[PATCH 00/32] python-team: Remove native inputs

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2 participants

Nicolas Graves
Sharlatan Hellseher

Owner: unassigned

Submitted by: Nicolas Graves

Severity: normal

Blocked by

69980

Debbugs page

Nicolas Graves wrote 10 months ago

Recipients:(address . guix-patches@gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510074844.2703-1-ngraves@ngraves.fr

This is a full rewrite of patch series 70735 which I couldn't fully
submit because debbugs doesn't seem to like when more than 100 patches
are sent in 2h. It is therefore much more concise.
Here's an adapted copy of the original cover-letter message:

How did I proceed ?

1) Identify packages we often don't need as native-inputs.
2) Systematically remove these packages when they are in native-inputs.
3) Iterate : try to rebuild needed packages, and fixes along the way (these can be updates, packages
rewrites, inputs additions...). Said fixes have been sent in patch series 70855. Back up from the native-input removal when it's not trivial, except for some specific cases (these are present as their own patches).
4) Stop when everything rebuilds properly, except for some specific cases.

   The packages that need rebuilding are identified from :
   guix graph --type=reverse-package -M 1 python-codecov python-coverage python-black python-isort
python-pycodestyle python-pep8 python-pyflakes python-flake8 python-pylint python-mypy
python-coveralls python-twine python-pytest-isort python-pytest-flake8 python-pytest-cov
python-pytest-black python-pytest-pep8 python-pytest-mypy pre-commit | grep label | cut -d\" -f4 |
cut -d@ -f1 | sort | uniq

   Some are removed from this list where the package was propagated rather than native, or when the
package is left unchanged (e.g. open-adventure), or for those specific cases :
   - "chirp"  ; needs to rebuild webkitgtk, no thanks
   - "cpplint"  ; has been updated on master + requires pytest-runner==5.6
   - "python-modin"  ; this is broken by pandas upgrade, will fix this independently
   - "python-libcst"  ; broken upstream but unchanged
   - "python-schema-salad"  ; broken upstream but unchanged
   - "python-dolfin-adjoint"  ; timeout, but probably works.
   - "reprotest"  ; needs to rebuild the whole openjdk, no thanks.

This patch series is built upon python-team's branch, with Vinicius' patch series 69980 and my patch
series 70855 on top.

Now, what about results in package node graph reduction?

Here's a summary of number of packages under guix refresh -l :

| package              | master | python-team+patch series |
|----------------------+--------+--------------------------|
| python-codecov       |      6 |                        1 |
| python-coverage      |   2359 |                      497 |
| python-black         |    332 |                       37 |
| python-isort         |    275 |                      153 |
| python-pycodestyle   |    392 |                      184 |
| python-pep8          |    219 |                      215 |
| python-pyflakes      |    392 |                      190 |
| python-flake8        |    377 |                      158 |
| python-pylint        |    235 |                        8 |
| python-mypy          |    347 |                      310 |
| python-coveralls     |     23 |                        1 |
| python-twine         |     28 |                      137 |
| python-pytest-isort  |    180 |                      145 |
| python-pytest-flake8 |    303 |                        8 |
| python-pytest-cov    |   2309 |                      286 |
| python-pytest-black  |    278 |                        7 |
| python-pytest-pep8   |     31 |                       31 |
| python-pytest-mypy   |    280 |                      307 |
| pre-commit           |    128 |                        1 |
| python-tox           |    166 |                        5 |

This means e.g. that an update of python-pylint will trigger 8 packages rebuilds rather than 235.


Nicolas Graves (32):
  guix: import: pypi: Ignore pypi-ignored-inputs.
  build-system/pyproject: Ignore unwanted pytest flags.
  build-system/pyproject: Remove python-black input.
  build-system/pyproject: Remove python-pylint native-input.
  build-system/pyproject: Remove python-flake8 inputs.
  build-system/pyproject: Remove python-coverage input.
  gnu: python-cram: Remove python-coverage native-input.
  gnu: u-boot-tools: Remove python-coverage native-input.
  gnu: python-aiosqlite: Remove python-coverage native-input.
  gnu: python-openid: Remove python-coverage native-input.
  build-system/pyproject: Remove python-coveralls native-input.
  build-system/pyproject: Remove python-pycodestyle native-input.
  gnu: python-versioneer: Remove python-pycodestyle native-input.
  gnu: python-versioneer: Remove python-pyflakes native-input.
  gnu: python-re-assert: Remove python-covdefaults native-input.
  build-system/pyproject: Remove python-codecov native-input.
  build-system/pyproject: Remove python-tox native-input.
  build-system/pyproject: Remove python-mypy native-input.
  gnu: python-immutables: Remove python-mypy native-input.
  build-system/pyproject: Remove python-isort native-input.
  build-system/pyproject: Remove python-twine native-input.
  build-system/pyproject: Remove python-pytest-cov native-input.
  gnu: python-tinycss2: Remove python-pytest-cov native-input.
  gnu: python-django-contact-form: Remove python-pytest-cov
    native-input.
  gnu: python-dateutil: Remove python-pytest-cov native-input.
  build-system/pyproject: Remove python-pytest-isort native-input.
  build-system/pyproject: Remove python-pytest-black native-input.
  build-system/pyproject: Remove python-pytest-flake8 native-input.
  build-system/pyproject: Remove python-pytest-mypy inputs.
  build-system/pyproject: Stop hiding options.
  gnu: python-linear-operator: Remove python-flake8-print native-input
  gnu: abjad-ext-ipython: Remove uneeded inputs.

 gnu/packages/android.scm              |   6 +-
 gnu/packages/astronomy.scm            |  33 +-
 gnu/packages/audio.scm                |   2 +-
 gnu/packages/backup.scm               |   2 +-
 gnu/packages/bioinformatics.scm       |  31 +-
 gnu/packages/bootloaders.scm          |  17 +-
 gnu/packages/build-tools.scm          |   1 -
 gnu/packages/check.scm                |  21 +-
 gnu/packages/cpp.scm                  |   4 +-
 gnu/packages/databases.scm            |  17 +-
 gnu/packages/dav.scm                  |   4 -
 gnu/packages/diffoscope.scm           |   2 -
 gnu/packages/django.scm               |  12 +-
 gnu/packages/ebook.scm                |   1 -
 gnu/packages/embedded.scm             |   1 -
 gnu/packages/engineering.scm          |   7 +-
 gnu/packages/finance.scm              |   6 +-
 gnu/packages/fontutils.scm            |   1 -
 gnu/packages/geo.scm                  |   9 +-
 gnu/packages/gettext.scm              |   4 -
 gnu/packages/gpodder.scm              |   3 +-
 gnu/packages/graph.scm                |   6 +-
 gnu/packages/graphviz.scm             |   5 -
 gnu/packages/jupyter.scm              |   8 +-
 gnu/packages/logging.scm              |   2 +-
 gnu/packages/machine-learning.scm     |  65 +---
 gnu/packages/mail.scm                 |   3 +-
 gnu/packages/mastodon.scm             |   1 -
 gnu/packages/messaging.scm            |   6 +-
 gnu/packages/music.scm                |  24 +-
 gnu/packages/package-management.scm   |   7 +-
 gnu/packages/patchutils.scm           |   2 +-
 gnu/packages/pdf.scm                  |   6 +-
 gnu/packages/potassco.scm             |   3 +-
 gnu/packages/protobuf.scm             |   4 +-
 gnu/packages/python-check.scm         |  33 +-
 gnu/packages/python-compression.scm   |  21 +-
 gnu/packages/python-crypto.scm        |   4 +-
 gnu/packages/python-science.scm       |  21 +-
 gnu/packages/python-web.scm           | 173 +++--------
 gnu/packages/python-xyz.scm           | 415 +++++++-------------------
 gnu/packages/radio.scm                |   3 +-
 gnu/packages/serialization.scm        |   1 -
 gnu/packages/simulation.scm           |   2 -
 gnu/packages/sphinx.scm               |   7 -
 gnu/packages/statistics.scm           |  14 +-
 gnu/packages/syndication.scm          |   8 +-
 gnu/packages/task-management.scm      |   1 -
 gnu/packages/telegram.scm             |   3 +-
 gnu/packages/terminals.scm            |   9 +-
 gnu/packages/textutils.scm            |   3 -
 gnu/packages/time.scm                 |  22 +-
 gnu/packages/version-control.scm      |   1 -
 gnu/packages/virtualization.scm       |   4 +-
 gnu/packages/vpn.scm                  |   2 -
 gnu/packages/web.scm                  |   6 +-
 gnu/packages/wm.scm                   |   2 -
 gnu/packages/xml.scm                  |   2 +-
 guix/build/pyproject-build-system.scm |  99 +++++-
 guix/import/pypi.scm                  |  21 +-
 guix/lint.scm                         |  12 +-
 tests/pypi.scm                        |   3 +-
 62 files changed, 413 insertions(+), 805 deletions(-)

-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 01/32] guix: import: pypi: Ignore pypi-ignored-inputs.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-1-ngraves@ngraves.fr

* guix/import/pypi.scm (pypi-ignored-inputs): New variable.

(compute-inputs): Use it.

* tests/pypi.scm (parse-requires.txt): Add ignored input to test the

feature.

* guix/lint.scm (check-inputs-should-be-native): Adapt list.

(check-inputs-should-not-be-an-input-at-all): Use pypi-ignored-list.

Change-Id: I774e526c5a090026e778ee44049637174a1dca95

---

guix/import/pypi.scm | 21 ++++++++++++++++++---

guix/lint.scm | 12 +++++++-----

tests/pypi.scm | 3 ++-

3 files changed, 27 insertions(+), 9 deletions(-)

Toggle diff (119 lines)diff --git a/guix/import/pypi.scm b/guix/import/pypi.scm
index 6719fde330a..d4b70061e86 100644
--- a/guix/import/pypi.scm
+++ b/guix/import/pypi.scm
@@ -14,6 +14,7 @@
 ;;; Copyright © 2022 Vivien Kraus <vivien@planete-kraus.eu>
 ;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2022 Hartmut Goebel <h.goebel@crazy-compilers.com>
+;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -61,6 +62,7 @@ (define-module (guix import pypi)
   #:use-module (guix upstream)
   #:use-module ((guix licenses) #:prefix license:)
   #:export (%pypi-base-url
+            pypi-ignored-inputs
             parse-requires.txt
             parse-wheel-metadata
             specification->requirement-name
@@ -77,6 +79,18 @@ (define %pypi-base-url
   ;; Base URL of the PyPI API.
   (make-parameter "https://pypi.org/pypi/"))
 
+(define pypi-ignored-inputs
+  ;; This list contains packages that are useful for development or quality
+  ;; testing, but that most of the time are not necessary to have as an input.
+  (list "argparse"  ; native
+        "tox" ; test wrapper for other environments
+        "codecov" "coverage"  ; coverage
+        "black" "isort" "pycodestyle" "pep8"  ; style
+        "pyflakes" "flake8" "pylint" "mypy"  ; style+lint
+        "coveralls" "twine"  ; upload integration tools
+        "pytest-isort" "pytest-flake8" "pytest-cov" "pytest-black"
+        "pytest-pep8" "pytest-mypy" "pytest-pep8" "pre-commit"))  ; variants
+
 (define non-empty-string-or-false
   (match-lambda
     ("" #f)
@@ -424,9 +438,10 @@ (define (compute-inputs source-url wheel-url archive)
   "Given the SOURCE-URL and WHEEL-URL of an already downloaded ARCHIVE, return
 the corresponding list of <upstream-input> records."
   (define (requirements->upstream-inputs deps type)
-    (filter-map (match-lambda
-                  ("argparse" #f)
-                  (name (upstream-input
+    (filter-map (lambda (name)
+                  (if (member name pypi-ignored-inputs)
+                      #f
+                      (upstream-input
                          (name name)
                          (downstream-name (python->package-name name))
                          (type type))))
diff --git a/guix/lint.scm b/guix/lint.scm
index 68d532968de..f689cc2a2a8 100644
--- a/guix/lint.scm
+++ b/guix/lint.scm
@@ -71,6 +71,7 @@ (define-module (guix lint)
                                     hg-reference-url)
   #:autoload   (guix bzr-download) (bzr-reference?
                                     bzr-reference-url)
+  #:use-module ((guix import pypi) #:select (pypi-ignored-inputs))
   #:use-module (guix import stackage)
   #:use-module (ice-9 match)
   #:use-module (ice-9 regex)
@@ -557,14 +558,12 @@ (define (check-inputs-should-be-native package)
             "m4"
             "qttools-5"
             "yasm" "nasm" "fasm"
-            "python-coverage"
             "python-cython"
             "python-docutils"
             "python-mock"
             "python-nose"
             "python-pbr"
             "python-pytest"
-            "python-pytest-cov"
             "python-setuptools-scm"
             "python-sphinx"
             "scdoc"
@@ -586,9 +585,12 @@ (define (check-inputs-should-be-native package)
 (define (check-inputs-should-not-be-an-input-at-all package)
   ;; Emit a warning if some inputs of PACKAGE are likely to should not be
   ;; an input at all.
-  (let ((input-names '("python-setuptools"
-                       "python-pip"
-                       "python-pre-commit")))
+  (let ((input-names (append
+                      '("python-setuptools"
+                        "python-pip"
+                        "pre-commit")
+                      (map (cut string-append "python-" <>)
+                           pypi-ignored-inputs))))
     (map (lambda (input)
            (make-warning
             package
diff --git a/tests/pypi.scm b/tests/pypi.scm
index 42b39cde730..fe01ab3beb3 100644
--- a/tests/pypi.scm
+++ b/tests/pypi.scm
@@ -97,6 +97,7 @@ (define test-requires.txt "\
 
 [test]
 pytest (>=2.5.0)
+pytest-cov  # read but ignored
 ")
 
 ;; Beaker contains only optional dependencies.
@@ -244,7 +245,7 @@ (define-syntax-rule (with-pypi responses body ...)
   (map specification->requirement-name test-specifications))
 
 (test-equal "parse-requires.txt"
-  (list '("foo" "bar") '("pytest"))
+  (list '("foo" "bar") '("pytest" "pytest-cov"))
   (mock ((ice-9 ports) call-with-input-file
          call-with-input-string)
         (parse-requires.txt test-requires.txt)))
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 02/32] build-system/pyproject: Ignore unwanted pytest flags.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-2-ngraves@ngraves.fr

* guix/build/pyproject-build-system.scm : Ignore unwanted pytest flags.

Change-Id: Ib9f1602e5af11227e5b7ce124f0f9be4fa2b78e4

---

guix/build/pyproject-build-system.scm | 99 ++++++++++++++++++++++++++-

1 file changed, 96 insertions(+), 3 deletions(-)

Toggle diff (137 lines)diff --git a/guix/build/pyproject-build-system.scm b/guix/build/pyproject-build-system.scm
index 947d240114a..2df9f2f4798 100644
--- a/guix/build/pyproject-build-system.scm
+++ b/guix/build/pyproject-build-system.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2021 Lars-Dominik Braun <lars@6xq.net>
 ;;; Copyright © 2022 Marius Bakke <marius@gnu.org>
+;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -35,7 +36,8 @@ (define-module (guix build pyproject-build-system)
             add-installed-pythonpath
             site-packages
             python-version
-            pyproject-build))
+            pyproject-build
+            with-guix-pytest-plugin))
 
 ;;; Commentary:
 ;;;
@@ -142,7 +144,94 @@ (define* (build #:key outputs build-backend backend-path configure-flags #:allow
      wheel-dir
      config-settings)))
 
-(define* (check #:key tests? test-backend test-flags #:allow-other-keys)
+(define pytest-default-ignore-alist
+  '(("cov" . ("--cov" "--cov-reset" "--cov-report" "--cov-config"
+              "--no-cov-on-fail" "--no-cov" "--cov-fail-under"
+              "--cov-append" "--cov-branch" "--cov-context"))
+    ("mypy" . ("--mypy" "--mypy-config-file" "--mypy-ignore-missing-imports"))
+    ("isort" . ("--isort"))
+    ("flake8" . ("--flake8"))
+    ("black" . ("--black"))
+    ("flakes" . ("--flakes"))
+    ("pep8" . ("--pep8"))))
+
+(define (pytest-ignore-flags-plugin flags)
+  "This function converts an list of flags into a string that can
+  be instantiated as a python pytest plugin."
+  (format #f "\
+import pytest
+
+def pytest_addoption(parser):
+    group = parser.getgroup('guix','Guix ignored options')
+    options = [~{~s, ~}]
+    for option in options:
+        group.addoption(option, action='append', nargs='?')"
+          flags))
+
+(define (call-with-guix-pytest-plugin inputs thunk)
+  "This function emulates command line options provided by pytest plugins in
+the absence of the plugins defining these options.
+
+This is done by selecting absent plugins, gettings their flags defined in
+PYTEST-DEFAULT-IGNORE-ALIST, and generating the plugin from there with
+PYTEST-IGNORE-FLAGS-PLUGIN."
+  (let* ((former-path (getenv "PYTHONPATH"))
+         (input-names
+          (map car
+               (filter (match-lambda
+                         ((name . _)
+                          (if (string-prefix? "python-pytest-" name)
+                              name
+                              #f))
+                         ( _ #f))
+                       inputs)))
+         (filtered-flags
+          (filter identity
+                  (append-map
+                   (match-lambda
+                     ((group . flags)
+                      (if (member (string-append "python-pytest-" group)
+                                  input-names)
+                          (list #f)
+                          flags))
+                     (_ (list #f)))
+                   pytest-default-ignore-alist)))
+         (dir (string-append
+               (if (access? (dirname (getcwd)) W_OK)
+                   (dirname (getcwd))
+                   ;; fallback if we're already out-of-source
+                   (getcwd))
+               "/.guix-pytest")))
+    (dynamic-wind
+      (lambda ()
+        (setenv "PYTHONPATH"
+                (string-append
+                 (if former-path
+                     (string-append former-path ":")
+                     "")
+                 dir))
+        (setenv "PYTEST_PLUGINS"
+                (string-append
+                 (if (getenv "PYTEST_PLUGINS")
+                     (string-append former-path ",")
+                     "")
+                 "pytest_guix_plugin"))
+        (mkdir-p dir)
+        (with-output-to-file (string-append dir "/__init__.py")
+          (lambda _ (display "")))
+        (with-output-to-file (string-append dir "/pytest_guix_plugin.py")
+          (lambda _
+            (display (pytest-ignore-flags-plugin filtered-flags)))))
+      thunk
+      (lambda ()
+        (setenv "PYTHONPATH" former-path)
+        (unsetenv "PYTEST_PLUGINS")))))
+
+(define-syntax-rule (with-guix-pytest-plugin inputs exp ...)
+  "Evaluate EXP in a context where the Guix pytest plugin is added."
+  (call-with-guix-pytest-plugin inputs (lambda () exp ...)))
+
+(define* (check #:key inputs tests? test-backend test-flags #:allow-other-keys)
   "Run the test suite of a given Python package."
   (if tests?
       ;; Unfortunately with PEP 517 there is no common method to specify test
@@ -165,7 +254,8 @@ (define* (check #:key tests? test-backend test-flags #:allow-other-keys)
         (format #t "Using ~a~%" use-test-backend)
         (match use-test-backend
           ('pytest
-           (apply invoke pytest "-vv" test-flags))
+           (with-guix-pytest-plugin inputs
+             (apply invoke pytest "-vv" test-flags)))
           ('nose
            (apply invoke nosetests "-v" test-flags))
           ('nose2
@@ -386,3 +476,6 @@ (define* (pyproject-build #:key inputs (phases %standard-phases)
   (apply python:python-build #:inputs inputs #:phases phases args))
 
 ;;; pyproject-build-system.scm ends here
+;;; Local Variables:
+;;; eval: (put 'with-guix-pytest-plugin 'scheme-indent-function 1)
+;;; End:
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 03/32] build-system/pyproject: Remove python-black input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-3-ngraves@ngraves.fr

* gnu/packages/bioinformatics.scm (python-doubletdetection,

python-liana-py, scvelo)[native-inputs]: Remove python-black.

* gnu/packages/databases.scm (datasette):

[arguments]<#:test-flags>: Ignore black tests.

<#:phases>: Remove parts related to black in relax-requirements

added phase.

[native-inputs]: Remove python-black.

* gnu/packages/finance.scm (python-trezor)[native-inputs]: Remove

python-black.

* gnu/packages/graph.scm (python-graphtools)[native-inputs]: Remove

python-black.

* gnu/packages/machine-learning.scm (python-funsor,

python-imbalanced-learn, python-hyperopt, python-captum,

python-pyro-ppl)[native-inputs]: Remove python-black.

* gnu/packages/python-check.scm (python-vcrpy)[native-inputs]:

Remove python-black.

* gnu/packages/python-web.scm (python-ovh, python-openai,

python-starsessions-for-pytorch-lightning)[native-inputs]: Remove

python-black.

* gnu/packages/python-xyz.scm (python-pydantic-cli, python-imageio,

python-update-checker, python-eliot, python-minikanren,

python-jupytext)[native-inputs]: Remove python-black.

(ptpython)[propagated-inputs]: Remove python-black.

* gnu/packages/virtualization.scm (python-transient)[native-inputs]:

Remove python-black.

Change-Id: Ie8098afda264bf9a5ab2cfe5d915bc7a41fdc604

---

gnu/packages/bioinformatics.scm | 11 +++--------

gnu/packages/databases.scm | 8 ++------

gnu/packages/finance.scm | 1 -

gnu/packages/graph.scm | 1 -

gnu/packages/machine-learning.scm | 11 +++--------

gnu/packages/python-check.scm | 3 +--

gnu/packages/python-web.scm | 8 +++-----

gnu/packages/python-xyz.scm | 15 +++++----------

gnu/packages/virtualization.scm | 2 +-

9 files changed, 18 insertions(+), 42 deletions(-)

Toggle diff (271 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a611caf715a..253c36947c3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2152,8 +2152,7 @@ (define-public python-doubletdetection
            python-scipy
            python-tqdm))
     (native-inputs
-     (list python-black
-           python-flake8
+     (list python-flake8
            python-poetry-core
            python-pytest))
     (home-page "https://github.com/JonathanShor/DoubletDetection")
@@ -2278,10 +2277,7 @@ (define-public python-liana-py
                              python-tqdm
                              tzdata))
     (native-inputs
-     (list python-black
-           python-poetry-core
-           python-pytest
-           python-pytest-cov))
+     (list python-poetry-core python-pytest python-pytest-cov))
     (home-page "https://github.com/saezlab/liana-py")
     (synopsis "LIANA is a ligand-receptor analysis framework")
     (description "This is a Ligand-Receptor inference framework.  The
@@ -21837,8 +21833,7 @@ (define-public scvelo
            python-umap-learn
            pybind11))
     (native-inputs
-     (list python-black
-           python-flake8
+     (list python-flake8
            python-hypothesis
            python-pytest
            python-setuptools-scm
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 67e6ced7c32..96b2c2a0437 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -5537,16 +5537,13 @@ (define-public datasette
                     " or test_custom_query_with_unicode_characters"
                     " or test_searchmode)")
               "-n" (number->string (parallel-job-count))
-              "-m" "not serial")        ;cannot run in parallel
+              "-m" "not serial"  ;cannot run in parallel
+              "--ignore=tests/test_black.py")
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'relax-requirements
             (lambda _
-              ;; The package needlessly specifies exact versions
-              ;; of dependencies, when it works fine with others.
               (substitute* "setup.py"
-                (("(black)==[0-9\\.]+" _ package)
-                 package)
                 (("click-default-group-wheel")
                  "click-default-group")))))))
     (propagated-inputs
@@ -5569,7 +5566,6 @@ (define-public datasette
            python-uvicorn))
     (native-inputs
      (list python-beautifulsoup4
-           python-black
            python-cogapp
            python-pip
            python-pytest
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index 3c32a220c4e..7d1efde8187 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -1149,7 +1149,6 @@ (define-public python-trezor
            python-typing-extensions))
     (native-inputs ; Only needed for running the tests
      (list protobuf
-           python-black
            python-isort
            python-pillow
            python-protobuf
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index eda8365a424..033027a5aa9 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -476,7 +476,6 @@ (define-public python-graphtools
     (native-inputs
      (list util-linux ;for lscpu
            python-anndata
-           python-black
            python-coverage
            python-coveralls
            python-nose
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index ba6f51b3f11..e63dd0f0678 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -175,8 +175,7 @@ (define-public python-funsor
     (propagated-inputs (list python-makefun python-multipledispatch
                              python-numpy python-opt-einsum
                              python-typing-extensions))
-    (native-inputs (list python-black
-                         python-flake8
+    (native-inputs (list python-flake8
                          python-isort
                          python-nbsphinx
                          python-pandas
@@ -1923,8 +1922,7 @@ (define-public python-imbalanced-learn
                               (getcwd)))))))
     (propagated-inputs (list python-joblib python-numpy python-scikit-learn
                              python-scipy python-threadpoolctl))
-    (native-inputs (list python-black
-                         python-flake8
+    (native-inputs (list python-flake8
                          python-keras
                          python-mypy
                          python-pandas
@@ -2359,8 +2357,7 @@ (define-public python-hyperopt
            python-six
            python-tqdm))
     (native-inputs
-     (list python-black
-           python-nose
+     (list python-nose
            python-pymongo
            python-pytest
            python-wheel))
@@ -4525,7 +4522,6 @@ (define-public python-captum
      (list python-matplotlib python-numpy python-pytorch python-tqdm))
     (native-inputs (list jupyter
                          python-annoy
-                         python-black
                          python-flake8
                          python-flask
                          python-flask-compress
@@ -5063,7 +5059,6 @@ (define-public python-pyro-ppl
     (native-inputs
      (list ninja
            jupyter
-           python-black
            python-flake8
            python-graphviz
            python-isort
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 5571cee2088..83fd723d12b 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -411,8 +411,7 @@ (define-public python-vcrpy
     (propagated-inputs
      (list python-pyyaml python-six python-wrapt python-yarl))
     (native-inputs
-     (list python-black
-           python-coverage
+     (list python-coverage
            python-flake8
            python-flask
            python-httplib2
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 61ea8a63558..a7794741f42 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -977,8 +977,7 @@ (define-public python-ovh
     (build-system pyproject-build-system)
     (arguments (list #:tests? #f))      ; XXX: tests require networking
     (propagated-inputs (list python-requests))
-    (native-inputs (list python-black
-                         python-coverage
+    (native-inputs (list python-coverage
                          python-flake8
                          python-isort
                          python-pytest
@@ -2174,7 +2173,7 @@ (define-public python-openai
  and not test_file_cli")))
     (propagated-inputs (list python-aiohttp python-requests python-tqdm
                              python-typing-extensions))
-    (native-inputs (list python-black python-pytest python-pytest-asyncio
+    (native-inputs (list python-pytest python-pytest-asyncio
                          python-pytest-mock python-setuptools python-wheel))
     (home-page "https://github.com/openai/openai-python")
     (synopsis "Python client library for the OpenAI API")
@@ -8968,8 +8967,7 @@ (define-public python-starsessions-for-pytorch-lightning
            python-itsdangerous
            python-starlette-for-fastapi-0.88))
     (native-inputs
-     (list python-black
-           python-flake8
+     (list python-flake8
            python-httpx
            python-mypy
            python-poetry-core
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 3f86ea8224b..7eff059637e 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -478,7 +478,6 @@ (define-public python-jupytext
     (native-inputs
      (list git-minimal
            python-autopep8
-           python-black
            python-flake8
            python-gitpython
            python-isort
@@ -8029,8 +8028,7 @@ (define-public python-pydantic-cli
     (propagated-inputs
      (list python-pydantic))
     (native-inputs
-     (list python-black
-           python-mypy
+     (list python-mypy
            python-pytest))
     (home-page "https://github.com/mpkocher/pydantic-cli")
     (synopsis "Turn Pydantic defined data models into CLI tools")
@@ -10802,7 +10800,7 @@ (define-public python-imageio
     (propagated-inputs
      (list python-imageio-ffmpeg python-numpy python-pillow python-tifffile python-setuptools))
     (native-inputs
-     (list python-black python-flake8 python-fsspec python-pytest
+     (list python-flake8 python-fsspec python-pytest
            python-pytest-cov python-wheel))
     (home-page "https://imageio.github.io/")
     (synopsis "Library for reading and writing a wide range of image data")
@@ -22108,8 +22106,7 @@ (define-public ptpython
     (arguments
      `(#:tests? #f)) ;there are no tests
     (propagated-inputs
-     (list python-appdirs python-black python-jedi python-prompt-toolkit
-           python-pygments))
+     (list python-appdirs python-jedi python-prompt-toolkit python-pygments))
     (home-page "https://github.com/jonathanslenders/ptpython")
     (synopsis "Python Read-Eval-Print-Loop with nice IDE-like features")
     (description
@@ -27291,7 +27288,7 @@ (define-public python-update-checker
         (base32 "04yb5a9mi45ax50m2m0ih6gdvkk1j7gfmy83dd58i1f59axlabba"))))
     (build-system python-build-system)
     (propagated-inputs (list python-requests))
-    (native-inputs (list python-black python-flake8 python-pytest))
+    (native-inputs (list python-flake8 python-pytest))
     (home-page "https://github.com/bboe/update_checker")
     (synopsis "Python module that will check for package updates")
     (description "This package provides a Python module that will check for
@@ -31399,8 +31396,7 @@ (define-public python-eliot
      (list python-boltons python-pyrsistent python-six
            python-zope-interface))
     (native-inputs
-     (list python-black
-           python-coverage
+     (list python-coverage
            python-dask
            python-flake8
            python-hypothesis
@@ -34155,7 +34151,6 @@ (define-public python-minikanren
            python-pytest
            python-pytest-cov
            python-pylint
-           python-black
            python-sympy
            python-versioneer
            python-coverage))
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index 20cbb0b8bed..b564bd043cb 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -2809,7 +2809,7 @@ (define-public python-transient
            python-requests
            python-toml))
     (native-inputs
-     (list python-black python-mypy python-pyhamcrest python-twine
+     (list python-mypy python-pyhamcrest python-twine
            python-setuptools python-wheel))
     (home-page "https://github.com/ALSchwalm/transient")
     (synopsis "QEMU Wrapper written in Python")
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 04/32] build-system/pyproject: Remove python-pylint native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-4-ngraves@ngraves.fr

* gnu/packages/potassco.scm (python-clingraph):

[native-inputs]: Remove python-pylint.

* gnu/packages/python-xyz.scm (python-mediapy, python-fastjsonschema,

python-trio)[native-inputs]: Remove python-pylint.

* gnu/packages/syndication.scm (rtv, tuir)[native-inputs]: Remove

python-pylint.

* gnu/packages/terminals.scm (python-halo, python-log-symbols,

python-spinners)[native-inputs]: Remove python-pylint.

Change-Id: If6a20e0b790f7157013a6868bba9e4a8d7e5ba28

---

gnu/packages/potassco.scm | 3 +--

gnu/packages/python-xyz.scm | 3 ---

gnu/packages/syndication.scm | 2 --

gnu/packages/terminals.scm | 6 +++---

4 files changed, 4 insertions(+), 10 deletions(-)

Toggle diff (95 lines)diff --git a/gnu/packages/potassco.scm b/gnu/packages/potassco.scm
index 9af307b4a90..054f9e9b180 100644
--- a/gnu/packages/potassco.scm
+++ b/gnu/packages/potassco.scm
@@ -563,8 +563,7 @@ (define-public python-clingraph
                              python-jsonschema
                              python-networkx
                              python-setuptools))
-    (native-inputs (list dot2tex graphviz python-pylint python-pytest
-                         python-wheel))
+    (native-inputs (list dot2tex graphviz python-pytest python-wheel))
     (home-page "https://github.com/potassco/clingraph")
     (synopsis "Visualizer for graphs defined as logic programs")
     (description
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 7eff059637e..e558dcdc83a 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4440,7 +4440,6 @@ (define-public python-mediapy
                              python-pillow))
     (native-inputs
      (list python-flit-core
-           python-pylint
            python-pytest
            python-pytest-xdist))
     (home-page "https://github.com/google/mediapy")
@@ -17184,7 +17183,6 @@ (define-public python-fastjsonschema
      (list python-colorama
            python-json-spec
            python-jsonschema
-           python-pylint
            python-pytest
            python-pytest-benchmark
            python-pytest-cache
@@ -29072,7 +29070,6 @@ (define-public python-trio
      (list python-astor
            python-ipython
            python-jedi
-           python-pylint
            python-pyopenssl
            python-pytest
            python-pytest-xdist
diff --git a/gnu/packages/syndication.scm b/gnu/packages/syndication.scm
index a2d8c61be45..29febdf3453 100644
--- a/gnu/packages/syndication.scm
+++ b/gnu/packages/syndication.scm
@@ -437,7 +437,6 @@ (define-public rtv
            python-coveralls
            python-coverage
            python-mock
-           python-pylint
            python-pytest
            python-vcrpy))
     (home-page "https://github.com/michael-lazar/rtv")
@@ -472,7 +471,6 @@ (define-public tuir
      (list python-coverage
            python-coveralls
            python-mock
-           python-pylint
            python-pytest
            python-vcrpy
            python-setuptools
diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index 98a6bf6684a..26af13af498 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -1196,7 +1196,7 @@ (define-public python-halo
     (build-system pyproject-build-system)
     (propagated-inputs (list python-colorama python-log-symbols python-six
                              python-spinners python-termcolor))
-    (native-inputs (list python-coverage python-nose python-pylint python-tox
+    (native-inputs (list python-coverage python-nose python-tox
                          python-twine python-setuptools python-wheel))
     (home-page "https://github.com/manrajgrover/halo")
     (synopsis "Python library to display graphical spinners in the terminal")
@@ -1224,7 +1224,7 @@ (define-public python-log-symbols
                      (("(.*)==(.*)$" _ dep ver)
                       (string-append dep ">=" ver))))))))
     (propagated-inputs (list python-colorama))
-    (native-inputs (list python-coverage python-nose python-pylint
+    (native-inputs (list python-coverage python-nose
                          python-setuptools python-tox python-wheel))
     (home-page "https://github.com/manrajgrover/py-log-symbols")
     (synopsis "Python library with graphical symbols for logging on the terminal")
@@ -1252,7 +1252,7 @@ (define-public python-spinners
                    (substitute* "requirements-dev.txt"
                      (("(.*)==(.*)$" _ dep ver)
                       (string-append dep ">=" ver))))))))
-    (native-inputs (list python-coverage python-nose python-pylint
+    (native-inputs (list python-coverage python-nose
                          python-setuptools python-tox python-wheel))
     (home-page "https://github.com/manrajgrover/py-spinners")
     (synopsis "Python library with graphical spinners for the terminal")
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 05/32] build-system/pyproject: Remove python-flake8 inputs.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-5-ngraves@ngraves.fr

* gnu/packages/astronomy.scm (python-crds)[native-inputs]: Remove

python-flake8.

* gnu/packages/bioinformatics.scm (python-doubletdetection,

python-biom-format)[native-inputs]: Remove python-flake8.

* gnu/packages/ebook.scm (calibre)[native-inputs]: Remove

python-flake8.

* gnu/packages/engineering.scm (python-scikit-rf)[native-inputs]:

Remove python-flake8.

* gnu/packages/finance.scm (python-mt-940)[native-inputs]: Remove

python-flake8.

* gnu/packages/geo.scm (python-geopy)[native-inputs]: Remove

python-flake8.

* gnu/packages/gettext.scm (python-mdpo)[native-inputs]: Remove

python-flake8.

* gnu/packages/graph.scm (python-pygsp)[native-inputs]: Remove

python-flake8.

* gnu/packages/graphviz.scm (python-uqbar)[native-inputs]: Remove

python-flake8.

* gnu/packages/machine-learning.scm (python-funsor,

python-imbalanced-learn, python-captum, python-pyro-api,

python-pyro-ppl, python-linear-operator,

python-gpytorch)[native-inputs]: Remove python-flake8.

* gnu/packages/music.scm (python-mutagen):

[arguments]<#:test-flags>: Ignore flake8 quality tests.

[native-inputs]: Remove python-flake8.

* gnu/packages/protobuf.scm (python-pure-protobuf):

[arguments]<#:phases>: Remove flake8 invocation from check phase.

[native-inputs]: Remove python-flake8.

* gnu/packages/python-web.scm (python-ovh, python-furl,

python-httplib2, python-http-ece, python-woob,

python-starsessions-for-pytorch-lightning)[native-inputs]: Remove

python-flake8.

* gnu/packages/python-xyz.scm (python-apispec,

python-apispec-webframeworks, python-apprise, python-colorful,

python-pymd4c, python-pyls-black, python-docx, python-flasgger,

python-imageio, python-importlib-ressources, python-jaraco-test,

python-seaborn, python-progressbar2, python-inflect,

python-argcomplete, python-diff-cover, python-validators,

python-marshmallow, python-marshmallow-jsonapi, python-yq,

python-update-checker, python-eliot, python-dateparser,

python-jinja2-cli, python-nikola, python-verspec, python-mike,

python-arpeggio, python-versioneer, python-codespell)[native-inputs]:

Remove python-flake8.

* gnu/packages/simulation.scm (python-dolfin-adjoint)[native-inputs]:

Remove python-flake8.

* gnu/packages/sphinx.scm (python-sphinx,

python-sphinx-5)[propagated-inputs]: Remove python-flake8.

* gnu/packages/statistics.scm (python-statsmodels)[native-inputs]:

Remove python-flake8.

* gnu/packages/vpn.scm (sshuttle)[native-inputs]: Remove

python-flake8.

* gnu/packages/wm.scm (qtile)[native-inputs]: Remove python-flake8.

* gnu/packages/textutils.scm (python-panflute)[native-inputs]: Remove

python-flake8.

Change-Id: I196a9c0b7497106c8f98598535cb8e0ea667481c

---

gnu/packages/astronomy.scm | 3 +-

gnu/packages/bioinformatics.scm | 7 +---

gnu/packages/ebook.scm | 1 -

gnu/packages/engineering.scm | 1 -

gnu/packages/finance.scm | 4 +-

gnu/packages/geo.scm | 1 -

gnu/packages/gettext.scm | 1 -

gnu/packages/graph.scm | 3 +-

gnu/packages/graphviz.scm | 1 -

gnu/packages/machine-learning.scm | 15 ++------

gnu/packages/music.scm | 5 ++-

gnu/packages/protobuf.scm | 4 +-

gnu/packages/python-web.scm | 12 ++----

gnu/packages/python-xyz.scm | 62 +++++++++++--------------------

gnu/packages/simulation.scm | 1 -

gnu/packages/sphinx.scm | 2 -

gnu/packages/statistics.scm | 1 -

gnu/packages/textutils.scm | 1 -

gnu/packages/vpn.scm | 1 -

gnu/packages/wm.scm | 1 -

20 files changed, 37 insertions(+), 90 deletions(-)

Toggle diff (399 lines)diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 32c6f30e8f6..ede10ab927a 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2186,8 +2186,7 @@ (define-public python-crds
                              python-roman-datamodels
                              python-stsynphot
                              python-requests))
-    (native-inputs (list python-flake8
-                         python-ipython
+    (native-inputs (list python-ipython
                          python-lockfile
                          python-mock
                          python-nose
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 253c36947c3..4f3a3d0ba01 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2152,8 +2152,7 @@ (define-public python-doubletdetection
            python-scipy
            python-tqdm))
     (native-inputs
-     (list python-flake8
-           python-poetry-core
+     (list python-poetry-core
            python-pytest))
     (home-page "https://github.com/JonathanShor/DoubletDetection")
     (synopsis
@@ -3005,7 +3004,6 @@ (define-public python-biom-format
     (propagated-inputs
      (list python-anndata
            python-click
-           python-flake8
            python-future
            python-h5py
            python-numpy
@@ -21833,8 +21831,7 @@ (define-public scvelo
            python-umap-learn
            pybind11))
     (native-inputs
-     (list python-flake8
-           python-hypothesis
+     (list python-hypothesis
            python-pytest
            python-setuptools-scm
            python-wheel))
diff --git a/gnu/packages/ebook.scm b/gnu/packages/ebook.scm
index 16d4fcd6e36..3d536e59add 100644
--- a/gnu/packages/ebook.scm
+++ b/gnu/packages/ebook.scm
@@ -154,7 +154,6 @@ (define-public calibre
     (native-inputs
      (list bash-minimal
            pkg-config
-           python-flake8
            python-pyqt-builder
            qtbase-5                     ; for qmake
            xdg-utils))
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index f082f346278..610fb53087b 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -2679,7 +2679,6 @@ (define-public python-scikit-rf
                              python-qtpy
                              python-scipy))
     (native-inputs (list python-coverage
-                         python-flake8
                          python-nbval
                          python-networkx
                          python-pytest
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index 7d1efde8187..7579001dd1f 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -2307,9 +2307,7 @@ (define-public python-mt-940
                         ;; Remove custom --cov flags.
                         (delete-file "pytest.ini")
                         (invoke "pytest" "-vv")))))))
-    (native-inputs (list python-flake8
-                         python-pytest
-                         python-pyyaml))
+    (native-inputs (list python-pytest python-pyyaml))
     (home-page "https://mt940.readthedocs.io/")
     (synopsis "Python parser for MT940-encoded SWIFT data")
     (description
diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 81a854f8a2a..69cc7e6ddc5 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -3265,7 +3265,6 @@ (define-public python-geopy
     (native-inputs
      (list python-async-generator
            python-coverage
-           python-flake8
            python-isort
            python-pytest
            python-pytest-aiohttp
diff --git a/gnu/packages/gettext.scm b/gnu/packages/gettext.scm
index 1408cc4cb46..bbb19bd4cb8 100644
--- a/gnu/packages/gettext.scm
+++ b/gnu/packages/gettext.scm
@@ -214,7 +214,6 @@ (define-public mdpo
     (build-system python-build-system)
     (native-inputs
      (list python-bump2version
-           python-flake8
            python-flake8-implicit-str-concat
            python-flake8-print
            python-isort
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 033027a5aa9..eb8aa17fdfe 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -564,8 +564,7 @@ (define-public python-pygsp
                 "")))))))
     (propagated-inputs (list python-numpy python-scikit-image python-scipy))
     (native-inputs
-     (list python-coverage python-coveralls python-flake8
-           python-pytest))
+     (list python-coverage python-coveralls python-pytest))
     (home-page "https://github.com/epfl-lts2/pygsp")
     (synopsis "Graph Signal Processing in Python")
     (description "The PyGSP is a Python package to ease signal processing on
diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm
index db40b99928a..b396a97c0bc 100644
--- a/gnu/packages/graphviz.scm
+++ b/gnu/packages/graphviz.scm
@@ -217,7 +217,6 @@ (define-public python-uqbar
 and not test_sphinx_book_text_broken_strict")))
     (native-inputs
      (list graphviz
-           python-flake8
            python-isort
            python-mypy
            python-pytest
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index e63dd0f0678..b4f0f65c837 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -175,8 +175,7 @@ (define-public python-funsor
     (propagated-inputs (list python-makefun python-multipledispatch
                              python-numpy python-opt-einsum
                              python-typing-extensions))
-    (native-inputs (list python-flake8
-                         python-isort
+    (native-inputs (list python-isort
                          python-nbsphinx
                          python-pandas
                          python-pillow
@@ -1922,8 +1921,7 @@ (define-public python-imbalanced-learn
                               (getcwd)))))))
     (propagated-inputs (list python-joblib python-numpy python-scikit-learn
                              python-scipy python-threadpoolctl))
-    (native-inputs (list python-flake8
-                         python-keras
+    (native-inputs (list python-keras
                          python-mypy
                          python-pandas
                          python-pytest
@@ -4522,7 +4520,6 @@ (define-public python-captum
      (list python-matplotlib python-numpy python-pytorch python-tqdm))
     (native-inputs (list jupyter
                          python-annoy
-                         python-flake8
                          python-flask
                          python-flask-compress
                          python-ipython
@@ -5009,8 +5006,7 @@ (define-public python-pyro-api
     (build-system python-build-system)
     (arguments '(#:tests? #false)) ;requires pyro
     (native-inputs
-     (list python-flake8
-           python-ipython
+     (list python-ipython
            python-pytest
            python-sphinx
            python-sphinx-rtd-theme))
@@ -5059,7 +5055,6 @@ (define-public python-pyro-ppl
     (native-inputs
      (list ninja
            jupyter
-           python-flake8
            python-graphviz
            python-isort
            python-lap
@@ -5106,8 +5101,7 @@ (define-public python-linear-operator
                              python-pytorch
                              python-scipy
                              python-typeguard))
-    (native-inputs (list python-flake8
-                         python-flake8-print
+    (native-inputs (list python-flake8-print
                          python-pytest
                          python-setuptools
                          python-setuptools-scm
@@ -5138,7 +5132,6 @@ (define-public python-gpytorch
                                        " and not test_t_matmul_matrix"))))
     (propagated-inputs (list python-linear-operator python-scikit-learn))
     (native-inputs (list python-coverage
-                         python-flake8
                          python-flake8-print
                          python-nbval
                          python-pytest
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 6b765dcb3d6..3af2b79b419 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -3968,6 +3968,7 @@ (define-public python-mutagen
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags '(list "--ignore=tests/quality/test_flake8.py")
        #:phases
        #~(modify-phases %standard-phases
            (add-before 'check 'remove-hypothesis-deadlines
@@ -3978,8 +3979,8 @@ (define-public python-mutagen
                  (("( +)@given" all spaces)
                   (string-append spaces "@settings(deadline=None)\n" all))))))))
     (native-inputs
-     (list python-pytest python-hypothesis python-flake8
-           python-setuptools python-wheel))
+     (list python-pytest python-hypothesis python-setuptools python-wheel))
+    (home-page "https://mutagen.readthedocs.io/")
     (synopsis "Read and write audio tags")
     (description "Mutagen is a Python module to handle audio metadata.  It
 supports ASF, FLAC, M4A, Monkey’s Audio, MP3, Musepack, Ogg FLAC, Ogg Speex, Ogg
diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm
index 8ca730df3c3..502ad09a3a6 100644
--- a/gnu/packages/protobuf.scm
+++ b/gnu/packages/protobuf.scm
@@ -469,7 +469,7 @@ (define-public python-pure-protobuf
         (base32 "15dp5pvazd0jx4wzzh79080ah7hkpd3axh40al9vhzs2hf3v90hx"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-flake8 python-pytest python-pytest-cov python-isort))
+     (list python-pytest python-pytest-cov python-isort))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
@@ -477,8 +477,6 @@ (define-public python-pure-protobuf
            (lambda _
              (invoke "pytest" "--cov-report" "term-missing" "--cov"
                      "pure_protobuf")
-             (invoke "flake8" "pure_protobuf" "tests"
-                     "--ignore=F541")
              (invoke "isort" "-rc" "-c" "pure_protobuf" "tests"))))))
     (home-page "https://pypi.org/project/pure-protobuf/")
     (synopsis "Protobuf implementation using dataclasses")
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index a7794741f42..4cf064e0742 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -978,7 +978,6 @@ (define-public python-ovh
     (arguments (list #:tests? #f))      ; XXX: tests require networking
     (propagated-inputs (list python-requests))
     (native-inputs (list python-coverage
-                         python-flake8
                          python-isort
                          python-pytest
                          python-pytest-cov
@@ -1239,8 +1238,6 @@ (define-public python-furl
     (build-system python-build-system)
     (propagated-inputs
      (list python-six python-orderedmultidict))
-    (native-inputs
-     (list python-flake8))
     (home-page "https://github.com/gruns/furl")
     (synopsis "URL manipulation in Python")
     (description "Furl provides an easy-to-use alternative to the
@@ -1273,7 +1270,6 @@ (define-public python-httplib2
                  (("==") ">=")))))))
     (native-inputs
      (list python-cryptography
-           python-flake8
            python-future
            python-mock
            python-pytest
@@ -7307,7 +7303,7 @@ (define-public python-http-ece
     (propagated-inputs
      (list python-cryptography))
     (native-inputs
-     (list python-coverage python-flake8 python-mock python-nose))
+     (list python-coverage python-mock python-nose))
     (home-page "https://github.com/web-push-libs/encrypted-content-encoding")
     (synopsis "Encrypted Content Encoding for HTTP")
     (description
@@ -8327,8 +8323,7 @@ (define-public python-woob
            python-six
            python-unidecode))
     (native-inputs
-     (list python-coverage python-flake8 python-nose python-selenium
-           python-xunitparser))
+     (list python-coverage python-nose python-selenium python-xunitparser))
     (home-page "https://woob.tech/")
     (synopsis "Woob, Web Outside Of Browsers")
     (description "Woob is a collection of applications able to interact with
@@ -8967,8 +8962,7 @@ (define-public python-starsessions-for-pytorch-lightning
            python-itsdangerous
            python-starlette-for-fastapi-0.88))
     (native-inputs
-     (list python-flake8
-           python-httpx
+     (list python-httpx
            python-mypy
            python-poetry-core
            python-pytest
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e558dcdc83a..fa77102857c 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -320,7 +320,6 @@ (define-public python-apprise
     (native-inputs (list python-babel
                          python-coverage
                          python-cryptography
-                         python-flake8
                          python-paho-mqtt
                          python-pytest
                          python-pytest-cov
@@ -1183,8 +1182,7 @@ (define-public python-colorful
         (base32 "0kyy9qhvrb5m9h8xmri7c88i0k1g5qc7017anw39gx44an7mn33y"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage python-flake8 python-pytest python-setuptools
-           python-wheel))
+     (list python-coverage python-pytest python-setuptools python-wheel))
     (propagated-inputs
      (list python-colorama))
     (home-page "http://github.com/timofurrer/colorful")
@@ -2370,7 +2368,7 @@ (define-public python-pymd4c
     (inputs
      (list md4c))
     (native-inputs
-     (list python-flake8 python-pkgconfig pkg-config))
+     (list python-pkgconfig pkg-config))
     (home-page "https://github.com/dominickpastore/pymd4c")
     (synopsis "Python bindings for MD4C")
     (description
@@ -3028,7 +3026,7 @@ (define-public python-pyls-black
     (propagated-inputs
      (list python-black python-lsp-server python-tomli))
     (native-inputs
-     (list python-flake8 python-isort python-mypy python-pytest
+     (list python-isort python-mypy python-pytest
            python-pytest-runner python-setuptools python-wheel))
     (home-page "https://github.com/rupert/pyls-black")
     (synopsis "Black plugin for the Python Language Server")
@@ -7006,7 +7004,6 @@ (define-public python-docx
     (build-system pyproject-build-system)
     (native-inputs
      (list behave
-           python-flake8
            python-mock
            python-pyparsing
            python-pytest
@@ -10799,7 +10796,7 @@ (define-public python-imageio
     (propagated-inputs
      (list python-imageio-ffmpeg python-numpy python-pillow python-tifffile python-setuptools))
     (native-inputs
-     (list python-flake8 python-fsspec python-pytest
+     (list python-fsspec python-pytest
            python-pytest-cov python-wheel))
     (home-page "https://imageio.github.io/")
     (synopsis "Library for reading and writing a wide range of image data")
@@ -11577,8 +11574,7 @@ (define-public python-importlib-resources
              (setenv "PYTHONPATH"
                      (string-append (getcwd) "/_custom_build")))))))
     (native-inputs
-     (list python-flake8
-           python-pytest
+     (list python-pytest
            python-pytest-black
            python-pytest-checkdocs
            python-pytest-cov
@@ -11900,8 +11896,7 @@ (define-public python-jaraco-test
     (arguments
      (list #:test-flags '(list "-k" "http")))
     (propagated-inputs (list python-jaraco-context python-jaraco-functools))
-    (native-inputs (list python-flake8
-                         python-pytest
+    (native-inputs (list python-pytest
                          python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-cov
@@ -13706,8 +13701,7 @@ (define-public python-seaborn
            python-scipy
            python-statsmodels))
     (native-inputs
-     (list python-flake8
-           python-flit-core
+     (list python-flit-core
            python-ipykernel
            python-nbconvert
            python-numpydoc
@@ -18691,8 +18685,7 @@ (define-public python-progressbar2
     (propagated-inputs
      (list python-six python-utils))
     (native-inputs
-     (list python-flake8
-           python-fre

This message was truncated. Download the full message here.

Nicolas Graves wrote 10 months ago

[PATCH 07/32] gnu: python-cram: Remove python-coverage native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-7-ngraves@ngraves.fr

* gnu/packages/python-xyz.scm (python-cram):
  [native-inputs]: Remove python-coverage.
  [build-system]: Move to pyproject-build-system.
  [arguments]<#:phases>: Adapt check and patch-source phases
  to coverage removal.

Change-Id: I83fafcdcfbc977f9d3e3411d01d23d9a0e120ec6
---
 gnu/packages/python-xyz.scm | 16 ++++------------
 1 file changed, 4 insertions(+), 12 deletions(-)

Toggle diff (36 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e84ce7df3eb..108b32d0459 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -15081,25 +15081,17 @@ (define-public python-cram
                ;; causes the line showing the default shell to break into two
                ;; lines, but the test expects a single line...
                (("env\\['COLUMNS'\\] = '80'")
-                "env['COLUMNS'] = '160'"))
-
-             (substitute* "Makefile"
-               ;; Recent versions of python-coverage have caused the test
-               ;; coverage to decrease (as of version 0.7).  Allow that.
-               (("--fail-under=100")
-                "--fail-under=90"))
-
-             #t))
+                "env['COLUMNS'] = '160'"))))
          (replace 'check
            ;; The test phase uses the built library and executable.
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (add-installed-pythonpath inputs outputs)
              (setenv "PATH" (string-append (getenv "PATH") ":"
                                            (assoc-ref outputs "out") "/bin"))
-             (invoke "make" "test"))))))
-    (build-system python-build-system)
+             (invoke "make" "quicktest"))))))
+    (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage python-setuptools python-wheel which))
+     (list python-setuptools python-wheel which))
     (synopsis "Simple testing framework for command line applications")
     (description
      "Cram is a functional testing framework for command line applications.
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 06/32] build-system/pyproject: Remove python-coverage input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-6-ngraves@ngraves.fr

* gnu/packages/android.scm (python-androguard):

[native-inputs]: Remove python-coverage.

[arguments]<#:phases>: Adapt 'check phase replacement.

* gnu/packages/astronomy.scm (python-asdf-astropy, python-astropy,

python-poliastro)[native-inputs]: Remove python-coverage.

* gnu/packages/bioinformatics.scm (python-ega-download-client,

python-scikit-bio, python-cooler)[native-inputs]: Remove

python-coverage.

* gnu/packages/check.scm (python-pytest-randomly,

python-pytest-flakes, python-aiounittest)[native-inputs]: Remove

python-coverage.

* gnu/packages/cpp.scm (cpplint)[native-inputs]: Remove

python-coverage.

* gnu/packages/diffoscope.scm (reprotest)[native-inputs]: Remove

python-coverage.

* gnu/packages/django.scm (python-django-haystack)[native-inputs]:

Remove python-coverage.

* gnu/packages/engineering.scm (python-scikit-rf)[native-inputs]:

Remove python-coverage.

* gnu/packages/geo.scm (python-geopy)[native-inputs]: Remove

python-coverage.

* gnu/packages/gpodder.scm (gpodder)[native-inputs]: Remove

python-coverage.

* gnu/packages/graph.scm (python-graphtools,

python-pygsp)[native-inputs]: Remove python-coverage.

* gnu/packages/jupyter.scm (python-jupyter-packaging)[native-inputs]:

Remove python-coverage.

* gnu/packages/machine-learning.scm (onnx, onnx-optimizer,

python-lightning-utilities, python-pytorch-lightning,

python-torchmetrics, python-gpytorch)[native-inputs]: Remove

python-coverage.

* gnu/packages/music.scm (python-pylast)[native-inputs]: Remove

python-coverage.

* gnu/packages/package-management.scm (python-anaconda-client,

conda)[native-inputs]: Remove python-coverage.

* gnu/packages/python-check.scm (python-vcrpy,

python-re-assert)[native-inputs]: Remove python-coverage.

* gnu/packages/python-compression.scm (python-multivolumefile,

python-pybcj, python-bcj-cffi, python-pyppmd, python-ppmd-cffi,

python-py7zr)[native-inputs]: Remove python-coverage.

* gnu/packages/python-web.scm (python-ovh, python-flask-misaka,

python-zope-interface, python-zope-hookable, python-url,

python-transaction, python-sanic, python-woob,

python-flask-combo-jsonapi)[native-inputs]: Remove python-coverage.

* gnu/packages/python-xyz.scm (python-apprise, python-arpeggio,

python-affine, python-colorful, python-lunr, python-mdit-py-plugins,

python-bidict, python-sh, python-cftime, python-can,

python-jsonargparse, python-extension-helpers, python-pyjwt,

python-virtualenv-clone, python-lsp-server, python-pikepdf,

python-tasklogger, python-notebook, python-structlog, binwalk,

python-argcomplete, python-attrs, python-yq, python-stone,

python-identify, python-nodeenv, python-anyio, python-forbiddenfruit,

python-watchgod, python-eliot, python-pem, python-scikit-build,

python-minikanren, nikola, python-verspec, python-mike)

[native-inputs]: Remove python-coverage.

* gnu/packages/simulation.scm (python-dolfin-adjoint)[native-inputs]:

Remove python-coverage.

* gnu/packages/statistics.scm (python-emcee,

python-rpy2)[native-inputs]: Remove python-coverage.

* gnu/packages/syndication.scm (rtv, tuir)[native-inputs]: Remove

python-coverage.

* gnu/packages/terminals.scm (python-halo, python-log-symbols,

python-spinners)[native-inputs]: Remove python-coverage.

* gnu/packages/textutils.scm (python-panflute)[native-inputs]: Remove

python-coverage.

* gnu/packages/version-control.scm (pre-commit)[native-inputs]: Remove

python-coverage.

* gnu/packages/web.scm (python-httpretty)[native-inputs]: Remove

python-coverage.

* gnu/packages/xml.scm (python-xmltodict)[native-inputs]: Remove

python-coverage.

Change-Id: I66b28e624aac94f1a2f6e4fae5cdb444193cd8d9

---

gnu/packages/android.scm | 6 +--

gnu/packages/astronomy.scm | 7 +--

gnu/packages/bioinformatics.scm | 8 ++--

gnu/packages/check.scm | 7 ++-

gnu/packages/cpp.scm | 3 +-

gnu/packages/diffoscope.scm | 1 -

gnu/packages/django.scm | 1 -

gnu/packages/engineering.scm | 3 +-

gnu/packages/geo.scm | 1 -

gnu/packages/gpodder.scm | 3 +-

gnu/packages/graph.scm | 3 +-

gnu/packages/jupyter.scm | 2 +-

gnu/packages/machine-learning.scm | 10 +---

gnu/packages/music.scm | 3 +-

gnu/packages/package-management.scm | 6 +--

gnu/packages/python-check.scm | 5 +-

gnu/packages/python-compression.scm | 12 ++---

gnu/packages/python-web.scm | 20 ++++----

gnu/packages/python-xyz.scm | 72 +++++++++--------------------

gnu/packages/simulation.scm | 1 -

gnu/packages/statistics.scm | 6 +--

gnu/packages/syndication.scm | 4 +-

gnu/packages/terminals.scm | 8 ++--

gnu/packages/textutils.scm | 1 -

gnu/packages/version-control.scm | 1 -

gnu/packages/web.scm | 3 +-

gnu/packages/xml.scm | 2 +-

27 files changed, 63 insertions(+), 136 deletions(-)

Toggle diff (381 lines)diff --git a/gnu/packages/android.scm b/gnu/packages/android.scm
index cbfbd6522f4..ab42f2be980 100644
--- a/gnu/packages/android.scm
+++ b/gnu/packages/android.scm
@@ -1072,11 +1072,9 @@ (define-public python-androguard
          (replace 'check
            ;; Adapted from .travis.yml
            (lambda _
-             (invoke "nosetests" "--with-coverage" "--with-timer"
-                     "--timer-top-n" "50"))))))
+             (invoke "nosetests" "--with-timer" "--timer-top-n" "50"))))))
     (native-inputs
-     (list python-codecov python-coverage python-mock python-nose
-           python-nose-timer))
+     (list python-codecov python-mock python-nose python-nose-timer))
     (propagated-inputs
      (list python-asn1crypto
            python-colorama
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index ede10ab927a..0ff2511208d 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1678,7 +1678,6 @@ (define-public python-astropy
     (native-inputs
      (list pkg-config
            python-colorlog
-           python-coverage
            python-cython-3
            python-extension-helpers
            python-h5py
@@ -2604,8 +2603,7 @@ (define-public python-poliastro
             (lambda _
               (setenv "HOME" "/tmp"))))))
     (native-inputs
-     (list python-coverage
-           python-hypothesis
+     (list python-hypothesis
            python-mypy
            python-flit-core
            python-pytest
@@ -4953,8 +4951,7 @@ (define-public python-asdf-astropy
                    (add-before 'check 'set-home-env
                      (lambda _ (setenv "HOME" "/tmp"))))))
     (native-inputs
-     (list python-coverage
-           python-h5py
+     (list python-h5py
            python-pandas
            python-pytest
            python-pytest-astropy
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4f3a3d0ba01..eabee35f70f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2766,8 +2766,7 @@ (define-public python-ega-download-client
                (("==") ">=")))))))
     (propagated-inputs (list python-htsget python-psutil python-requests
                              python-tqdm python-urllib3))
-    (native-inputs (list python-coverage
-                         python-mock
+    (native-inputs (list python-mock
                          python-pyfakefs
                          python-pytest
                          python-responses
@@ -5359,7 +5358,7 @@ (define-public python-scikit-bio
            python-requests
            python-scipy))
     (native-inputs
-     (list python-coverage python-pytest))
+     (list python-pytest))
     (home-page "https://scikit-bio.org")
     (synopsis "Data structures, algorithms and educational resources for bioinformatics")
     (description
@@ -17971,8 +17970,7 @@ (define-public python-cooler
            python-scipy
            python-simplejson))
     (native-inputs
-     (list python-coverage
-           python-hatchling
+     (list python-hatchling
            python-isort
            python-pytest
            python-pytest-cov))
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 880d3cb46f3..b7116b3f0e2 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -1617,8 +1617,7 @@ (define-public python-pytest-randomly
                          "not reordered "
                          "and not test_it_runs_before_stepwise "
                          "and not test_entrypoint_injection"))))))))
-    (native-inputs (list python-coverage
-                         python-factory-boy
+    (native-inputs (list python-factory-boy
                          python-faker
                          python-numpy
                          python-pytest-xdist))
@@ -2715,7 +2714,7 @@ (define-public python-pytest-flakes
              (add-installed-pythonpath inputs outputs)
              (invoke "py.test" "-vv" "-k" "not test_syntax_error"))))))
     (native-inputs
-     (list python-coverage python-pytest python-pytest-pep8))
+     (list python-pytest python-pytest-pep8))
     (propagated-inputs
      (list python-pyflakes))
     (home-page "https://github.com/fschulze/pytest-flakes")
@@ -3568,7 +3567,7 @@ (define-public python-aiounittest
                       #t)))))
     (propagated-inputs (list python-wrapt))
     (native-inputs
-     (list python-coverage python-nose))
+     (list python-nose))
     (home-page
      "https://github.com/kwarunek/aiounittest")
     (synopsis "Test asyncio code more easily")
diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index 8a0bd62d6b6..ba2698056da 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -1189,8 +1189,7 @@ (define-public cpplint
                    (setenv "GUIX_PYTHONPATH"
                            (getenv "TMP_PYTHONPATH")))))))
     (native-inputs
-     (list python-coverage
-           python-pytest
+     (list python-pytest
            python-pytest-cov
            python-pytest-runner
            python-testfixtures))
diff --git a/gnu/packages/diffoscope.scm b/gnu/packages/diffoscope.scm
index fd2146456d6..67567a6b310 100644
--- a/gnu/packages/diffoscope.scm
+++ b/gnu/packages/diffoscope.scm
@@ -269,7 +269,6 @@ (define-public reprotest
      `(("diffoscope" ,diffoscope)
        ("help2man" ,help2man)
        ("libfaketime" ,libfaketime)
-       ("python-coverage" ,python-coverage)
        ("python-docutils" ,python-docutils)
        ("python-magic " ,python-magic)
        ("python-pytest " ,python-pytest)
diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index 4a271eaf0b5..298968d37c6 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -495,7 +495,6 @@ (define-public python-django-haystack
      (list python-django))
     (native-inputs
      (list gdal
-           python-coverage
            python-dateutil
            python-geopy
            python-mock
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index 610fb53087b..2620d5272b6 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -2678,8 +2678,7 @@ (define-public python-scikit-rf
                              python-pyqtgraph
                              python-qtpy
                              python-scipy))
-    (native-inputs (list python-coverage
-                         python-nbval
+    (native-inputs (list python-nbval
                          python-networkx
                          python-pytest
                          python-pytest-cov
diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 69cc7e6ddc5..806120e939d 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -3264,7 +3264,6 @@ (define-public python-geopy
      (list python-geographiclib))
     (native-inputs
      (list python-async-generator
-           python-coverage
            python-isort
            python-pytest
            python-pytest-aiohttp
diff --git a/gnu/packages/gpodder.scm b/gnu/packages/gpodder.scm
index f9102d3a447..0786010471f 100644
--- a/gnu/packages/gpodder.scm
+++ b/gnu/packages/gpodder.scm
@@ -64,7 +64,6 @@ (define-public gpodder
     (build-system python-build-system)
     (native-inputs
      (list intltool
-           python-coverage
            python-minimock
            python-pytest
            python-pytest-cov
@@ -173,7 +172,7 @@ (define-public python-mygpoclient
          "1fi5x6k1mngr0iviw2s4n1f3y2x7pwqy5ivkcrjdprzvwr37f0mh"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-coverage python-minimock python-nose))
+     (list python-minimock python-nose))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index eb8aa17fdfe..f83a23dd0be 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -476,7 +476,6 @@ (define-public python-graphtools
     (native-inputs
      (list util-linux ;for lscpu
            python-anndata
-           python-coverage
            python-coveralls
            python-nose
            python-nose2
@@ -564,7 +563,7 @@ (define-public python-pygsp
                 "")))))))
     (propagated-inputs (list python-numpy python-scikit-image python-scipy))
     (native-inputs
-     (list python-coverage python-coveralls python-pytest))
+     (list python-coveralls python-pytest))
     (home-page "https://github.com/epfl-lts2/pygsp")
     (synopsis "Graph Signal Processing in Python")
     (description "The PyGSP is a Python package to ease signal processing on
diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm
index e2bef079ba0..456b0544a9a 100644
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -486,7 +486,7 @@ (define-public python-jupyter-packaging
      (list python-deprecation python-packaging python-setuptools
            python-tomlkit python-wheel))
     (native-inputs
-     (list python-pypa-build python-coverage python-pytest
+     (list python-pypa-build python-pytest
            python-pytest-cov python-pytest-mock))
     (home-page "https://jupyter.org")
     (synopsis "Jupyter packaging utilities")
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index b4f0f65c837..e6f6bfe410d 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1364,7 +1364,6 @@ (define args
      (list cmake
            googletest
            pybind11
-           python-coverage
            python-nbval
            python-pytest
            python-pytest-runner))
@@ -1443,8 +1442,7 @@ (define-public onnx-optimizer
         #~(modify-phases #$phases
             (delete 'relax-requirements)))))
     (native-inputs
-     (list cmake python-pytest python-pytest-runner python-nbval
-           python-coverage))
+     (list cmake python-pytest python-pytest-runner python-nbval))
     (inputs
      (list onnx protobuf pybind11))
     (propagated-inputs
@@ -4487,7 +4485,6 @@ (define-public python-lightning-utilities
     (build-system python-build-system)
     (propagated-inputs (list python-importlib-metadata python-packaging
                              python-typing-extensions))
-    (native-inputs (list python-coverage))
     (home-page "https://github.com/Lightning-AI/utilities")
     (synopsis "PyTorch Lightning sample project")
     (description "This package provides common Python utilities and GitHub
@@ -4700,7 +4697,6 @@ (define-public python-pytorch-lightning
     (native-inputs
      (list python-aiohttp
            python-cloudpickle
-           python-coverage
            python-flaky
            python-pympler
            python-pytest
@@ -4730,7 +4726,6 @@ (define-public python-torchmetrics
            python-typing-extensions))
     (native-inputs
      (list python-cloudpickle
-           python-coverage
            python-fire
            python-mir-eval
            python-mypy
@@ -5131,8 +5126,7 @@ (define-public python-gpytorch
            #~(list "-k" (string-append "not test_deprecated_methods"
                                        " and not test_t_matmul_matrix"))))
     (propagated-inputs (list python-linear-operator python-scikit-learn))
-    (native-inputs (list python-coverage
-                         python-flake8-print
+    (native-inputs (list python-flake8-print
                          python-nbval
                          python-pytest
                          python-setuptools
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 3af2b79b419..5420a140657 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -4069,8 +4069,7 @@ (define-public python-pylast
     ;; https://github.com/pylast/pylast/issues/105
     (arguments '(#:tests? #f))
     (native-inputs
-     (list python-coverage python-pytest python-flaky python-pyyaml
-           python-setuptools-scm))
+     (list python-pytest python-flaky python-pyyaml python-setuptools-scm))
     (home-page "https://github.com/pylast/pylast")
     (synopsis "Python interface to Last.fm and Libre.fm")
     (description "A Python interface to Last.fm and other API-compatible
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index feed16ebcef..4e7e46bf1b3 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -1100,8 +1100,7 @@ (define-public python-anaconda-client
      (list python-clyent python-nbformat python-pyyaml python-requests
            python-setuptools))
     (native-inputs
-     (list python-coverage
-           python-dateutil
+     (list python-dateutil
            python-freezegun
            python-mock
            python-pillow
@@ -1286,8 +1285,7 @@ (define-public conda
            ;; XXX: This is dragged in by libarchive and is needed at runtime.
            zstd))
     (native-inputs
-     (list python-coverage
-           python-flaky
+     (list python-flaky
            python-pytest-timeout
            python-pytest-xprocess
            python-wheel))
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 83fd723d12b..574a93782ce 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -411,8 +411,7 @@ (define-public python-vcrpy
     (propagated-inputs
      (list python-pyyaml python-six python-wrapt python-yarl))
     (native-inputs
-     (list python-coverage
-           python-flake8
+     (list python-flake8
            python-flask
            python-httplib2
            python-ipaddress
@@ -1145,7 +1144,7 @@ (define-public python-re-assert
            (lambda _
              (invoke "pytest" "-vv"))))))
     (native-inputs
-     (list python-covdefaults python-coverage python-pytest))
+     (list python-covdefaults python-pytest))
     (propagated-inputs
      (list python-regex))
     (home-page "https://github.com/asottile/re-assert")
diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm
index 34a9cd73a20..b2d789c92d0 100644
--- a/gnu/packages/python-compression.scm
+++ b/gnu/packages/python-compression.scm
@@ -109,7 +109,6 @@ (define-public python-multivolumefile
     (build-system pyproject-build-system)
     (native-inputs
      (list python-setuptools-scm
-           python-coverage
            python-coveralls
            python-hypothesis
            python-pyannotate
@@ -247,8 +246,7 @@ (define-public python-pybcj
     (build-system pyproject-build-system)
     (propagated-inputs (list python-importlib-metadata))
     (native-inputs
-     (list python-coverage
-           python-hypothesis
+     (list python-hypothesis
            python-pytest
            python-pytest-cov
            python-setuptools-scm
@@ -281,8 +279,7 @@ (define-public python-bcj-cffi
     (propagated-inputs
      (list python-cffi python-toml python-setuptools-scm))
     (native-inputs
-     (list python-setuptools python-coverage python-pytest
-           python-pytest-cov))
+     (list python-setuptools python-pytest python-pytest-cov))
     (home-page "https

This message was truncated. Download the full message here.

Nicolas Graves wrote 10 months ago

[PATCH 08/32] gnu: u-boot-tools: Remove python-coverage native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-8-ngraves@ngraves.fr

* gnu/packages/bootloaders.scm (u-boot-tools):

[native-inputs]: Remove python-coverage.

[arguments]<#:phases>: Adapt patch phase.

Change-Id: I94394544079197b4a3f8c53cc0b3d78d1f5dc8be

---

gnu/packages/bootloaders.scm | 17 ++++-------------

1 file changed, 4 insertions(+), 13 deletions(-)

Toggle diff (44 lines)diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm
index 0e7bc66bd75..cf568b2bd6a 100644
--- a/gnu/packages/bootloaders.scm
+++ b/gnu/packages/bootloaders.scm
@@ -802,8 +802,7 @@ (define-public u-boot-tools
     (name "u-boot-tools")
     (native-inputs
      (modify-inputs (package-native-inputs u-boot)
-       (prepend python-coverage
-                python-filelock
+       (prepend python-filelock
                 python-pycryptodomex
                 python-pytest
                 python-pytest-xdist
@@ -820,14 +819,6 @@ (define-public u-boot-tools
                (("/bin/false") (which "false")))
              (substitute* "tools/dtoc/fdt_util.py"
                (("'cc'") "'gcc'"))
-             (substitute* "tools/u_boot_pylib/test_util.py"
-               ;; python3-coverage is simply called coverage in guix.
-               (("python3-coverage") "coverage")
-
-               ;; Don't require 100% coverage since it's brittle and can
-               ;; fail with newer versions of coverage or dependencies.
-               (("raise ValueError\\('Test coverage failure'\\)")
-                "print('Continuing anyway since Guix does not care :O')"))
              (substitute* "test/run"
                ;; Make it easier to find test failures.
                (("#!/bin/bash") "#!/bin/bash -x")
@@ -838,9 +829,9 @@ (define-public u-boot-tools
                ;; FIXME: test_spl fails, needs further investiation
                (("test_ofplatdata or test_handoff or test_spl")
                 "test_ofplatdata or test_handoff")
-               ;; FIXME: code coverage not working
-               (("run_test \"binman code coverage\"")
-                "# run_test \"binman code coverage\"")
+               ;; Disable code coverage tests.
+               (("run_test \"(\\w+) code coverage\"" all)
+                (string-append "# " all))
                ;; This test would require internet access.
                (("\\./tools/buildman/buildman") (which "true")))
              (substitute* "test/py/tests/test_sandbox_exit.py"
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 09/32] gnu: python-aiosqlite: Remove python-coverage native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-9-ngraves@ngraves.fr

* gnu/packages/databases.scm (python-aiosqlite):

[arguments]<#:phases>: Adapt check phase.

[native-inputs]: Remove python-coverage.

Change-Id: I165d174426022f0603223e3def91ffe280f15899

---

gnu/packages/databases.scm | 5 +----

1 file changed, 1 insertion(+), 4 deletions(-)

Toggle diff (19 lines)diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 96b2c2a0437..f9202639c53 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -3935,11 +3935,8 @@ (define-public python-aiosqlite
                         (replace 'check
                           (lambda* (#:key tests? #:allow-other-keys)
                             (when tests?
-                              (invoke "python" "-m" "coverage" "run" "-m"
-                                      "aiosqlite.tests")
-                              (invoke "python" "-m" "coverage" "report")))))))
+                              (invoke "python" "-m" "aiosqlite.tests")))))))
     (native-inputs (list python-flit-core
-                         python-coverage
                          python-mypy))
     (home-page "https://github.com/jreese/aiosqlite")
     (synopsis
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 10/32] gnu: python-openid: Remove python-coverage native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-10-ngraves@ngraves.fr

* gnu/packages/python-web.scm (python-openid):

[native-inputs]: Remove python-coverage.

[arguments]<#:phases>: Rewrite check phase.

Change-Id: Id4ea5abc531f5fd84b60ff22407eb608f1e6ac29

---

gnu/packages/python-web.scm | 17 +++++++++--------

1 file changed, 9 insertions(+), 8 deletions(-)

Toggle diff (33 lines)diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 942999f6cf9..fe79f629bb8 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -2341,17 +2341,18 @@ (define-public python-openid
          "1bxf9a3ny1js422j962zfzl4a9dhj192pvai05whn7j0iy9gdyrk"))))
     (build-system python-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-        (replace 'check
-          (lambda* (#:key tests? #:allow-other-keys)
-            (when tests?
-              (invoke "coverage" "run" "-m"
-                      "unittest" "openid.test.test_suite")))))))
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (if tests?
+                  (invoke "python" "-m" "unittest" "openid.test.test_suite")
+                  (format #t "test suite not run~%")))))))
     (propagated-inputs
      (list python-defusedxml))
     (native-inputs
-     (list python-coverage python-psycopg2 python-django))
+     (list python-psycopg2 python-django))
     (home-page "https://github.com/necaris/python3-openid")
     (synopsis "OpenID support for servers and consumers")
     (description "This library provides OpenID authentication for Python, both
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 11/32] build-system/pyproject: Remove python-coveralls native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-11-ngraves@ngraves.fr

* gnu/packages/geo.scm (python-cartopy)[native-inputs]: Remove

python-coveralls.

* gnu/packages/graph.scm (python-graphtools,

python-pygsp)[native-inputs]: Remove python-coveralls.

* gnu/packages/python-compression.scm (python-multivolumefile,

python-py7zr)[native-inputs]: Remove python-coveralls.

* gnu/packages/python-science.scm (python-trimesh)[native-inputs]:

Remove python-coveralls.

* gnu/packages/python-web.scm (python-flask-combo-jsonapi)

[native-inputs]: Remove python-coveralls.

* gnu/packages/python-xyz.scm (python-affine, python-cftime,

python-ddlparse, python-tasklogger, python-minikanren,

python-arpeggio)[native-inputs]: Remove python-coveralls.

* gnu/packages/syndication.scm (rtv, tuir)[native-inputs]: Remove

python-coveralls.

* gnu/packages/telegram.scm (tgcli)[native-inputs]: Remove

python-coveralls.

Change-Id: I47b3c21f985175876618f1457b242e6841eb6d3b

---

gnu/packages/geo.scm | 3 +--

gnu/packages/graph.scm | 3 +--

gnu/packages/python-compression.scm | 2 --

gnu/packages/python-science.scm | 3 +--

gnu/packages/python-web.scm | 3 +--

gnu/packages/python-xyz.scm | 12 ++++--------

gnu/packages/syndication.scm | 4 +---

gnu/packages/telegram.scm | 3 +--

8 files changed, 10 insertions(+), 23 deletions(-)

Toggle diff (179 lines)diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 806120e939d..be96e6800a3 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -1479,8 +1479,7 @@ (define-public python-cartopy
     (inputs
      (list geos))
     (native-inputs
-     (list python-coveralls
-           python-cython
+     (list python-cython
            python-pytest
            python-pytest-cov
            python-pytest-mpl
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index f83a23dd0be..d66a3676fd2 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -476,7 +476,6 @@ (define-public python-graphtools
     (native-inputs
      (list util-linux ;for lscpu
            python-anndata
-           python-coveralls
            python-nose
            python-nose2
            python-pandas
@@ -563,7 +562,7 @@ (define-public python-pygsp
                 "")))))))
     (propagated-inputs (list python-numpy python-scikit-image python-scipy))
     (native-inputs
-     (list python-coveralls python-pytest))
+     (list python-pytest))
     (home-page "https://github.com/epfl-lts2/pygsp")
     (synopsis "Graph Signal Processing in Python")
     (description "The PyGSP is a Python package to ease signal processing on
diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm
index b2d789c92d0..5faf7b2a3cb 100644
--- a/gnu/packages/python-compression.scm
+++ b/gnu/packages/python-compression.scm
@@ -109,7 +109,6 @@ (define-public python-multivolumefile
     (build-system pyproject-build-system)
     (native-inputs
      (list python-setuptools-scm
-           python-coveralls
            python-hypothesis
            python-pyannotate
            python-pytest
@@ -474,7 +473,6 @@ (define-public python-py7zr
      (list python-setuptools
            python-wheel
            python-setuptools-scm
-           python-coveralls
            python-libarchive-c
            python-py-cpuinfo
            python-pyannotate
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index f82feab0963..9301e82bb60 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -653,8 +653,7 @@ (define-public python-trimesh
                 (("\\$MESH_PRE")
                  "'$MESH_PRE'")))))))
     (native-inputs
-     (list python-coveralls
-           python-pyinstrument
+     (list python-pyinstrument
            python-pytest
            python-pytest-cov))
     (propagated-inputs
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index fe79f629bb8..0e969eef306 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -8370,8 +8370,7 @@ (define-public python-flask-combo-jsonapi
            python-simplejson
            python-six))
     (native-inputs
-     (list python-coveralls
-           python-pytest
+     (list python-pytest
            python-pytest-runner))
     (home-page "https://github.com/AdCombo/flask-combo-jsonapi")
     (synopsis "Flask extension to quickly create JSON:API 1.0 REST Web APIs")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 108b32d0459..c2926bf7497 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1019,7 +1019,7 @@ (define-public python-affine
                (base32
                 "1shyvajayyzbkp9dihb4mz835jnkp0kqqbyjfqci6v43da6q2kd2"))))
     (build-system pyproject-build-system)
-    (propagated-inputs (list python-coveralls python-pydocstyle
+    (propagated-inputs (list python-pydocstyle
                              python-pytest python-pytest-cov))
     (native-inputs (list python-flit-core))
     (home-page "https://github.com/rasterio/affine")
@@ -3070,7 +3070,6 @@ (define-public python-cftime
      (list python-numpy))
     (native-inputs
      (list python-check-manifest
-           python-coveralls
            python-cython
            python-pytest-cov
            python-sphinx
@@ -5678,7 +5677,6 @@ (define-public python-ddlparse
     (build-system pyproject-build-system)
     (native-inputs
      (list python-codecov
-           python-coveralls
            python-pytest
            python-pytest-cov
            python-setuptools
@@ -16022,7 +16020,7 @@ (define-public python-tasklogger
         (base32 "1901mibcp6aiyjy8afnybrxnb0dkbdxlbvjqbr3gginlw7dr18xh"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-deprecated))
-    (native-inputs (list python-coveralls python-nose2
+    (native-inputs (list python-nose2
                          python-numpy python-setuptools python-wheel))
     (home-page "https://github.com/scottgigante/tasklogger")
     (synopsis "Extension to the core Python logging library")
@@ -34093,8 +34091,7 @@ (define-public python-minikanren
                         (invoke "python" "-m" "pytest" "-v" "tests/" "kanren/"))
                       #t)))))
     (native-inputs
-     (list python-coveralls
-           python-pydocstyle
+     (list python-pydocstyle
            python-pytest
            python-pytest-cov
            python-pylint
@@ -35928,8 +35925,7 @@ (define-public python-arpeggio
                (base32
                 "0ggdsck1wpladd5bh9drhkmm86bblgk2wagrhn3sdf4v04wkic6n"))))
     (build-system python-build-system)
-    (native-inputs (list python-coveralls
-                         python-mike
+    (native-inputs (list python-mike
                          python-mkdocs
                          python-pytest
                          python-pytest-runner
diff --git a/gnu/packages/syndication.scm b/gnu/packages/syndication.scm
index 0a6ff765c30..a9980f1777d 100644
--- a/gnu/packages/syndication.scm
+++ b/gnu/packages/syndication.scm
@@ -434,7 +434,6 @@ (define-public rtv
            python-requests python-six))
     (native-inputs
      (list ncurses
-           python-coveralls
            python-mock
            python-pytest
            python-vcrpy))
@@ -467,8 +466,7 @@ (define-public tuir
      (list python-beautifulsoup4 python-decorator python-kitchen
            python-requests python-six))
     (native-inputs
-     (list python-coveralls
-           python-mock
+     (list python-mock
            python-pytest
            python-vcrpy
            python-setuptools
diff --git a/gnu/packages/telegram.scm b/gnu/packages/telegram.scm
index 358374a5bb7..c5930180e6a 100644
--- a/gnu/packages/telegram.scm
+++ b/gnu/packages/telegram.scm
@@ -790,8 +790,7 @@ (define-public tgcli
                (add-installed-pythonpath inputs outputs)
                (invoke "pytest" "tests")))))))
     (native-inputs
-     `(("coveralls" ,python-coveralls)
-       ("pytest" ,python-pytest)
+     `(("pytest" ,python-pytest)
        ("pytest-click" ,python-pytest-click)
        ("pytest-cov" ,python-pytest-cov)
        ("mkdocs" ,python-mkdocs)
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 13/32] gnu: python-versioneer: Remove python-pycodestyle native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-13-ngraves@ngraves.fr

* gnu/packages/python-xyz.scm (python-versioneer):

[arguments]<#:phases>: Remove pycodestyle invocation in check phase.

[native-inputs]: Remove python-pycodestyle.

Change-Id: Ida3fd1e16cb8656be2af666203a82cb9f6d65f75

---

gnu/packages/python-xyz.scm | 6 ++----

1 file changed, 2 insertions(+), 4 deletions(-)

Toggle diff (20 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 18e4d21f136..8e54608678d 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -32658,11 +32658,9 @@ (define-public python-versioneer
                 (invoke "python" "setup.py" "make_long_version_py_git")
                 (invoke "pyflakes" "setup.py" "versioneer.py" "git_version.py")
                 (invoke "python" "test/run_pyflakes_src.py")
-                (invoke "pyflakes" "test")
-                (invoke "pycodestyle" "--max-line-length=88"
-                        "git_version.py" "versioneer.py")))))))
+                (invoke "pyflakes" "test")))))))
     (native-inputs
-     (list git-minimal python-pycodestyle python-pyflakes
+     (list git-minimal python-pyflakes
            python-pypa-build python-setuptools python-wheel))
     (propagated-inputs
      (list python-tomli))
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 15/32] gnu: python-re-assert: Remove python-covdefaults native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-15-ngraves@ngraves.fr

* gnu/packages/python-check.scm (python-re-assert):

[native-inputs]: Remove python-covdefaults.

Change-Id: Ib30c58b69aef7f255e5893ae6f9a33bdf41ac85d

---

gnu/packages/python-check.scm | 2 +-

1 file changed, 1 insertion(+), 1 deletion(-)

Toggle diff (15 lines)diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 574a93782ce..3281e5a772b 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -1144,7 +1144,7 @@ (define-public python-re-assert
            (lambda _
              (invoke "pytest" "-vv"))))))
     (native-inputs
-     (list python-covdefaults python-pytest))
+     (list python-pytest))
     (propagated-inputs
      (list python-regex))
     (home-page "https://github.com/asottile/re-assert")
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 16/32] build-system/pyproject: Remove python-codecov native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-16-ngraves@ngraves.fr

* gnu/packages/android.scm (python-androguard)[native-inputs]: Remove

python-codecov.

* gnu/packages/astronomy.scm (python-wiimatch, python-tweakwcs)

[native-inputs]: Remove python-codecov.

* gnu/packages/python-check.scm (python-pytest-trio):

[arguments]<#:test-flags>: Remove --cov flag.

[native-inputs]: Remove python-pytest-cov.

* gnu/packages/python-xyz.scm (python-can,

python-ddlparse)[native-inputs]: Remove python-codecov.

Change-Id: Ic7d3789b3b30d3263f61442bb4e55fd332a4d2f6

---

gnu/packages/android.scm | 2 +-

gnu/packages/astronomy.scm | 8 +++-----

gnu/packages/python-check.scm | 5 ++---

gnu/packages/python-xyz.scm | 4 +---

4 files changed, 7 insertions(+), 12 deletions(-)

Toggle diff (86 lines)diff --git a/gnu/packages/android.scm b/gnu/packages/android.scm
index ab42f2be980..7cc1fa4ef05 100644
--- a/gnu/packages/android.scm
+++ b/gnu/packages/android.scm
@@ -1074,7 +1074,7 @@ (define-public python-androguard
            (lambda _
              (invoke "nosetests" "--with-timer" "--timer-top-n" "50"))))))
     (native-inputs
-     (list python-codecov python-mock python-nose python-nose-timer))
+     (list python-mock python-nose python-nose-timer))
     (propagated-inputs
      (list python-asn1crypto
            python-colorama
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 0ff2511208d..c2d874f8f3f 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4605,8 +4605,7 @@ (define-public python-tweakwcs
            python-stsci-imagestats
            python-stsci-stimage))
     (native-inputs
-     (list python-codecov
-           python-pytest
+     (list python-pytest
            python-pytest-cov
            python-scipy
            python-setuptools
@@ -5272,9 +5271,8 @@ (define-public python-wiimatch
                 "15kq7z30m9i286ncs9xvpaq3dq1p5fa47jz21prq146qwr7j6dm8"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-numpy python-scipy python-setuptools))
-    (native-inputs (list python-codecov python-pytest python-pytest-cov
-                         python-pytest-doctestplus python-setuptools-scm
-                         python-wheel))
+    (native-inputs (list python-pytest python-pytest-cov python-wheel
+                         python-pytest-doctestplus python-setuptools-scm))
     (home-page "https://github.com/spacetelescope/wiimatch")
     (synopsis
      "Optimal matching of weighted N-dimensional image intensity data")
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 3281e5a772b..5345a15e108 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -1191,7 +1191,7 @@ (define-public python-pytest-trio
     (arguments
      (list
       #:test-flags '(list "-W" "error" "-ra" "-v" "--pyargs"
-                          "pytest_trio" "--verbose" "--cov" "-k"
+                          "pytest_trio" "--verbose" "-k"
                           (string-append
                            ;; Needs network
                            "not test_async_yield_fixture_with_nursery"
@@ -1199,8 +1199,7 @@ (define-public python-pytest-trio
                            ;; No keyboard interrupt in our build environment.
                            " and not test_actual_test"))))
     (native-inputs
-     (list python-hypothesis python-pytest python-pytest-cov
-           python-setuptools python-wheel))
+     (list python-hypothesis python-pytest python-setuptools python-wheel))
     (propagated-inputs
       (list python-async-generator python-outcome python-pytest python-trio))
     (home-page "https://github.com/python-trio/pytest-trio")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index c4167de452d..ca6d5279d19 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3572,7 +3572,6 @@ (define-public python-can
            python-setuptools))
     (native-inputs
      (list ;; python-canalystii ; Not packed yet
-           python-codecov
            python-future
            python-hypothesis
            python-mock
@@ -5675,8 +5674,7 @@ (define-public python-ddlparse
         (base32 "1nh8m6rxslwk05daxshxmgk41qfp18yynydba49b13l4m8dnh634"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-codecov
-           python-pytest
+     (list python-pytest
            python-pytest-cov
            python-setuptools
            python-tox
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 12/32] build-system/pyproject: Remove python-pycodestyle native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-12-ngraves@ngraves.fr

* gnu/packages/python-science.scm (python-scipy):

[native-inputs]: Remove python-pycodestyle.

* gnu/packages/python-xyz.scm (python-jsonargparse, python-lsp-server,

python-orderedmultidict, python-progressbar2, python-stem)

[native-inputs]: Remove python-pycodestyle.

Change-Id: I4518bae13aa0e688bc6e0bb40c07082414e8130f

---

gnu/packages/python-science.scm | 1 -

gnu/packages/python-xyz.scm | 7 ++-----

2 files changed, 2 insertions(+), 6 deletions(-)

Toggle diff (60 lines)diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 9301e82bb60..e20cb56db9c 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -296,7 +296,6 @@ (define-public python-scipy
            python-doit
            python-hypothesis
            python-pooch
-           python-pycodestyle
            python-pydevtool
            python-pytest
            python-pytest-cov
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index c2926bf7497..18e4d21f136 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4510,7 +4510,6 @@ (define-public python-jsonargparse
            python-typeshed-client))
     (native-inputs
      (list python-attrs
-           python-pycodestyle
            python-pydantic
            python-pytest
            python-pytest-subtests
@@ -8180,7 +8179,6 @@ (define-public python-lsp-server
            python-jedi
            python-lsp-jsonrpc
            python-pluggy
-           python-pycodestyle
            python-pydocstyle
            python-ujson
            python-whatthepatch
@@ -9915,7 +9913,7 @@ (define-public python-orderedmultidict
     (propagated-inputs
      (list python-six))
     (native-inputs
-     (list python-flake8 python-pycodestyle python-setuptools python-wheel))
+     (list python-flake8 python-setuptools python-wheel))
     (home-page "https://github.com/gruns/orderedmultidict")
     (synopsis "Python Ordered Multivalue Dictionary - omdict")
     (description "This package contains a library for ordered multivalue
@@ -18660,7 +18658,6 @@ (define-public python-progressbar2
      (list python-six python-utils))
     (native-inputs
      (list python-freezegun
-           python-pycodestyle
            python-pytest
            python-pytest-cache
            python-pytest-cov
@@ -22174,7 +22171,7 @@ (define-public python-stem
              (invoke "./run_tests.py" "--unit")
              #t)))))
     (native-inputs
-     (list python-mock python-pycodestyle python-pyflakes))
+     (list python-mock python-pyflakes))
     (home-page "https://stem.torproject.org/")
     (synopsis
      "Python controller library that allows applications to interact with Tor")
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 14/32] gnu: python-versioneer: Remove python-pyflakes native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-14-ngraves@ngraves.fr

* gnu/packages/python-xyz.scm (python-versioneer):

[arguments]<#:phases>: Remove pyflakes tests.

[native-inputs]: Remove python-pyflakes.

Change-Id: If2b8ab397f2ad25f73c434d28d8382f13d417f94

---

gnu/packages/python-xyz.scm | 8 ++------

1 file changed, 2 insertions(+), 6 deletions(-)

Toggle diff (22 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 8e54608678d..c4167de452d 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -32655,13 +32655,9 @@ (define-public python-versioneer
                 (invoke "python" "test/git/test_git.py" "-v")
                 ;; Some invocation tests require the network.
                 ;;(invoke "python" "test/git/test_invocations.py" "-v")
-                (invoke "python" "setup.py" "make_long_version_py_git")
-                (invoke "pyflakes" "setup.py" "versioneer.py" "git_version.py")
-                (invoke "python" "test/run_pyflakes_src.py")
-                (invoke "pyflakes" "test")))))))
+                (invoke "python" "setup.py" "make_long_version_py_git")))))))
     (native-inputs
-     (list git-minimal python-pyflakes
-           python-pypa-build python-setuptools python-wheel))
+     (list git-minimal python-pypa-build python-setuptools python-wheel))
     (propagated-inputs
      (list python-tomli))
     (home-page "https://github.com/python-versioneer/python-versioneer")
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 17/32] build-system/pyproject: Remove python-tox native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-17-ngraves@ngraves.fr

* gnu/packages/check.scm (python-pytest-regressions)[native-inputs]:

Remove python-tox.

* gnu/packages/diffoscope.scm (reprotest)[native-inputs]: Remove

python-tox.

* gnu/packages/django.scm (python-django-extensions)[native-inputs]:

Remove python-tox.

* gnu/packages/logging.scm (tailon)[native-inputs]: Remove python-tox.

* gnu/packages/messaging.scm (python-harmony)[native-inputs]: Remove

python-tox.

* gnu/packages/python-check.scm (python-vcrpy)[native-inputs]: Remove

python-tox.

* gnu/packages/python-web.scm (python-omnipath,

python-sanic)[native-inputs]: Remove python-tox.

* gnu/packages/python-xyz.scm (python-lunr, python-bidict,

python-jsonargparse, python-ddlparse, python-virtualenv-clone,

python-honcho, python-pdfminer-six, python-shshsh,

python-marshmallow-jsonapi, python-apispec-webframeworks, bpython,

python-loguru, python-ansicolors)[native-inputs]: Remove python-tox.

* gnu/packages/radio.scm (chirp)[native-inputs]: Remove python-tox.

* gnu/packages/terminals.scm (python-halo, python-log-symbols,

python-spinners)[native-inputs]: Remove python-tox.

Change-Id: I39dadb40a73ad1c64ba8b9ef9d1b3fe7d1498b5a

---

gnu/packages/check.scm | 1 -

gnu/packages/diffoscope.scm | 1 -

gnu/packages/django.scm | 1 -

gnu/packages/logging.scm | 2 +-

gnu/packages/messaging.scm | 2 --

gnu/packages/python-check.scm | 1 -

gnu/packages/python-web.scm | 2 --

gnu/packages/python-xyz.scm | 27 ++++++++-------------------

gnu/packages/radio.scm | 3 +--

gnu/packages/terminals.scm | 6 +++---

10 files changed, 13 insertions(+), 33 deletions(-)

Toggle diff (263 lines)diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index b7116b3f0e2..6042f763f15 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -3675,7 +3675,6 @@ (define-public python-pytest-regressions
            python-pandas
            python-pillow
            python-restructuredtext-lint
-           python-tox
            python-setuptools-scm
            python-pytest))
     (home-page "https://github.com/ESSS/pytest-regressions")
diff --git a/gnu/packages/diffoscope.scm b/gnu/packages/diffoscope.scm
index 67567a6b310..bfe4ce99fdc 100644
--- a/gnu/packages/diffoscope.scm
+++ b/gnu/packages/diffoscope.scm
@@ -273,7 +273,6 @@ (define-public reprotest
        ("python-magic " ,python-magic)
        ("python-pytest " ,python-pytest)
        ("python-tlsh" ,python-tlsh)
-       ("python-tox" ,python-tox)
        ("unzip" ,unzip)
        ("xxd" ,xxd)))
     (build-system python-build-system)
diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index 298968d37c6..f5b1e0462bb 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -260,7 +260,6 @@ (define-public python-django-extensions
     (native-inputs
      (list python-mock
            python-factory-boy
-           python-tox
            python-pytest
            python-pytest-cov
            python-pytest-django
diff --git a/gnu/packages/logging.scm b/gnu/packages/logging.scm
index a757c22154f..3c593001d00 100644
--- a/gnu/packages/logging.scm
+++ b/gnu/packages/logging.scm
@@ -134,7 +134,7 @@ (define-public tailon
          "0xkmrivzilsc9wqr8ms67v7399gxnh7pv5687k4rdpdgz4309fwc"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-tox python-wheel))
+     (list python-wheel))
     (inputs
      (list python-pyyaml-5 python-sockjs-tornado python-tornado-http-auth
            python-tornado python-deepmerge))
diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index cb72bfb3e25..35ff807e12c 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -3504,8 +3504,6 @@ (define-public python-harmony
                (base32
                 "1bm9xcnzpnpj6rlhbrnl2abwclzl7ivgh1vb5644y9mnhcs489js"))))
     (build-system python-build-system)
-    (native-inputs
-     (list python-tox))
     (inputs
      (list python-librecaptcha python-keyring python-requests))
     (synopsis "Discord account management")
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 5345a15e108..7f1c73ee0ad 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -419,7 +419,6 @@ (define-public python-vcrpy
            python-pytest
            python-pytest-cov
            python-pytest-httpbin
-           python-tox
            python-urllib3))
     (home-page "https://github.com/kevin1024/vcrpy")
     (synopsis "Automatically mock your HTTP interactions")
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 0e969eef306..fa908ceafd9 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -2137,7 +2137,6 @@ (define-public python-omnipath
            python-pytest-socket
            python-requests-mock
            python-setuptools-scm
-           python-tox
            python-setuptools
            python-wheel))
     (home-page "https://omnipathdb.org/")
@@ -7634,7 +7633,6 @@ (define-public python-sanic
            python-setuptools
            python-slotscheck
            python-towncrier
-           python-tox
            python-types-ujson
            python-uvicorn
            python-wheel))
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index ca6d5279d19..32a18f52d20 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1308,8 +1308,7 @@ (define-public python-lunr
      (list python-hatch-fancy-pypi-readme
            python-hatchling
            python-pytest
-           python-pytest-timeout
-           python-tox))
+           python-pytest-timeout))
     (propagated-inputs
      (list python-importlib-metadata python-typing-extensions))
     (home-page
@@ -2695,8 +2694,7 @@ (define-public python-bidict
            python-sortedcollections
            python-sortedcontainers
            python-sphinx
-           python-sphinx-autodoc-typehints
-           python-tox))
+           python-sphinx-autodoc-typehints))
     (arguments
      `(#:phases (modify-phases %standard-phases
                   (add-after 'unpack 'relax-reqs
@@ -4513,7 +4511,6 @@ (define-public python-jsonargparse
            python-pytest
            python-pytest-subtests
            python-responses
-           python-tox
            python-types-requests
            python-setuptools
            python-wheel))
@@ -5677,7 +5674,6 @@ (define-public python-ddlparse
      (list python-pytest
            python-pytest-cov
            python-setuptools
-           python-tox
            python-wheel))
     (propagated-inputs (list python-pyparsing))
     (home-page "https://github.com/shinichi-takii/ddlparse")
@@ -6219,7 +6215,6 @@ (define-public python-virtualenv-clone
                               (delete-file "tox.ini")
                               (invoke "pytest" "-vvv" "tests")))))))
     (native-inputs (list python-pytest
-                         python-tox
                          python-virtualenv
                          python-wheel
                          python-tomli
@@ -11332,7 +11327,7 @@ (define-public python-honcho
         (base32 "1y0r8dw4pqcq7r4n58ixjdg1iy60lp0gxsd7d2jmhals16ij71rj"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-pytest python-mock python-tox which)) ;for tests
+     (list python-pytest python-mock which)) ;for tests
     (propagated-inputs
      (list python-jinja2))
     (arguments
@@ -20125,7 +20120,7 @@ (define-public python-pdfminer-six
     (propagated-inputs
      (list python-chardet python-cryptography python-sortedcontainers))
     (native-inputs
-     (list python-nose python-tox))
+     (list python-nose))
     (home-page "https://github.com/pdfminer/pdfminer.six")
     (synopsis "PDF parser and analyzer")
     (description "@code{pdfminer.six} is a community maintained fork of
@@ -21272,9 +21267,7 @@ (define-public python-shshsh
          "1wzqyj1a6jj6cyv5ymzy834qm2lyq80yy1kfz0q0zayq9gm1cj7f"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-poetry-core
-           python-pytest
-           python-tox))
+     (list python-poetry-core python-pytest))
     (home-page "https://github.com/zqqqqz2000/shshsh")
     (synopsis "Write Shell commands simply and safely within Python")
     (description "This package provides a way to write Shell commands from
@@ -25140,8 +25133,7 @@ (define-public python-marshmallow-jsonapi
            python-flake8-bugbear
            python-flask
            python-mock
-           python-pytest
-           python-tox))
+           python-pytest))
     (home-page "https://github.com/marshmallow-code/marshmallow-jsonapi")
     (synopsis "JSON:API 1.0 formatting with Marshmallow")
     (description
@@ -25205,7 +25197,6 @@ (define-public python-apispec-webframeworks
            python-pytest
            python-pyyaml
            python-tornado
-           python-tox
            python-wheel))
     (home-page "https://github.com/marshmallow-code/apispec-webframeworks")
     (synopsis "Web framework plugins for apispec")
@@ -26663,7 +26654,7 @@ (define-public bpython
            python-watchdog
            python-jedi))
     (native-inputs
-     (list python-sphinx python-mock python-tox python-wheel))
+     (list python-sphinx python-mock python-wheel))
     (home-page "https://bpython-interpreter.org/")
     (synopsis "Fancy interface to the Python interpreter")
     (description "Bpython is a fancy interface to the Python
@@ -32923,7 +32914,6 @@ (define-public python-loguru
                          python-sphinx
                          python-sphinx-autobuild
                          python-sphinx-rtd-theme
-                         python-tox
                          python-setuptools
                          python-wheel))
     (home-page "https://github.com/Delgan/loguru")
@@ -35280,8 +35270,7 @@ (define-public python-ansicolors
         (base32 "1q3jqglkq4z0f6nkkn8bswcwqg012i2grrc27kabr8286dg4zycr"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-tox
-           python-pytest-cov
+     (list python-pytest-cov
            unzip))
     (home-page "https://github.com/jonathaneunice/colors/")
     (synopsis "ANSI colors for Python")
diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index 56e674a8edc..bfd601564d8 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -3171,8 +3171,7 @@ (define-public chirp
              python-pep8
              python-pytest
              python-pytest-mock
-             python-pyyaml
-             python-tox))
+             python-pyyaml))
       (inputs
        (list python-future
              python-importlib-resources
diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index e96ee664eff..a0acaa71769 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -1196,7 +1196,7 @@ (define-public python-halo
     (build-system pyproject-build-system)
     (propagated-inputs (list python-colorama python-log-symbols python-six
                              python-spinners python-termcolor))
-    (native-inputs (list python-nose python-tox
+    (native-inputs (list python-nose
                          python-twine python-setuptools python-wheel))
     (home-page "https://github.com/manrajgrover/halo")
     (synopsis "Python library to display graphical spinners in the terminal")
@@ -1224,7 +1224,7 @@ (define-public python-log-symbols
                      (("(.*)==(.*)$" _ dep ver)
                       (string-append dep ">=" ver))))))))
     (propagated-inputs (list python-colorama))
-    (native-inputs (list python-nose python-setuptools python-tox python-wheel))
+    (native-inputs (list python-nose python-setuptools python-wheel))
     (home-page "https://github.com/manrajgrover/py-log-symbols")
     (synopsis "Python library with graphical symbols for logging on the terminal")
     (description "This package provides a Python library with graphical symbols
@@ -1251,7 +1251,7 @@ (define-public python-spinners
                    (substitute* "requirements-dev.txt"
                      (("(.*)==(.*)$" _ dep ver)
                       (string-append dep ">=" ver))))))))
-    (native-inputs (list python-nose python-setuptools python-tox python-wheel))
+    (native-inputs (list python-nose python-setuptools python-wheel))
     (home-page "https://github.com/manrajgrover/py-spinners")
     (synopsis "Python library with graphical spinners for the terminal")
     (description "Spinners is a Python library that contains graphical spinners
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 19/32] gnu: python-immutables: Remove python-mypy native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-19-ngraves@ngraves.fr

* gnu/packages/python-xyz.scm (python-immutables):
  [origin]: Use git-fetch to use upstream test-data directory.
  [build-system]: Move to pyrpoject-build-system.
  [native-inputs]: Remove python-mypy.
  [arguments]<#:phases>: Add phase to remove python-mypy native-input.

Change-Id: Ie67f634ffecbc3711f354e915b2fab54a1639925
---
 gnu/packages/python-xyz.scm | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

Toggle diff (33 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index dd2b35eb35d..6fc3f0dbb06 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -15819,13 +15819,21 @@ (define-public python-immutables
     (version "0.18")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "immutables" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/MagicStack/immutables")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "1x4cinh0xbl6p6p2yfm2s07mxxy3lf0zzai9gqpydk4482bwfdjk"))))
+        (base32 "1xjbkgls0dqrvpg4yzkdzz6aayizxcv5chjc5gyynk196wyshw4m"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-mypy python-pytest
-                         python-setuptools python-wheel))
+    (arguments
+     (list #:phases #~(modify-phases %standard-phases
+                        (add-after 'unpack 'remove-mypy-dependency
+                          (lambda _
+                            (delete-file "tests/test_mypy.py")
+                            (delete-file "tests/conftest.py"))))))
+    (native-inputs (list python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/MagicStack/immutables")
     (synopsis "High-performance immutable mapping type for Python")
     (description
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 18/32] build-system/pyproject: Remove python-mypy native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-18-ngraves@ngraves.fr

* gnu/packages/astronomy.scm (python-poliastro)[native-inputs]: Remove

python-mypy.

* gnu/packages/databases.scm (python-psycopg2)[native-inputs]: Remove

python-mypy.

* gnu/packages/engineering.scm (uranium, cura)[native-inputs]: Remove

python-mypy.

* gnu/packages/graphviz.scm (python-uqbar)[native-inputs]: Remove

python-mypy.

* gnu/packages/machine-learning.scm (python-imbalanced-learn,

python-captum, python-torchmetrics, python-pyro-ppl)[native-inputs]:

Remove python-mypy.

* gnu/packages/python-science.scm (python-scipy)[native-inputs]:

Remove python-mypy.

* gnu/packages/python-web.scm (python-huggingface-hub, python-asgiref,

python-starsessions-for-pytorch-lightning,

python-fastapi)[native-inputs]: Remove python-mypy.

* gnu/packages/python-xyz.scm (python-pyls-black, kalamine,

python-pydantic-cli, python-marshmallow, python-apispec,

python-typeguard, python-trio-typing, python-verspec,

python-catalogue, python-duckdb)[native-inputs]: Remove python-mypy.

* gnu/packages/serialization.scm (python-msgspec)[native-inputs]: Remove

python-mypy.

* gnu/packages/virtualization.scm (python-transient)[native-inputs]:

Remove python-mypy.

Change-Id: I947656750aa0c7732291d826641736aaefab274e

---

gnu/packages/astronomy.scm | 1 -

gnu/packages/databases.scm | 1 -

gnu/packages/engineering.scm | 2 --

gnu/packages/graphviz.scm | 1 -

gnu/packages/machine-learning.scm | 4 ----

gnu/packages/python-science.scm | 1 -

gnu/packages/python-web.scm | 5 +----

gnu/packages/python-xyz.scm | 22 +++++++++-------------

gnu/packages/serialization.scm | 1 -

gnu/packages/virtualization.scm | 3 +--

10 files changed, 11 insertions(+), 30 deletions(-)

Toggle diff (272 lines)diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index c2d874f8f3f..426cfd8c88f 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2604,7 +2604,6 @@ (define-public python-poliastro
               (setenv "HOME" "/tmp"))))))
     (native-inputs
      (list python-hypothesis
-           python-mypy
            python-flit-core
            python-pytest
            python-pytest-cov
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index f9202639c53..ad27ec621ca 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -4112,7 +4112,6 @@ (define-public python-psycopg
                (delete 'sanity-check))))
     (native-inputs
      (list python-cython-3
-           python-mypy
            python-psycopg-pool
            python-pytest
            python-pytest-asyncio
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index 2620d5272b6..af79172e53b 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -3923,7 +3923,6 @@ (define-public uranium
            graphviz
            pkg-config
            python-pytest
-           python-mypy
            python-certifi
            python-twisted))
     (propagated-inputs
@@ -4126,7 +4125,6 @@ (define-public cura
     (build-system qt-build-system)
     (native-inputs
      (list python-certifi
-           python-mypy
            python-pytest
            python-requests))
     (inputs
diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm
index b396a97c0bc..ecc2dc2bb4c 100644
--- a/gnu/packages/graphviz.scm
+++ b/gnu/packages/graphviz.scm
@@ -218,7 +218,6 @@ (define-public python-uqbar
     (native-inputs
      (list graphviz
            python-isort
-           python-mypy
            python-pytest
            python-pytest-cov
            python-setuptools
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index e6f6bfe410d..3e3b7ab8ea8 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1920,7 +1920,6 @@ (define-public python-imbalanced-learn
     (propagated-inputs (list python-joblib python-numpy python-scikit-learn
                              python-scipy python-threadpoolctl))
     (native-inputs (list python-keras
-                         python-mypy
                          python-pandas
                          python-pytest
                          python-pytest-cov
@@ -4521,7 +4520,6 @@ (define-public python-captum
                          python-flask-compress
                          python-ipython
                          python-ipywidgets
-                         python-mypy
                          python-parameterized
                          python-pytest
                          python-pytest-cov
@@ -4728,7 +4726,6 @@ (define-public python-torchmetrics
      (list python-cloudpickle
            python-fire
            python-mir-eval
-           python-mypy
            python-pandas
            python-psutil
            python-pytest
@@ -5054,7 +5051,6 @@ (define-public python-pyro-ppl
            python-isort
            python-lap
            python-matplotlib
-           python-mypy
            python-nbformat
            python-nbsphinx
            python-nbstripout
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index e20cb56db9c..567fa5d1559 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -273,7 +273,6 @@ (define-public python-scipy
            '())
        (list python-matplotlib
              python-mpmath
-             python-mypy
              python-numpy
              python-numpydoc
              python-pydata-sphinx-theme
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index fa908ceafd9..04712745963 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -196,7 +196,6 @@ (define-public python-huggingface-hub
            python-fastapi
            python-jedi
            python-jinja2
-           python-mypy
            python-numpy
            python-pillow
            python-pydantic
@@ -717,7 +716,7 @@ (define-public python-asgiref
              (when tests?
                (invoke "pytest" "-vv")))))))
     (native-inputs
-     (list python-mypy python-pytest python-pytest-asyncio))
+     (list python-pytest python-pytest-asyncio))
     (propagated-inputs
      (list python-typing-extensions))
     (home-page "https://github.com/django/asgiref/")
@@ -8957,7 +8956,6 @@ (define-public python-starsessions-for-pytorch-lightning
            python-starlette-for-fastapi-0.88))
     (native-inputs
      (list python-httpx
-           python-mypy
            python-poetry-core
            python-pytest
            python-pytest-asyncio
@@ -9003,7 +9001,6 @@ (define-public python-fastapi
                          python-hatchling
                          python-isort
                          python-jose
-                         python-mypy
                          python-passlib
                          python-peewee
                          python-pytest
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 32a18f52d20..dd2b35eb35d 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3020,7 +3020,7 @@ (define-public python-pyls-black
     (propagated-inputs
      (list python-black python-lsp-server python-tomli))
     (native-inputs
-     (list python-isort python-mypy python-pytest
+     (list python-isort python-pytest
            python-pytest-runner python-setuptools python-wheel))
     (home-page "https://github.com/rupert/pyls-black")
     (synopsis "Black plugin for the Python Language Server")
@@ -6785,7 +6785,7 @@ (define-public kalamine
     ;; TODO: Add python-pytest-ruff to native-inputs once it has been
     ;; packaged.
     (native-inputs
-     (list python-hatchling python-mypy python-pytest))
+     (list python-hatchling python-pytest))
     (home-page "https://github.com/OneDeadKey/kalamine")
     (synopsis "Keyboard layout maker")
     (description
@@ -8002,8 +8002,7 @@ (define-public python-pydantic-cli
     (propagated-inputs
      (list python-pydantic))
     (native-inputs
-     (list python-mypy
-           python-pytest))
+     (list python-pytest))
     (home-page "https://github.com/mpkocher/pydantic-cli")
     (synopsis "Turn Pydantic defined data models into CLI tools")
     (description
@@ -23457,6 +23456,8 @@ (define-public python-duckdb
      (list
       #:test-flags
       '(list "--ignore=tests/slow/test_h2oai_arrow.py"
+             ;; stubs require mypy and don't actually check functionality.
+             "--ignore=tests/stubs/test_stubs.py"
              ;; Don't install anything, thank you.
              "-k" "not test_install_non_existent_extension")
       #:phases
@@ -23481,7 +23482,6 @@ (define-public python-duckdb
      (list pybind11
            python-fsspec
            python-google-cloud-storage
-           python-mypy
            python-numpy
            python-pandas
            python-psutil
@@ -25103,7 +25103,6 @@ (define-public python-marshmallow
      (list python-packaging))
     (native-inputs
      (list python-flake8-bugbear
-           python-mypy
            python-pytest
            python-pytz
            python-simplejson
@@ -25165,7 +25164,6 @@ (define-public python-apispec
     (native-inputs
      (list python-flake8-bugbear
            python-marshmallow
-           python-mypy
            python-pytest
            python-pyyaml
            python-setuptools
@@ -26582,8 +26580,7 @@ (define-public python-typeguard
                         ;; XXX: These fail when installed as a library:
                         ;; https://github.com/agronholm/typeguard/issues/176
                         "not usefixtures and not test_cached_module")))))))
-    (native-inputs (list python-mypy
-                         python-pytest
+    (native-inputs (list python-pytest
                          python-setuptools-scm
                          python-typing-extensions))
     (home-page "https://github.com/agronholm/typeguard")
@@ -29050,8 +29047,7 @@ (define-public python-trio-typing
     (native-inputs (list python-attrs python-pytest python-setuptools
                          python-wheel))
     (propagated-inputs
-     (list python-mypy python-mypy-extensions python-trio
-           python-typing-extensions))
+     (list python-mypy-extensions python-trio python-typing-extensions))
     (home-page "https://github.com/python-trio/trio-typing")
     (synopsis "Static type checking support for Trio and related projects")
     (description
@@ -35483,7 +35479,7 @@ (define-public python-verspec
                (base32
                 "07n06wv85fm4vl1ird2mja0823js3x322wgs9gdnq1djjyk4ql64"))))
     (build-system python-build-system)
-    (native-inputs (list python-mypy python-pretend python-pytest))
+    (native-inputs (list python-pretend python-pytest))
     (arguments
      `(#:phases (modify-phases %standard-phases
                   (replace 'check
@@ -36230,7 +36226,7 @@ (define-public python-catalogue
                 "0srdxiil2xys8q1gpc1nvzhvis3a33d8a7amk2i1rlpbg6p36pak"))))
     (build-system python-build-system)
     (native-inputs (list python-pytest))
-    (inputs (list python python-zipp python-typing-extensions python-mypy))
+    (inputs (list python python-zipp python-typing-extensions))
     (home-page "https://github.com/explosion/catalogue")
     (synopsis "Lightweight function registries for your library")
     (description
diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index 728d6404bb9..b39ce176502 100644
--- a/gnu/packages/serialization.scm
+++ b/gnu/packages/serialization.scm
@@ -719,7 +719,6 @@ (define-public python-msgspec
     (native-inputs (list python-attrs
                          python-gcovr
                          python-msgpack
-                         python-mypy
                          python-pytest
                          python-setuptools-scm
                          python-versioneer
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index b564bd043cb..b4dce1cc9d6 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -2809,8 +2809,7 @@ (define-public python-transient
            python-requests
            python-toml))
     (native-inputs
-     (list python-mypy python-pyhamcrest python-twine
-           python-setuptools python-wheel))
+     (list python-pyhamcrest python-twine python-setuptools python-wheel))
     (home-page "https://github.com/ALSchwalm/transient")
     (synopsis "QEMU Wrapper written in Python")
     (description
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 20/32] build-system/pyproject: Remove python-isort native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-20-ngraves@ngraves.fr

* gnu/packages/bioinformatics.scm (python-cooler,

scvelo)[native-inputs]: Remove python-isort.

* gnu/packages/databases.scm (aerich)[native-inputs]: Remove

python-isort.

* gnu/packages/django.scm (python-django-taggit)[native-inputs]:

Remove python-isort.

* gnu/packages/finance.scm (python-trezor)[native-inputs]: Remove

python-isort.

* gnu/packages/geo.scm (python-geopy)[native-inputs]: Remove

python-isort.

* gnu/packages/gettext.scm (mdpo)[native-inputs]: Remove python-isort.

* gnu/packages/graphviz.scm (python-uqbar)[native-inputs]: Remove

python-isort.

* gnu/packages/machine-learning.scm (python-funsor,

python-pyro-ppl)[native-inputs]: Remove python-isort.

* gnu/packages/mail.scm (python-hyperkitty, postorius)[native-inputs]:

Remove python-isort.

* gnu/packages/protobuf.scm (python-pure-protobuf)[native-inputs]:

Remove python-isort.

* gnu/packages/python-check.scm (python-pytest-toolbox)

[native-inputs]: Remove python-pytest-isort.

* gnu/packages/python-web.scm (python-ovh, python-tinycss2,

python-fastapi)[native-inputs]: Remove python-isort.

* gnu/packages/python-xyz.scm (python-jupytext, python-pyls-black,

python-eventlet, python-textdistance,

python-validators)[native-inputs]: Remove python-isort.

* gnu/packages/sphinx.scm (python-sphinx,

python-sphinx-5)[native-inputs]: Remove python-isort.

* gnu/packages/statistics.scm (python-statsmodels)[native-inputs]:

Remove python-isort.

* gnu/packages/virtualization.scm (python-qemu-qmp)[native-inputs]:

Remove python-isort.

Change-Id: I6dc9a49cdbb10ddd33ea32854f891312d3a29e53

---

gnu/packages/bioinformatics.scm | 2 --

gnu/packages/databases.scm | 1 -

gnu/packages/django.scm | 2 +-

gnu/packages/finance.scm | 1 -

gnu/packages/geo.scm | 1 -

gnu/packages/gettext.scm | 1 -

gnu/packages/graphviz.scm | 1 -

gnu/packages/machine-learning.scm | 4 +---

gnu/packages/mail.scm | 3 +--

gnu/packages/protobuf.scm | 2 +-

gnu/packages/python-check.scm | 3 +--

gnu/packages/python-web.scm | 4 +---

gnu/packages/python-xyz.scm | 7 ++-----

gnu/packages/sphinx.scm | 2 --

gnu/packages/statistics.scm | 1 -

gnu/packages/virtualization.scm | 1 -

16 files changed, 8 insertions(+), 28 deletions(-)

Toggle diff (277 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index eabee35f70f..3d5d381f0a0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -17971,7 +17971,6 @@ (define-public python-cooler
            python-simplejson))
     (native-inputs
      (list python-hatchling
-           python-isort
            python-pytest
            python-pytest-cov))
     ;; Almost all the projects of the Mirnylab are moved under Open2C umbrella
@@ -21815,7 +21814,6 @@ (define-public scvelo
     (propagated-inputs
      (list python-anndata
            python-hnswlib
-           python-isort
            python-igraph
            python-loompy
            python-louvain
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index ad27ec621ca..9ec7855109c 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -3251,7 +3251,6 @@ (define-public aerich
      (list poetry
            python-bandit
            python-cryptography
-           python-isort
            python-pydantic
            python-pytest
            python-pytest-asyncio
diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index f5b1e0462bb..48b1b38a97f 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -387,7 +387,7 @@ (define-public python-django-taggit
            (lambda _
              (invoke "python3" "-m" "django" "test" "--settings=tests.settings"))))))
     (propagated-inputs
-     (list python-django python-isort))
+     (list python-django))
     (native-inputs
      (list python-pytest python-mock))
     (home-page
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index 7579001dd1f..6f70d61f700 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -1149,7 +1149,6 @@ (define-public python-trezor
            python-typing-extensions))
     (native-inputs ; Only needed for running the tests
      (list protobuf
-           python-isort
            python-pillow
            python-protobuf
            python-pyqt
diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index be96e6800a3..73644ab2bb4 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -3263,7 +3263,6 @@ (define-public python-geopy
      (list python-geographiclib))
     (native-inputs
      (list python-async-generator
-           python-isort
            python-pytest
            python-pytest-aiohttp
            python-readme-renderer
diff --git a/gnu/packages/gettext.scm b/gnu/packages/gettext.scm
index bbb19bd4cb8..39215a0ccb6 100644
--- a/gnu/packages/gettext.scm
+++ b/gnu/packages/gettext.scm
@@ -216,7 +216,6 @@ (define-public mdpo
      (list python-bump2version
            python-flake8-implicit-str-concat
            python-flake8-print
-           python-isort
            python-pytest
            python-pytest-cov
            python-sphinx
diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm
index ecc2dc2bb4c..f6a58943ecb 100644
--- a/gnu/packages/graphviz.scm
+++ b/gnu/packages/graphviz.scm
@@ -217,7 +217,6 @@ (define-public python-uqbar
 and not test_sphinx_book_text_broken_strict")))
     (native-inputs
      (list graphviz
-           python-isort
            python-pytest
            python-pytest-cov
            python-setuptools
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 3e3b7ab8ea8..d4ce01b0c1b 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -175,8 +175,7 @@ (define-public python-funsor
     (propagated-inputs (list python-makefun python-multipledispatch
                              python-numpy python-opt-einsum
                              python-typing-extensions))
-    (native-inputs (list python-isort
-                         python-nbsphinx
+    (native-inputs (list python-nbsphinx
                          python-pandas
                          python-pillow
                          python-pyro-api
@@ -5048,7 +5047,6 @@ (define-public python-pyro-ppl
      (list ninja
            jupyter
            python-graphviz
-           python-isort
            python-lap
            python-matplotlib
            python-nbformat
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 5743558e76b..7c4b6f2cb26 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -3724,7 +3724,6 @@ (define-public python-hyperkitty
     (native-inputs
      (list python-beautifulsoup4
            python-elasticsearch
-           python-isort
            python-lxml
            python-mock
            python-whoosh))
@@ -3763,7 +3762,7 @@ (define-public postorius
      (list python-readme-renderer python-mailmanclient
            python-django python-django-mailman3))
     (native-inputs
-     (list python-beautifulsoup4 python-isort python-mock python-vcrpy))
+     (list python-beautifulsoup4 python-mock python-vcrpy))
     (home-page "https://gitlab.com/mailman/postorius")
     (synopsis "Web user interface for GNU Mailman")
     (description
diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm
index 502ad09a3a6..9c4d56bd384 100644
--- a/gnu/packages/protobuf.scm
+++ b/gnu/packages/protobuf.scm
@@ -469,7 +469,7 @@ (define-public python-pure-protobuf
         (base32 "15dp5pvazd0jx4wzzh79080ah7hkpd3axh40al9vhzs2hf3v90hx"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-pytest python-pytest-cov python-isort))
+     (list python-pytest python-pytest-cov))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 7f1c73ee0ad..d51c5e19bba 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -1487,8 +1487,7 @@ (define-public python-pytest-toolbox
                 (substitute* "setup.cfg"
                   ((".*timeout.*") ""))))))))
     (native-inputs
-     (list python-pydantic python-pytest python-pytest-isort
-           python-setuptools python-wheel))
+     (list python-pydantic python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/samuelcolvin/pytest-toolbox")
     (synopsis "Numerous useful plugins for Pytest")
     (description
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 04712745963..d4988620385 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -976,8 +976,7 @@ (define-public python-ovh
     (build-system pyproject-build-system)
     (arguments (list #:tests? #f))      ; XXX: tests require networking
     (propagated-inputs (list python-requests))
-    (native-inputs (list python-isort
-                         python-pytest
+    (native-inputs (list python-pytest
                          python-pytest-cov
                          python-setuptools
                          python-sphinx
@@ -8999,7 +8998,6 @@ (define-public python-fastapi
     (native-inputs (list python-databases
                          python-flask
                          python-hatchling
-                         python-isort
                          python-jose
                          python-passlib
                          python-peewee
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 6fc3f0dbb06..f467f5f5794 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -478,7 +478,6 @@ (define-public python-jupytext
            python-autopep8
            python-flake8
            python-gitpython
-           python-isort
            python-ipython-genutils
            python-jupyter-server
            python-pyaml
@@ -3020,7 +3019,7 @@ (define-public python-pyls-black
     (propagated-inputs
      (list python-black python-lsp-server python-tomli))
     (native-inputs
-     (list python-isort python-pytest
+     (list python-pytest
            python-pytest-runner python-setuptools python-wheel))
     (home-page "https://github.com/rupert/pyls-black")
     (synopsis "Black plugin for the Python Language Server")
@@ -4242,7 +4241,6 @@ (define-public python-eventlet
            python-hatchling
            python-hatch-vcs
            python-pytest
-           python-isort
            python-twine))
     (arguments
      (list
@@ -12910,7 +12908,6 @@ (define-public python-textdistance
              #t)))))
     (native-inputs
      (list python-hypothesis
-           python-isort
            python-numpy
            python-pytest
            python-pytest-runner
@@ -25041,7 +25038,7 @@ (define-public python-validators
     (propagated-inputs
      (list python-decorator python-six))
     (native-inputs
-     (list python-isort python-pytest))
+     (list python-pytest))
     (home-page "https://github.com/kvesteri/validators")
     (synopsis "Data validation library")
     (description
diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index 2057649ede5..e49e215de79 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -93,7 +93,6 @@ (define-public python-sphinx
            python-html5lib
            python-imagesize
            python-importlib-metadata
-           python-isort
            python-jinja2
            python-mypy
            python-packaging
@@ -191,7 +190,6 @@ (define-public python-sphinx-5
            python-html5lib
            python-imagesize
            python-importlib-metadata
-           python-isort
            python-jinja2
            python-mypy
            python-packaging
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index bfc69062587..de4fb6e3aa7 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2446,7 +2446,6 @@ (define-public python-statsmodels
     (native-inputs
      (list python-colorama
            python-cython
-           python-isort
            python-joblib
            python-matplotlib
            python-pytest
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index b4dce1cc9d6..90f46e6f23a 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -2031,7 +2031,6 @@ (define-public python-qemu-qmp
     (native-inputs
      (list python-avocado-framework
            python-flake8
-           python-isort
            python-pylint
            python-setuptools
            python-setuptools-scm
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 21/32] build-system/pyproject: Remove python-twine native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-21-ngraves@ngraves.fr

* gnu/packages/gettext.scm (mdpo)[native-inputs]: Remove python-twine.

* gnu/packages/machine-learning.scm (python-linear-operator,

python-gpytorch)[native-inputs]: Remove python-twine.

* gnu/packages/python-check.scm (python-testfixtures)[native-inputs]:

Remove python-twine.

* gnu/packages/python-web.scm (python-translation-finder)

[native-inputs]: Remove python-twine.

* gnu/packages/python-xyz.scm (python-cftime, python-eventlet,

python-eliot, python-arpeggio)[native-inputs]: Remove python-twine.

* gnu/packages/terminals.scm (python-halo)[native-inputs]: Remove

python-twine.

* gnu/packages/virtualization.scm (python-transient)[native-inputs]:

Remove python-twine.

Change-Id: Ie9ff17126810dc3e2b17ad42a1f765361401eae7

---

gnu/packages/gettext.scm | 1 -

gnu/packages/machine-learning.scm | 6 ++----

gnu/packages/python-check.scm | 2 +-

gnu/packages/python-web.scm | 2 +-

gnu/packages/python-xyz.scm | 6 +-----

gnu/packages/terminals.scm | 3 +--

gnu/packages/virtualization.scm | 2 +-

7 files changed, 7 insertions(+), 15 deletions(-)

Toggle diff (129 lines)diff --git a/gnu/packages/gettext.scm b/gnu/packages/gettext.scm
index 39215a0ccb6..b3c807c6774 100644
--- a/gnu/packages/gettext.scm
+++ b/gnu/packages/gettext.scm
@@ -221,7 +221,6 @@ (define-public mdpo
            python-sphinx
            python-sphinx-argparse
            python-sphinx-rtd-theme
-           python-twine
            python-yamllint))
     (propagated-inputs
      (list python-polib python-pymd4c))
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index d4ce01b0c1b..7c3faa94c5e 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -5093,8 +5093,7 @@ (define-public python-linear-operator
     (native-inputs (list python-flake8-print
                          python-pytest
                          python-setuptools
-                         python-setuptools-scm
-                         python-twine))
+                         python-setuptools-scm))
     (home-page "https://github.com/cornellius-gp/linear_operator/")
     (synopsis "Linear operator implementation")
     (description "LinearOperator is a PyTorch package for abstracting away the
@@ -5123,8 +5122,7 @@ (define-public python-gpytorch
     (native-inputs (list python-flake8-print
                          python-nbval
                          python-pytest
-                         python-setuptools
-                         python-twine))
+                         python-setuptools))
     (home-page "https://gpytorch.ai")
     (synopsis "Implementation of Gaussian Processes in PyTorch")
     (description
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index d51c5e19bba..4426e5af2f5 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -245,7 +245,7 @@ (define-public python-testfixtures
     (native-inputs
      (list python-pytest python-pytest-cov
            ;;("python-pytest-django" ,python-pytest-django)
-           python-twine python-wheel))
+           python-wheel))
     (synopsis "Tests components for Python")
     (description "Testfixtures is a collection of helpers and mock objects that
 are useful when writing automated tests in Python.")
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index d4988620385..3aadc9060a0 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -6221,7 +6221,7 @@ (define-public python-translation-finder
      (list python-chardet python-pathlib2 python-ruamel.yaml python-six))
     (native-inputs
      (list python-codecov python-codacy-coverage python-pytest-cov
-           python-pytest-runner python-twine))
+           python-pytest-runner))
     (home-page "https://weblate.org/")
     (synopsis "Translation file finder for Weblate")
     (description "This package provides a function to find translation file in
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f467f5f5794..4e6f0e1a29a 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3070,7 +3070,6 @@ (define-public python-cftime
            python-cython
            python-pytest-cov
            python-sphinx
-           python-twine
            python-wheel))
     (home-page "https://unidata.github.io/cftime/")
     (synopsis "Library for time handling")
@@ -4240,8 +4239,7 @@ (define-public python-eventlet
      (list python-black
            python-hatchling
            python-hatch-vcs
-           python-pytest
-           python-twine))
+           python-pytest))
     (arguments
      (list
       #:test-flags
@@ -31340,7 +31338,6 @@ (define-public python-eliot
            python-sphinx
            python-sphinx-rtd-theme
            python-testtools
-           python-twine
            python-twisted))
     (home-page "https://github.com/itamarst/eliot/")
     (synopsis "Eliot: the logging system that tells you why it happened")
@@ -35908,7 +35905,6 @@ (define-public python-arpeggio
                          python-mkdocs
                          python-pytest
                          python-pytest-runner
-                         python-twine
                          python-wheel))
     (home-page "https://github.com/textX/Arpeggio")
     (synopsis "Packrat parser interpreter for Python")
diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index a0acaa71769..6a1946719a6 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -1196,8 +1196,7 @@ (define-public python-halo
     (build-system pyproject-build-system)
     (propagated-inputs (list python-colorama python-log-symbols python-six
                              python-spinners python-termcolor))
-    (native-inputs (list python-nose
-                         python-twine python-setuptools python-wheel))
+    (native-inputs (list python-nose python-setuptools python-wheel))
     (home-page "https://github.com/manrajgrover/halo")
     (synopsis "Python library to display graphical spinners in the terminal")
     (description "Halo is a Python library to display graphical spinners in
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index 90f46e6f23a..cf090aec9fc 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -2808,7 +2808,7 @@ (define-public python-transient
            python-requests
            python-toml))
     (native-inputs
-     (list python-pyhamcrest python-twine python-setuptools python-wheel))
+     (list python-pyhamcrest python-setuptools python-wheel))
     (home-page "https://github.com/ALSchwalm/transient")
     (synopsis "QEMU Wrapper written in Python")
     (description
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 23/32] gnu: python-tinycss2: Remove python-pytest-cov native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-23-ngraves@ngraves.fr

* gnu/packages/python-web.scm (python-tinycss2):

[arguments]<#:phases>: Add phase remove-unwanted-dependency to

ignore coverage options.

[native-inputs]: Remove python-pytest-cov.

Change-Id: I853fe3371be84be1655db0ee8d1dca8d23c50ef9

---

gnu/packages/python-web.scm | 11 +++++++++--

1 file changed, 9 insertions(+), 2 deletions(-)

Toggle diff (27 lines)diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index c73bc6294e9..8c51282c9cb 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -5895,11 +5895,18 @@ (define-public python-tinycss2
        (sha256
         (base32 "0zyc48vbmczpqj7f3f0d7zb3bz29fyj50dg0m6bbwbr5i88kq3sq"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'remove-unwanted-dependencies
+            (lambda _
+              (substitute* "pyproject.toml"
+                (("^addopts.*") "")))))))
     (propagated-inputs
      (list python-webencodings))
     (native-inputs
-     (list python-flit python-pytest python-pytest-cov
-           python-pytest-flake8 python-pytest-isort))
+     (list python-flit python-pytest python-pytest-flake8 python-pytest-isort))
     (home-page "https://tinycss2.readthedocs.io/")
     (synopsis "Low-level CSS parser for Python")
     (description "@code{tinycss2} can parse strings, return Python objects
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 22/32] build-system/pyproject: Remove python-pytest-cov native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-22-ngraves@ngraves.fr

* gnu/packages/astronomy.scm (python-astroml, python-casa-formats-io,

python-cdflib, python-czml3, python-poliastro, python-tweakwcs,

python-wiimatch, python-stcal)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/audio.scm (python-pysox)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/backup.scm (borgmatic)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/bioinformatics.scm (python-biom-format, python-pyfaidx,

python-cooler, python-screed)[native-inputs]: Remove python-pytest-cov.

* gnu/packages/build-tools.scm (meson-python)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/check.scm (python-pytest-nunit, python-pytest-timeout,

python-pytest-enabler, python-pytest-perf,

python-pyhamcrest)[native-inputs]: Remove python-pytest-cov.

* gnu/packages/cpp.scm (cpplint)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/databases.scm (python-alembic)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/dav.scm (vdirsyncer, radicale)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/django.scm (python-django-extensions)[native-inputs]:

Remove python-pytest-cov.

* gnu/packages/embedded.scm (mbed-tools)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/engineering.scm (python-scikit-rf)[native-inputs]:

Remove python-pytest-cov.

* gnu/packages/fontutils.scm (psautohint)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/geo.scm (python-fiona, python-cartopy)[native-inputs]:

Remove python-pytest-cov.

* gnu/packages/gettext.scm (mdpo)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/graphviz.scm (python-graphviz, python-uqbar)

[native-inputs]: Remove python-pytest-cov.

* gnu/packages/jupyter.scm (python-jupyter-packaging,

python-jupyter-server, python-jupyterlite-core, python-ipydatawidgets)

[native-inputs]: Remove python-pytest-cov.

* gnu/packages/machine-learning.scm (python-persim,

python-scikit-learn-extra, python-imbalanced-learn,

python-keras-application, python-keras-preprocessing, python-keras,

python-tensorly, python-pytorch-geometric, python-captum,

python-torchmetrics, python-pyro-ppl)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/mastodon.scm (python-mastodon-py)[native-inputs]:

Remove python-pytest-cov.

* gnu/packages/messaging.scm (zulip-term)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/package-management.scm (python-conda-package-handling):

[native-inputs]: Remove python-pytest-cov.

* gnu/packages/patchutils.scm (pwclient)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/protobuf.scm (python-pure-protobuf)[native-inputs]:

Remove python-pytest-cov.

* gnu/packages/python-check.scm (python-testfixtures, python-vcrpy,

python-pytest-filter-subpackage, python-atpublic, python-sybil,

python-vulture)[native-inputs]: Remove python-pytest-cov.

* gnu/packages/python-compression.scm (python-multivolumefile,

python-pybcj, python-bcj-cffi, python-pyppmd, python-ppmd-cffi,

python-py7zr)[native-inputs]: Remove python-pytest-cov.

* gnu/packages/python-crypto.scm (python-trustme)[native-inputs]:

Remove python-pytest-cov.

(python-certauth)[native-inputs]: Remove python-pytest-cov. Add

python-pytest.

* gnu/packages/python-science.scm (python-scipy, python-trimesh,

python-pandaparallel, python-pyts, python-usetplot, python-pingouin,

python-opt-einsum, python-salib)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/python-web.scm (python-apiron, python-huggingface-hub,

python-portend, python-aiosignal, python-aiostream, python-ovh,

python-cbor2, python-httplib2, python-cheroot, parfive, python-jose,

python-pyscss, python-mechanicalsoup, python-priority, hypercorn,

python-aioftp, python-oauthlib, python-tinycss, python-cssselect2,

python-httpcore, python-wsgiprox, python-venusian, python-cloud-init,

python-siosocks, python-zeep, gunicorn)[native-inputs]: Remove

python-pytest-cov.

(python-warcio)[native-inputs]: Remove python-pytest-cov. Add

python-pytest.

* gnu/packages/python-xyz.scm (python-apprise, python-janus,

python-logbook, python-affine, python-mdit-py-plugins, python-pint,

python-rasterio, python-bidict, python-can, dosage, python-contourpy,

python-portalocker, python-extension-helpers, python-mizani,

python-cligj, python-ddlparse, python-robotframework-pythonlibcore,

python-lsp-server, python-sparse, python-pikepdf, python-imageio,

python-manimpango, python-importlib-resources, python-jaraco-classes,

python-jaraco-collections, python-jaraco-context,

python-jaraco-functools, python-jaraco-test, python-jaraco-text,

python-ipyparallel, python-three-merge, python-seaborn,

python-sentry-sdk, python-sniffio, python-get-version,

python-legacy-api-wrap, python-path, python-pip-run, python-debugpy,

python-notebook, python-ipywidgets, python-qstylizer,

python-cookiecutter, python-pyqtgraph, python-codespell,

python-inflect, python-lazy-loader, python-pymemcache, python-natsort,

python-mwclient, python-flasgger, python-tempora, python-outcome,

python-trio, python-apscheduler, python-iocapture, python-argh,

python-flit, python-watchdog, python-watchgod, python-cmd2,

python-inform, python-qtsass, python-scikit-build, python-minikanren,

python-tablib, nikola, python-ansicolors, python-shtab, python-scooby,

dynaconf, python-pyan3, python-numpydoc, python-loguru,

python-multidict)[native-inputs]: Remove python-pytest-cov.

* gnu/packages/sphinx.scm (python-sphinx-gallery)[native-inputs]:

Remove python-pytest-cov.

* gnu/packages/statistics.scm (python-pymc, python-emcee,

python-rpy2)[native-inputs]: Remove python-pytest-cov.

* gnu/packages/task-management.scm (todoman)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/textutils.scm (python-panflute)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/time.scm (python-arrow, python-tzlocal)[native-inputs]:

Remove python-pytest-cov.

* gnu/packages/vpn.scm (sshuttle)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/web.scm (anonip, python-tibanna)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/wm.scm (qtile)[native-inputs]: Remove

python-pytest-cov. Add python-coverage.

Change-Id: Ia8c96b18a60b6ceb00b345ef06351eae1a68e070

---

gnu/packages/astronomy.scm | 12 +--

gnu/packages/audio.scm | 2 +-

gnu/packages/backup.scm | 2 +-

gnu/packages/bioinformatics.scm | 9 +-

gnu/packages/build-tools.scm | 1 -

gnu/packages/check.scm | 8 +-

gnu/packages/cpp.scm | 1 -

gnu/packages/databases.scm | 2 +-

gnu/packages/dav.scm | 2 -

gnu/packages/django.scm | 1 -

gnu/packages/embedded.scm | 1 -

gnu/packages/engineering.scm | 1 -

gnu/packages/fontutils.scm | 1 -

gnu/packages/geo.scm | 3 +-

gnu/packages/gettext.scm | 1 -

gnu/packages/graphviz.scm | 2 -

gnu/packages/jupyter.scm | 7 +-

gnu/packages/machine-learning.scm | 20 ++---

gnu/packages/mastodon.scm | 1 -

gnu/packages/messaging.scm | 4 +-

gnu/packages/package-management.scm | 1 -

gnu/packages/patchutils.scm | 2 +-

gnu/packages/protobuf.scm | 2 +-

gnu/packages/python-check.scm | 11 +--

gnu/packages/python-compression.scm | 9 +-

gnu/packages/python-crypto.scm | 3 +-

gnu/packages/python-science.scm | 16 ++--

gnu/packages/python-web.scm | 58 ++++---------

gnu/packages/python-xyz.scm | 123 +++++++---------------------

gnu/packages/sphinx.scm | 1 -

gnu/packages/statistics.scm | 6 +-

gnu/packages/task-management.scm | 1 -

gnu/packages/textutils.scm | 1 -

gnu/packages/time.scm | 2 -

gnu/packages/vpn.scm | 1 -

gnu/packages/web.scm | 3 +-

gnu/packages/wm.scm | 1 -

37 files changed, 88 insertions(+), 234 deletions(-)

Toggle diff (290 lines)diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 426cfd8c88f..61ab7520aef 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -601,7 +601,7 @@ (define-public python-astroml
              (setenv "HOME" "/tmp"))))))
     (propagated-inputs (list python-astropy python-matplotlib python-numpy
                              python-scikit-learn python-scipy))
-    (native-inputs (list python-pytest-astropy-header python-pytest-cov
+    (native-inputs (list python-pytest-astropy-header python-pytest
                          python-pytest-doctestplus python-pytest-remotedata
                          python-setuptools python-wheel))
     (home-page "https://astroml.org")
@@ -2040,8 +2040,7 @@ (define-public python-casa-formats-io
             (lambda _
               (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (native-inputs
-     (list python-pytest python-pytest-cov python-pytest-openfiles
-           python-setuptools))
+     (list python-pytest python-pytest-openfiles python-setuptools))
     (propagated-inputs
      (list python-astropy python-click python-dask python-numpy))
     (home-page "https://casa-formats-io.readthedocs.io/")
@@ -2111,7 +2110,6 @@ (define-public python-cdflib
      (list python-astropy
            python-hypothesis
            python-pytest
-           python-pytest-cov
            python-pytest-remotedata
            python-setuptools-scm
            python-xarray
@@ -2228,7 +2226,6 @@ (define-public python-czml3
     (native-inputs
      (list python-astropy
            python-pytest
-           python-pytest-cov
            python-pytest-mypy
            python-setuptools
            python-wheel))
@@ -2606,7 +2603,6 @@ (define-public python-poliastro
      (list python-hypothesis
            python-flit-core
            python-pytest
-           python-pytest-cov
            python-pytest-doctestplus
            python-pytest-mpl
            python-pytest-mypy))
@@ -3386,7 +3382,6 @@ (define-public python-stcal
      (list python-cython-3
            python-psutil
            python-pytest
-           python-pytest-cov
            python-pytest-doctestplus
            python-setuptools-scm
            python-setuptools
@@ -4605,7 +4600,6 @@ (define-public python-tweakwcs
            python-stsci-stimage))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-scipy
            python-setuptools
            python-setuptools-scm))
@@ -5270,7 +5264,7 @@ (define-public python-wiimatch
                 "15kq7z30m9i286ncs9xvpaq3dq1p5fa47jz21prq146qwr7j6dm8"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-numpy python-scipy python-setuptools))
-    (native-inputs (list python-pytest python-pytest-cov python-wheel
+    (native-inputs (list python-pytest python-wheel
                          python-pytest-doctestplus python-setuptools-scm))
     (home-page "https://github.com/spacetelescope/wiimatch")
     (synopsis
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index e6d16211fd4..724430dae36 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -6197,7 +6197,7 @@ (define-public python-pysox
       (propagated-inputs
        (list python-numpy python-typing-extensions))
       (native-inputs
-       (list sox python-pytest python-pytest-cov python-soundfile))
+       (list sox python-pytest python-soundfile))
       (home-page "https://github.com/rabitt/pysox")
       (synopsis "Python wrapper around SoX")
       (description "@code{python-pysox} is a wrapper around the @command{sox}
diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index 663eb2568fe..566ea06338b 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -1357,7 +1357,7 @@ (define-public borgmatic
                   python-jsonschema
                   python-requests
                   python-ruamel.yaml))
-    (native-inputs (list python-flexmock python-pytest python-pytest-cov))
+    (native-inputs (list python-flexmock python-pytest))
     (home-page "https://torsion.org/borgmatic/")
     (synopsis "Simple, configuration-driven backup software")
     (description
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3d5d381f0a0..5a4cf23eabb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3010,7 +3010,7 @@ (define-public python-biom-format
            ;;python-scikit-bio ;mutually recursive dependency
            python-scipy))
     (native-inputs
-     (list python-cython python-pytest python-pytest-cov python-nose))
+     (list python-cython python-pytest python-nose))
     (home-page "https://www.biom-format.org")
     (synopsis "Biological Observation Matrix (BIOM) format utilities")
     (description
@@ -10187,7 +10187,7 @@ (define-public python-screed
         (base32 "0slva743xn93h4sl5zg2as4ricnnj5pp6nw9dm4qclk4i9xglkvk"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-pytest-cov
+     (list python-pytest
            python-pytest-runner
            python-setuptools
            python-wheel))
@@ -17920,7 +17920,6 @@ (define-public python-pyfaidx
            python-mock
            python-numpy
            python-pytest
-           python-pytest-cov
            python-wheel))
     (propagated-inputs (list python-setuptools))
     (home-page "http://mattshirley.com")
@@ -17970,9 +17969,7 @@ (define-public python-cooler
            python-scipy
            python-simplejson))
     (native-inputs
-     (list python-hatchling
-           python-pytest
-           python-pytest-cov))
+     (list python-hatchling python-pytest))
     ;; Almost all the projects of the Mirnylab are moved under Open2C umbrella
     (home-page "https://github.com/open2c/cooler")
     (synopsis "Sparse binary format for genomic interaction matrices")
diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm
index 8fec2f8e2f2..29974dfd8b6 100644
--- a/gnu/packages/build-tools.scm
+++ b/gnu/packages/build-tools.scm
@@ -376,7 +376,6 @@ (define-public meson-python
            python-cython
            python-gitpython
            python-pytest
-           python-pytest-cov
            python-pytest-mock))
     (home-page "https://github.com/mesonbuild/meson-python")
     (synopsis "Meson-based build backend for Python")
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 6042f763f15..6b16ec7711b 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -1530,7 +1530,7 @@ (define-public python-pytest-nunit
     (build-system pyproject-build-system)
     (arguments (list #:tests? #false)) ;no tests included
     (propagated-inputs (list python-attrs python-pytest))
-    (native-inputs (list python-pytest python-pytest-cov python-setuptools
+    (native-inputs (list python-pytest python-setuptools
                          python-wheel python-xmlschema))
     (home-page "https://github.com/pytest-dev/pytest-nunit")
     (synopsis "Pytest plugin for generating NUnit3 test result XML output")
@@ -1796,7 +1796,7 @@ (define-public python-pytest-timeout
                       (add-installed-pythonpath inputs outputs)
                       (invoke "pytest" "-vv"))))))
     (propagated-inputs
-     (list python-pytest python-pytest-cov))
+     (list python-pytest))
     (native-inputs
      (list python-pexpect))
     (home-page "https://github.com/pytest-dev/pytest-timeout")
@@ -2493,7 +2493,6 @@ (define-public python-pytest-enabler
     (native-inputs (list python-pytest
                          python-pytest-black
                          python-pytest-checkdocs
-                         python-pytest-cov
                          python-pytest-flake8
                          python-pytest-mypy
                          python-setuptools
@@ -2667,7 +2666,6 @@ (define-public python-pytest-perf
      (list python-pytest
            python-pytest-black
            python-pytest-checkdocs
-           python-pytest-cov
            python-pytest-enabler
            python-pytest-flake8
            python-pytest-mypy
@@ -3242,7 +3240,7 @@ (define-public python-pyhamcrest
                (base32
                 "05kdzlhs2kvj82pfca13qszszcj6dyrk4b9pbr46x06sq2s4qyls"))))
     (native-inputs                      ;all native inputs are for tests
-     (list python-pytest-cov python-mock python-pytest python-hypothesis))
+     (list python-mock python-pytest python-hypothesis))
     (build-system python-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases
diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index ba2698056da..9c693fb16c3 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -1190,7 +1190,6 @@ (define-public cpplint
                            (getenv "TMP_PYTHONPATH")))))))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-pytest-runner
            python-testfixtures))
     (home-page "https://github.com/cpplint/cpplint")
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 9ec7855109c..8abea7ec385 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -3763,7 +3763,7 @@ (define-public python-alembic
         (base32 "0lxi2g2025lz5k7k5dd5fc1lfijqi2yw6qqyjzp073z6laa8cckw"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-mock python-pytest-cov))
+     (list python-mock python-pytest))
     (propagated-inputs
      (list python-dateutil python-sqlalchemy python-mako python-editor))
     (home-page "https://bitbucket.org/zzzeek/alembic")
diff --git a/gnu/packages/dav.scm b/gnu/packages/dav.scm
index b30b1ef5a59..0612a72c831 100644
--- a/gnu/packages/dav.scm
+++ b/gnu/packages/dav.scm
@@ -58,7 +58,6 @@ (define-public radicale
     (build-system python-build-system)
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-pytest-flake8
            python-pytest-isort
            python-pytest-runner
@@ -146,7 +145,6 @@ (define-public vdirsyncer
            python-trustme
            python-pytest
            python-pytest-asyncio
-           python-pytest-cov
            python-pytest-httpserver
            radicale))
     (inputs
diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index 48b1b38a97f..3ab2bc139d1 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -261,7 +261,6 @@ (define-public python-django-extensions
      (list python-mock
            python-factory-boy
            python-pytest
-           python-pytest-cov
            python-pytest-django
            python-shortuuid))
     (home-page
diff --git a/gnu/packages/embedded.scm b/gnu/packages/embedded.scm
index 1da41415194..542895c8779 100644
--- a/gnu/packages/embedded.scm
+++ b/gnu/packages/embedded.scm
@@ -1798,7 +1798,6 @@ (define-public mbed-tools
                (invoke "pytest" "-vv")))))))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-factory-boy
            python-requests-mock
            python-semver))
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index af79172e53b..eaff8546dc4 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -2681,7 +2681,6 @@ (define-public python-scikit-rf
     (native-inputs (list python-nbval
                          python-networkx
                          python-pytest
-                         python-pytest-cov
                          python-pytest-mock
                          python-pyvisa))
     (home-page "https://scikit-rf.org/")
diff --git a/gnu/packages/fontutils.scm b/gnu/packages/fontutils.scm
index 84eb33d19bf..46b06765f0c 100644
--- a/gnu/packages/fontutils.scm
+++ b/gnu/packages/fontutils.scm
@@ -856,7 +856,6 @@ (define-public psautohint
     (native-inputs
      (list psautohint-font-data
            python-pytest
-           python-pytest-cov
            python-pytest-xdist
            python-setu

This message was truncated. Download the full message here.

Nicolas Graves wrote 10 months ago

[PATCH 25/32] gnu: python-dateutil: Remove python-pytest-cov native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-25-ngraves@ngraves.fr

* gnu/packages/time.scm (python-dateutil):

[native-inputs]: Remove python-pytest-cov.

[arguments]<#:phases>: Add remove-pytest-cov-dep phase.

Change-Id: Id82a147d6e40383ecc2661ac896b65b858c181e0

---

gnu/packages/time.scm | 20 +++++++++++++-------

1 file changed, 13 insertions(+), 7 deletions(-)

Toggle diff (34 lines)diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm
index 1064467020f..ad33306c7cf 100644
--- a/gnu/packages/time.scm
+++ b/gnu/packages/time.scm
@@ -246,14 +246,20 @@ (define-public python-dateutil
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags '(list  ; avoid freezegun dependency
-                     "--ignore=dateutil/test/test_utils.py"
-                     "--ignore=dateutil/test/test_rrule.py"
-                     ;; XXX: Fails to get timezone from /etc/localtime.
-                     "--ignore=dateutil/test/test_tz.py")))
+      #:test-flags '(list "dateutil/test" "docs"
+                          ;; avoid freezegun dependency
+                          "--ignore=dateutil/test/test_utils.py"
+                          "--ignore=dateutil/test/test_rrule.py"
+                          ;; XXX: Fails to get timezone from /etc/localtime.
+                          "--ignore=dateutil/test/test_tz.py")
+      #:phases #~(modify-phases %standard-phases
+                   (add-after 'unpack 'remove-pytest-cov-dep
+                     (lambda _
+                       (substitute* "dateutil/test/conftest.py"
+                         (("item\\.add_marker\\(pytest\\.mark\\.no_cover\\)")
+                          "pass")))))))
     (native-inputs
-     (list python-pytest python-pytest-cov python-setuptools
-           python-setuptools-scm python-wheel))
+     (list python-pytest python-setuptools python-setuptools-scm python-wheel))
     (propagated-inputs
      (list python-six))
     (home-page "https://dateutil.readthedocs.io/en/stable/")
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 26/32] build-system/pyproject: Remove python-pytest-isort native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-26-ngraves@ngraves.fr

* gnu/packages/dav.scm (radicale):

[native-inputs]: Remove python-pytest-isort.

* gnu/packages/python-web.scm (python-tinycss):

[arguments]<#:test-flags>: Ignore isort tests.

[native-inputs]: Remove python-pytest-isort.

Change-Id: I706e8c310adbeda49b91c6815d299172ce05df22

---

gnu/packages/dav.scm | 1 -

gnu/packages/python-web.scm | 4 ++--

2 files changed, 2 insertions(+), 3 deletions(-)

Toggle diff (30 lines)diff --git a/gnu/packages/dav.scm b/gnu/packages/dav.scm
index 0612a72c831..99284220846 100644
--- a/gnu/packages/dav.scm
+++ b/gnu/packages/dav.scm
@@ -59,7 +59,6 @@ (define-public radicale
     (native-inputs
      (list python-pytest
            python-pytest-flake8
-           python-pytest-isort
            python-pytest-runner
            python-waitress))
     (propagated-inputs
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 8c51282c9cb..340ef0836b4 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -5862,9 +5862,9 @@ (define-public python-tinycss
     (build-system pyproject-build-system)
     (arguments
      (list #:test-flags
-           '(list "-k" "not test_speedups")))
+           '(list "-k" "not ISORT and not test_speedups")))
     (native-inputs
-     (list python-pytest-flake8 python-pytest-isort
+     (list python-pytest-flake8
            python-pytest-runner python-setuptools python-wheel))
     (home-page "https://tinycss.readthedocs.io/")
     (synopsis "Complete yet simple CSS parser for Python")
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 27/32] build-system/pyproject: Remove python-pytest-black native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-27-ngraves@ngraves.fr

* gnu/packages/check.scm (python-pytest-perf, python-pytest-enabler)

[native-inputs]: Remove python-pytest-black.

* gnu/packages/python-web.scm (python-portend)[native-inputs]:

Remove python-pytest-black.

* gnu/packages/python-xyz.scm (python-importlib-resources,

python-jaraco-classes, python-jaraco-collections,

python-jaraco-context, python-jaraco-functools, python-jaraco-test,

python-jaraco-text, python-legacy-api-wrap, python-path,

python-pip-run, python-inflect, python-isort, python-tempora,

python-sparse)[native-inputs]: Remove python-pytest-black.

Change-Id: Ib46f1c4a3cc33821cda3d7b2172d36158aa812c9

---

gnu/packages/check.scm | 2 --

gnu/packages/python-web.scm | 1 -

gnu/packages/python-xyz.scm | 22 +++++-----------------

3 files changed, 5 insertions(+), 20 deletions(-)

Toggle diff (165 lines)diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 6b16ec7711b..f8ead8df4e4 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2491,7 +2491,6 @@ (define-public python-pytest-enabler
            python-jaraco-functools
            python-toml))
     (native-inputs (list python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-flake8
                          python-pytest-mypy
@@ -2664,7 +2663,6 @@ (define-public python-pytest-perf
                            "and not upstream_url"))))
     (native-inputs
      (list python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-enabler
            python-pytest-flake8
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 340ef0836b4..5f19d93ea19 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -311,7 +311,6 @@ (define-public python-portend
     (propagated-inputs (list python-tempora))
     ;; TODO: Add python-pytest-ruff to native-inputs once it has been packaged.
     (native-inputs (list python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-enabler
                          python-pytest-mypy
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index bc4761e4c38..9c15ca8e566 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -8686,7 +8686,7 @@ (define-public python-sparse
      (list python-numba python-numpy python-scipy))
     (native-inputs
      (list python-dask python-importlib-metadata python-pytest
-           python-pytest-black python-setuptools))
+           python-setuptools))
     (home-page "https://github.com/pydata/sparse/")
     (synopsis "Library for multi-dimensional sparse arrays")
     (description
@@ -11523,7 +11523,6 @@ (define-public python-importlib-resources
                      (string-append (getcwd) "/_custom_build")))))))
     (native-inputs
      (list python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-enabler
            python-pytest-flake8
@@ -11653,7 +11652,6 @@ (define-public python-jaraco-classes
       #:test-flags '(list "-k" "not project")))
     (native-inputs
      (list python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-flake8
            python-pytest-mypy
@@ -11686,7 +11684,6 @@ (define-public python-jaraco-collections
     ;; TODO: Add python-pytest-ruff to native-inputs once it has been
     ;; packaged.
     (native-inputs (list python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-enabler
                          python-pytest-mypy
@@ -11746,7 +11743,6 @@ (define-public python-jaraco-context
            #:test-flags '(list "-k" "not project")))
     (native-inputs
      (list python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-flake8
            python-pytest-mypy
@@ -11780,7 +11776,6 @@ (define-public python-jaraco-functools
     (native-inputs
      (list python-jaraco-classes
            python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-flake8
            python-pytest-mypy
@@ -11840,7 +11835,6 @@ (define-public python-jaraco-test
      (list #:test-flags '(list "-k" "http")))
     (propagated-inputs (list python-jaraco-context python-jaraco-functools))
     (native-inputs (list python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-enabler
                          python-pytest-flake8
@@ -11873,7 +11867,6 @@ (define-public python-jaraco-text
     ;; TODO: Add python-pytest-ruff to native-inputs once it has been
     ;; packaged.
     (native-inputs (list python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-enabler
                          python-pytest-mypy
@@ -16255,8 +16248,7 @@ (define-public python-legacy-api-wrap
          "06qhp0g543dy98vpa41hwdalvdbsjfc3ldk474yr9sd75mhl8jh3"))))
     (build-system python-build-system)
     (propagated-inputs
-     (list python-get-version python-pytest python-pytest-black
-           python-setuptools))
+     (list python-get-version python-pytest python-setuptools))
     (home-page "https://github.com/flying-sheep/legacy-api-wrap")
     (synopsis "Legacy API wrapper")
     (description "This module defines a decorator to wrap legacy APIs.  The
@@ -16516,7 +16508,6 @@ (define-public python-path
                python-packaging
                python-pygments
                python-pytest
-               python-pytest-black
                python-pytest-checkdocs
                python-pytest-enabler
                python-pytest-flake8
@@ -16621,7 +16612,6 @@ (define-public python-pip-run
        (append python-nbformat
                python-pygments
                python-pytest
-               python-pytest-black
                python-pytest-checkdocs
                python-pytest-enabler
                python-pytest-flake8
@@ -21059,7 +21049,6 @@ (define-public python-inflect
     (propagated-inputs (list python-pydantic))
     (native-inputs (list python-pygments
                          python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-enabler
                          python-pytest-flake8
@@ -24089,7 +24078,8 @@ (define-public python-isort
     (arguments
      (list
       #:test-flags '(list "tests/unit/" "-k" "not test_gitignore"
-                          "--ignore=tests/unit/test_deprecated_finders.py")
+                          "--ignore=tests/unit/test_deprecated_finders.py"
+                          "--ignore=tests/unit/profiles/test_black.py")
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'install 'install-example-plugins
@@ -24107,8 +24097,7 @@ (define-public python-isort
                 (apply invoke "pip" "--no-cache-dir" "--no-input"
                        "install"  "--user" "--no-deps" example-whls)))))))
     (native-inputs
-     (list python-black
-           python-colorama
+     (list python-colorama
            python-hypothesmith
            python-libcst-minimal
            python-natsort
@@ -25908,7 +25897,6 @@ (define-public python-tempora
     (native-inputs
      (list python-freezegun
            python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-enabler
            python-pytest-flake8
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 24/32] gnu: python-django-contact-form: Remove python-pytest-cov native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-24-ngraves@ngraves.fr

* gnu/packages/django.scm (python-django-contact-form):

[native-inputs]: Remove python-pytest-cov.

[build-system]: Upgrade to pyproject-build-system.

[arguments]<#:phases>: Remove coverage tests for check phase.

Change-Id: I4d0fc406401b7e923f7efa084dbe8ea3753e50fc

---

gnu/packages/django.scm | 7 ++-----

1 file changed, 2 insertions(+), 5 deletions(-)

Toggle diff (25 lines)diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index 3ab2bc139d1..726dd77639e 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -838,16 +838,13 @@ (define-public python-django-contact-form
               (sha256
                (base32
                 "1my9hkrylckp5vfqg9b0kncrdlxjnwxll56sdciqn4v19i4wbq1y"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
          (replace 'check
            (lambda _
-             (invoke "coverage" "run" "--source" "contact_form"
-                     "runtests.py"))))))
-    (native-inputs
-     (list python-coverage))
+             (invoke "python" "runtests.py"))))))
     (propagated-inputs
      (list python-django))
     (home-page "https://github.com/ubernostrum/django-contact-form")
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 28/32] build-system/pyproject: Remove python-pytest-flake8 native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-28-ngraves@ngraves.fr

* gnu/packages/check.scm (python-pytest-enabler, python-pytest-perf):

[native-inputs]: Remove python-pytest-flake8.

* gnu/packages/dav.scm (radicale)[native-inputs]: Remove

python-pytest-flake8.

* gnu/packages/jupyter.scm (python-nbstripout)[native-inputs]:

Remove python-pytest-flake8.

* gnu/packages/python-check.scm (python-pytest-csv):

[arguments]<#:test-flags>: Ignore flake8 test.

[native-inputs]: Remove python-pytest-flake8.

* gnu/packages/python-web.scm (python-mechanicalsoup,

python-tinycss2)[native-inputs]: Remove python-pytest-flake8.

(python-tinycss):

[arguments]<#:test-flags>: Ignore flake8 tests.

[native-inputs]: Remove python-pytest-flake8.

* gnu/packages/python-xyz.scm (python-importlib-resources,

python-jaraco-classes, python-jaraco-context, python-jaraco-functools,

python-jaraco-packaging, python-jaraco-test, python-path,

python-pip-run, python-inflect, python-tempora, python-cairosvg)

[native-inputs]: Remove python-pytest-flake8.

Change-Id: I60ad04391d1c4b081e3293d50b3ac93c6430c7bf

---

gnu/packages/check.scm | 2 --

gnu/packages/dav.scm | 1 -

gnu/packages/jupyter.scm | 1 -

gnu/packages/python-check.scm | 5 +++--

gnu/packages/python-web.scm | 10 ++++------

gnu/packages/python-xyz.scm | 12 +-----------

6 files changed, 8 insertions(+), 23 deletions(-)

Toggle diff (192 lines)diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index f8ead8df4e4..e8f121e9fe9 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2492,7 +2492,6 @@ (define-public python-pytest-enabler
            python-toml))
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
-                         python-pytest-flake8
                          python-pytest-mypy
                          python-setuptools
                          python-setuptools-scm
@@ -2665,7 +2664,6 @@ (define-public python-pytest-perf
      (list python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools
            python-wheel))
diff --git a/gnu/packages/dav.scm b/gnu/packages/dav.scm
index 99284220846..b5a1ba749d8 100644
--- a/gnu/packages/dav.scm
+++ b/gnu/packages/dav.scm
@@ -58,7 +58,6 @@ (define-public radicale
     (build-system python-build-system)
     (native-inputs
      (list python-pytest
-           python-pytest-flake8
            python-pytest-runner
            python-waitress))
     (propagated-inputs
diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm
index c25663e4da6..4bc0bc2a8f4 100644
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -817,7 +817,6 @@ (define-public python-nbstripout
     (native-inputs
      (list python-pytest
            python-pytest-cram
-           python-pytest-flake8
            python-pytest-runner
            python-setuptools
            python-wheel))
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index fdef98f6c8a..4b5ca23569a 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -214,9 +214,10 @@ (define-public python-pytest-csv
         (base32
          "17518f2fn5l98lyk9p8r7215c1whi61imzrh6ahrmcksr8w0zz04"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list #:test-flags '(list "--ignore=tests/test_flake8.py")))
     (native-inputs
-     (list python-pytest-flake8
-           python-pytest-xdist
+     (list python-pytest-xdist
            python-setuptools
            python-tabulate
            python-wheel))
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 5f19d93ea19..2a7d083b9de 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1578,8 +1578,7 @@ (define-public python-mechanicalsoup
     (propagated-inputs
      (list python-beautifulsoup4 python-lxml python-requests python-six))
     (native-inputs
-     (list python-pytest-flake8
-           python-pytest-httpbin
+     (list python-pytest-httpbin
            python-pytest-mock
            python-pytest-runner
            python-requests-mock
@@ -5861,10 +5860,9 @@ (define-public python-tinycss
     (build-system pyproject-build-system)
     (arguments
      (list #:test-flags
-           '(list "-k" "not ISORT and not test_speedups")))
+           '(list "-k" "not ISORT and not FLAKE8 and not test_speedups")))
     (native-inputs
-     (list python-pytest-flake8
-           python-pytest-runner python-setuptools python-wheel))
+     (list python-pytest-runner python-setuptools python-wheel))
     (home-page "https://tinycss.readthedocs.io/")
     (synopsis "Complete yet simple CSS parser for Python")
     (description
@@ -5905,7 +5903,7 @@ (define-public python-tinycss2
     (propagated-inputs
      (list python-webencodings))
     (native-inputs
-     (list python-flit python-pytest python-pytest-flake8 python-pytest-isort))
+     (list python-flit python-pytest python-pytest-isort))
     (home-page "https://tinycss2.readthedocs.io/")
     (synopsis "Low-level CSS parser for Python")
     (description "@code{tinycss2} can parse strings, return Python objects
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 9c15ca8e566..1b3837dddc4 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -11525,7 +11525,6 @@ (define-public python-importlib-resources
      (list python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools-57
            python-setuptools-scm))
@@ -11653,7 +11652,6 @@ (define-public python-jaraco-classes
     (native-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools
            python-setuptools-scm
@@ -11744,7 +11742,6 @@ (define-public python-jaraco-context
     (native-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools
            python-setuptools-scm
@@ -11777,7 +11774,6 @@ (define-public python-jaraco-functools
      (list python-jaraco-classes
            python-pytest
            python-pytest-checkdocs
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools
            python-setuptools-scm
@@ -11807,7 +11803,6 @@ (define-public python-jaraco-packaging
     (propagated-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-flake8
            python-rst.linker
            python-setuptools
            python-setuptools-scm
@@ -11837,7 +11832,6 @@ (define-public python-jaraco-test
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-flake8
                          python-pytest-mypy
                          python-setuptools
                          python-wheel))
@@ -16510,7 +16504,6 @@ (define-public python-path
                python-pytest
                python-pytest-checkdocs
                python-pytest-enabler
-               python-pytest-flake8
                python-pytest-mypy)))
     (properties (alist-delete 'hidden?
                               (package-properties
@@ -16614,7 +16607,6 @@ (define-public python-pip-run
                python-pytest
                python-pytest-checkdocs
                python-pytest-enabler
-               python-pytest-flake8
                python-pytest-mypy)))
     (properties (alist-delete 'hidden? (package-properties
                                         python-pip-run-bootstrap)))))
@@ -21051,7 +21043,6 @@ (define-public python-inflect
                          python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-flake8
                          python-pytest-mypy
                          ;; For the version number
                          python-setuptools-scm
@@ -25899,7 +25890,6 @@ (define-public python-tempora
            python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-flake8
            python-pytest-freezegun
            python-pytest-mypy
            python-setuptools-scm
@@ -29569,7 +29559,7 @@ (define-public python-cairosvg
      (list python-cairocffi python-cssselect2 python-defusedxml
            python-pillow python-tinycss2))
     (native-inputs
-     (list python-pytest-flake8 python-pytest-isort python-pytest-runner
+     (list python-pytest-isort python-pytest-runner
            python-setuptools python-wheel))
     (home-page "https://cairosvg.org/")
     (synopsis "SVG to PDF/PS/PNG converter based on Cairo")
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 29/32] build-system/pyproject: Remove python-pytest-mypy inputs.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-29-ngraves@ngraves.fr

* gnu/packages/astronomy.scm (python-czml3, python-poliastro)

[native-inputs]: Remove python-pytest-mypy.

* gnu/packages/check.scm (python-pytest-perf)[native-inputs]: Remove

python-pytest-mypy.

* gnu/packages/python-web.scm (python-portend)[native-inputs]: Remove

python-pytest-mypy.

* gnu/packages/python-xyz.scm (python-importlib-resources,

python-jaraco-classes, python-jaraco-collections,

python-jaraco-context, python-jaraco-functools, python-jaraco-test,

python-jaraco-text, python-path, python-pip-run, python-inflect,

python-tempora, python-loguru, python-portalocker)[native-inputs]: Remove

python-pytest-mypy.

* gnu/packages/sphinx.scm (python-sphinx, python-sphinx-5):

[propagated-inputs]: Remove python-mypy.

Change-Id: Ia36ca82e0327a886f9c5317e9ef4ffc35dc8ac9d

---

gnu/packages/astronomy.scm | 4 +---

gnu/packages/check.scm | 1 -

gnu/packages/python-web.scm | 1 -

gnu/packages/python-xyz.scm | 17 ++---------------

gnu/packages/sphinx.scm | 2 --

5 files changed, 3 insertions(+), 22 deletions(-)

Toggle diff (180 lines)diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 61ab7520aef..2b78738f5a8 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2226,7 +2226,6 @@ (define-public python-czml3
     (native-inputs
      (list python-astropy
            python-pytest
-           python-pytest-mypy
            python-setuptools
            python-wheel))
     (home-page "https://github.com/poliastro/czml3")
@@ -2604,8 +2603,7 @@ (define-public python-poliastro
            python-flit-core
            python-pytest
            python-pytest-doctestplus
-           python-pytest-mpl
-           python-pytest-mypy))
+           python-pytest-mpl))
     (propagated-inputs
      (list python-astropy
            python-astroquery
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index e8f121e9fe9..8eac2b13563 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2664,7 +2664,6 @@ (define-public python-pytest-perf
      (list python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-mypy
            python-setuptools
            python-wheel))
     (propagated-inputs
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 2a7d083b9de..425aa9d5d0f 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -313,7 +313,6 @@ (define-public python-portend
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-mypy
                          python-setuptools
                          python-wheel))
     (home-page "https://github.com/jaraco/portend")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 1b3837dddc4..733a60b087d 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4928,7 +4928,6 @@ (define-public python-portalocker
                 "0lawjm736vs86wlnxc3qqh37l11z0yx81xq3dmrw33m86kaq2bh3"))))
     (build-system pyproject-build-system)
     (native-inputs (list python-pytest
-                         python-pytest-mypy
                          python-pytest-timeout
                          python-redis
                          python-setuptools
@@ -11525,7 +11524,6 @@ (define-public python-importlib-resources
      (list python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-mypy
            python-setuptools-57
            python-setuptools-scm))
     (propagated-inputs
@@ -11652,7 +11650,6 @@ (define-public python-jaraco-classes
     (native-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-mypy
            python-setuptools
            python-setuptools-scm
            python-wheel))
@@ -11684,7 +11681,6 @@ (define-public python-jaraco-collections
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-mypy
                          python-setuptools
                          python-wheel))
     (home-page "https://github.com/jaraco/jaraco.collections")
@@ -11742,7 +11738,6 @@ (define-public python-jaraco-context
     (native-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-mypy
            python-setuptools
            python-setuptools-scm
            python-wheel))
@@ -11774,7 +11769,6 @@ (define-public python-jaraco-functools
      (list python-jaraco-classes
            python-pytest
            python-pytest-checkdocs
-           python-pytest-mypy
            python-setuptools
            python-setuptools-scm
            python-wheel))
@@ -11832,7 +11826,6 @@ (define-public python-jaraco-test
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-mypy
                          python-setuptools
                          python-wheel))
     (home-page "https://github.com/jaraco/jaraco.test")
@@ -11863,7 +11856,6 @@ (define-public python-jaraco-text
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-mypy
                          python-setuptools
                          python-wheel))
     (home-page "https://github.com/jaraco/jaraco.text")
@@ -16503,8 +16495,7 @@ (define-public python-path
                python-pygments
                python-pytest
                python-pytest-checkdocs
-               python-pytest-enabler
-               python-pytest-mypy)))
+               python-pytest-enabler)))
     (properties (alist-delete 'hidden?
                               (package-properties
                                python-path-bootstrap)))))
@@ -16606,8 +16597,7 @@ (define-public python-pip-run
                python-pygments
                python-pytest
                python-pytest-checkdocs
-               python-pytest-enabler
-               python-pytest-mypy)))
+               python-pytest-enabler)))
     (properties (alist-delete 'hidden? (package-properties
                                         python-pip-run-bootstrap)))))
 
@@ -21043,7 +21033,6 @@ (define-public python-inflect
                          python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-mypy
                          ;; For the version number
                          python-setuptools-scm
                          python-setuptools
@@ -25891,7 +25880,6 @@ (define-public python-tempora
            python-pytest-checkdocs
            python-pytest-enabler
            python-pytest-freezegun
-           python-pytest-mypy
            python-setuptools-scm
            python-types-freezegun
            python-types-pytz
@@ -32828,7 +32816,6 @@ (define-public python-loguru
     (propagated-inputs (list python-colorama))
     (native-inputs (list python-colorama
                          python-freezegun
-                         python-mypy
                          python-pre-commit
                          python-pytest
                          python-pytest-mypy-plugins
diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index 669120cad0a..35eaef3036e 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -94,7 +94,6 @@ (define-public python-sphinx
            python-imagesize
            python-importlib-metadata
            python-jinja2
-           python-mypy
            python-packaging
            python-pygments
            python-requests
@@ -191,7 +190,6 @@ (define-public python-sphinx-5
            python-imagesize
            python-importlib-metadata
            python-jinja2
-           python-mypy
            python-packaging
            python-pygments
            python-requests
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 30/32] build-system/pyproject: Stop hiding options.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-30-ngraves@ngraves.fr

* gnu/packages/pdf.scm (python-pydyf, weasyprint)[arguments]
<#:test-flags>: Remove arguments hiding coverage options.

* gnu/packages/python-crypto.scm (python-keyring)
[arguments]<#:test-flags>: Remove arguments hiding coverage options.

* gnu/packages/python-web.scm (python-asgi-csrf, python-asgi-lifespan,
python-openapi-schema-validator, python-openapi-spec-validator,
python-openapi-core)[arguments]<#:test-flags>: Remove arguments hiding
coverage options.
(python-openapi-schema-validator, python-openapi-spec-validator)
[arguments]<#:phases>: Remove 'remove-coverage-pytest-options phase.
(python-cssselect2, python-tinycss2)[arguments]: Remove uneeded field.
(python-jsonpickle)[arguments]<#:test-flags>: Remove uneeded
test-flags.

* gnu/packages/python-xyz.scm (python-cattrs)
[arguments]<#:phases>: Remove arguments hiding coverage options.

Change-Id: Ibe08ecfebf8a24259c8658918d98fe9e5a8925b7
---
 gnu/packages/pdf.scm           |  6 +---
 gnu/packages/python-crypto.scm |  1 -
 gnu/packages/python-web.scm    | 51 ++++------------------------------
 gnu/packages/python-xyz.scm    |  4 +--
 4 files changed, 7 insertions(+), 55 deletions(-)

Toggle diff (164 lines)diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm
index 4e260d614de..16d4d9336e3 100644
--- a/gnu/packages/pdf.scm
+++ b/gnu/packages/pdf.scm
@@ -816,9 +816,6 @@ (define-public python-pydyf
        (sha256
         (base32 "18q43g5d9455msipcgd5fvnh8m4a2rz189slzfg80yycjw66rshs"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:test-flags #~'("-c" "/dev/null")))
     (propagated-inputs (list python-pillow))
     (native-inputs
      (list ghostscript
@@ -1635,8 +1632,7 @@ (define-public weasyprint
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags #~(list "-c" "/dev/null"
-                           "-n" (number->string (parallel-job-count)))
+      #:test-flags #~(list "-n" (number->string (parallel-job-count)))
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-library-paths
diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm
index 6965a330624..6139856a906 100644
--- a/gnu/packages/python-crypto.scm
+++ b/gnu/packages/python-crypto.scm
@@ -288,7 +288,6 @@ (define-public python-keyring
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags '(list "-c" "/dev/null") ;avoid extra test dependencies
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'check 'workaround-test-failure
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 425aa9d5d0f..a149e561243 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -738,10 +738,7 @@ (define-public python-asgi-csrf
     (build-system pyproject-build-system)
     (arguments
      (list #:test-flags
-           ;; Provide a null config to avoid the extraneous dependency on
-           ;; python-pytest-coverage.
-           #~(list "-c" "/dev/null"
-                   ;; Disable two failing tests (see:
+           #~(list ;; Disable two failing tests (see:
                    ;; https://github.com/simonw/asgi-csrf/issues/24).
                    "-k" (string-append
                          "not (test_multipart "
@@ -780,8 +777,7 @@ (define-public python-asgi-lifespan
     (arguments
      (list
       #:test-flags
-      '(list "-c" "/dev/null"           ;ignore coverage-related options
-             "-k"
+      '(list "-k"
              (string-append
               ;; XXX: Some tests fail because of a 'lifespan.shutdown.failed'
               ;; extra event, perhaps because our version of trio is older.
@@ -1528,10 +1524,7 @@ (define-public python-jsonpickle
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags
-      ;; Prevent running the flake8 and black pytest plugins, which only tests
-      ;; style and frequently causes harmless failures.
-      '(list "-o" "addopts=''" "tests")
+      #:test-flags '(list "tests")
       #:phases
       '(modify-phases %standard-phases
          (add-before 'check 'pre-check
@@ -2178,13 +2171,7 @@ (define-public python-openapi-schema-validator
      (list
       #:test-flags
       ;; This one returns 5 instead of 4 elements
-      '(list "-k" "not test_array_prefixitems_invalid")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'remove-coverage-pytest-options
-            (lambda _
-              (substitute* "pyproject.toml"
-                (("^--cov.*") "")))))))
+      '(list "-k" "not test_array_prefixitems_invalid")))
     (native-inputs (list python-poetry-core python-pytest))
     (propagated-inputs
      (list python-isodate
@@ -2222,13 +2209,7 @@ (define-public python-openapi-spec-validator
      (list
       ;; These tests attempt to fetch resources from the Internet
       #:test-flags '(list "--ignore-glob=tests/integration/validation/**"
-                          "-k" "not example")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'remove-coverage-pytest-options
-            (lambda _
-              (substitute* "pyproject.toml"
-                (("^--cov.*") "")))))))
+                          "-k" "not example")))
     (native-inputs
      (list python-poetry-core
            python-pytest))
@@ -2267,9 +2248,6 @@ (define-public python-openapi-core
      (list
       #:test-flags
       '(list "tests/unit"
-             ;; Ignore Pytest configuration in setup.cfg that adds
-             ;; unwanted flake8 and coverage options.
-             "-c" "/dev/null"
              "-k" (string-append
                    ;; Type mismatches
                    "not TestFlaskOpenAPIRequest"
@@ -5891,14 +5869,6 @@ (define-public python-tinycss2
        (sha256
         (base32 "0zyc48vbmczpqj7f3f0d7zb3bz29fyj50dg0m6bbwbr5i88kq3sq"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'check 'remove-unwanted-dependencies
-            (lambda _
-              (substitute* "pyproject.toml"
-                (("^addopts.*") "")))))))
     (propagated-inputs
      (list python-webencodings))
     (native-inputs
@@ -5925,17 +5895,6 @@ (define-public python-cssselect2
        (sha256
         (base32 "1j2fcr217rsvkipsg6zjq03rl64rxnvb5hqqpx0dv58fhspvkywk"))))
     (build-system pyproject-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'disable-linters
-           ;; Their check fails; none of our business.
-           (lambda _
-             (substitute* '("setup.py" "pyproject.toml")
-               (("'pytest-flake8',") "")
-               (("'pytest-isort',") "")
-               (("--flake8") "")
-               (("--isort") "")))))))
     (propagated-inputs
      (list python-tinycss2))
     (native-inputs
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 733a60b087d..2bfeecf33e0 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21316,9 +21316,7 @@ (define-public python-cattrs
               (substitute* "pyproject.toml"
                 ;; Fix version string
                 (("dynamic = \\[\"version\"\\]")
-                 (string-append "version = \"" #$version "\""))
-                ;; Just run pytest with no frills
-                (("addopts = \"-l.*") "")))))))
+                 (string-append "version = \"" #$version "\""))))))))
     (native-inputs
      (list python-hatchling
            python-hatch-vcs
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 31/32] gnu: python-linear-operator: Remove python-flake8-print native-input

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-31-ngraves@ngraves.fr

* gnu/packages/machine-learning.scm (python-linear-operator):

[native-inputs]: Remove pytest-flake8-print.

Change-Id: Iba2670b47e479c20a3f4ae1c703ad9fe815e3764

---

gnu/packages/machine-learning.scm | 3 +--

1 file changed, 1 insertion(+), 2 deletions(-)

Toggle diff (16 lines)diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index a3c598ba1c8..cc33a3e9762 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -5082,8 +5082,7 @@ (define-public python-linear-operator
                              python-pytorch
                              python-scipy
                              python-typeguard))
-    (native-inputs (list python-flake8-print
-                         python-pytest
+    (native-inputs (list python-pytest
                          python-setuptools
                          python-setuptools-scm))
     (home-page "https://github.com/cornellius-gp/linear_operator/")
-- 
2.41.0

Nicolas Graves wrote 10 months ago

[PATCH 32/32] gnu: abjad-ext-ipython: Remove uneeded inputs.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240510075605.6303-32-ngraves@ngraves.fr

* gnu/packages/music.scm (abjad-ext-ipython):
  [arguments]<#:phases>: Remove unwanted dev dependencies in phase
  losen-requirements.
  [native-inputs]: Remove python-black, python-flake8, python-isort,
  python-mypy, python-pytest-cov, python-iniconfig,
  python-pytest-helpers-namespace.
  [propagated-inputs]: Remove python-sphinx-autodoc-typehints.

Change-Id: Id337da7731bc04d69831096b31f52e0e4c6a13c0
---
 gnu/packages/music.scm | 16 +++++-----------
 1 file changed, 5 insertions(+), 11 deletions(-)

Toggle diff (37 lines)diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 5420a140657..45daa9438ae 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -1790,7 +1790,9 @@ (define-public abjad-ext-ipython
              (substitute* "setup.py"
                ;; Don't require a specific version of abjad.
                (("abjad==")
-                "abjad>="))))
+                "abjad>=")
+               ;; XXX: Remove unwanted dev dependencies.
+               (("\"(black|flake8|isort|mypy|pytest)[^,]*,") ""))))
          (replace 'check
            (lambda* (#:key tests? inputs outputs #:allow-other-keys)
              (when tests?
@@ -1800,17 +1802,9 @@ (define-public abjad-ext-ipython
                (invoke "jupyter" "nbconvert" "--to=html"
                "--ExecutePreprocessor.enabled=True" "tests/test.ipynb")))))))
     (native-inputs
-     (list lilypond
-           python-black
-           python-flake8
-           python-iniconfig
-           python-isort
-           python-mypy
-           python-pytest
-           python-pytest-cov
-           python-pytest-helpers-namespace))
+     (list lilypond python-pytest))
     (propagated-inputs
-     (list abjad jupyter python-sphinx-autodoc-typehints))
+     (list abjad jupyter))
     (home-page "https://abjad.github.io")
     (synopsis "Abjad IPython Extension")
     (description
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 00/32] Remove unwanted native-inputs.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-1-ngraves@ngraves.fr

Simply rebased the v1, ontop of 69980.

Nicolas Graves (32):
  guix: import: pypi: Ignore pypi-ignored-inputs.
  build-system/pyproject: Ignore unwanted pytest flags.
  build-system/pyproject: Remove python-black input.
  build-system/pyproject: Remove python-pylint native-input.
  build-system/pyproject: Remove python-flake8 inputs.
  build-system/pyproject: Remove python-coverage input.
  gnu: python-cram: Remove python-coverage native-input.
  gnu: u-boot-tools: Remove python-coverage native-input.
  gnu: python-aiosqlite: Remove python-coverage native-input.
  gnu: python-openid: Remove python-coverage native-input.
  build-system/pyproject: Remove python-coveralls native-input.
  build-system/pyproject: Remove python-pycodestyle native-input.
  gnu: python-versioneer: Remove python-pycodestyle native-input.
  gnu: python-versioneer: Remove python-pyflakes native-input.
  gnu: python-re-assert: Remove python-covdefaults native-input.
  build-system/pyproject: Remove python-codecov native-input.
  build-system/pyproject: Remove python-tox native-input.
  build-system/pyproject: Remove python-mypy native-input.
  gnu: python-immutables: Remove python-mypy native-input.
  build-system/pyproject: Remove python-isort native-input.
  build-system/pyproject: Remove python-twine native-input.
  build-system/pyproject: Remove python-pytest-cov native-input.
  gnu: python-tinycss2: Remove python-pytest-cov native-input.
  gnu: python-django-contact-form: Remove python-pytest-cov
    native-input.
  gnu: python-dateutil: Remove python-pytest-cov native-input.
  build-system/pyproject: Remove python-pytest-isort native-input.
  build-system/pyproject: Remove python-pytest-black native-input.
  build-system/pyproject: Remove python-pytest-flake8 native-input.
  build-system/pyproject: Remove python-pytest-mypy inputs.
  build-system/pyproject: Stop hiding options.
  gnu: python-linear-operator: Remove python-flake8-print native-input
  gnu: abjad-ext-ipython: Remove uneeded inputs.

 gnu/packages/android.scm              |   6 +-
 gnu/packages/astronomy.scm            |  31 +-
 gnu/packages/audio.scm                |   2 +-
 gnu/packages/backup.scm               |   2 +-
 gnu/packages/bioinformatics.scm       |  31 +-
 gnu/packages/bootloaders.scm          |  17 +-
 gnu/packages/build-tools.scm          |   1 -
 gnu/packages/check.scm                |  21 +-
 gnu/packages/cpp.scm                  |   4 +-
 gnu/packages/databases.scm            |  17 +-
 gnu/packages/dav.scm                  |   4 -
 gnu/packages/diffoscope.scm           |   2 -
 gnu/packages/django.scm               |  12 +-
 gnu/packages/ebook.scm                |   1 -
 gnu/packages/embedded.scm             |   1 -
 gnu/packages/engineering.scm          |   7 +-
 gnu/packages/finance.scm              |   6 +-
 gnu/packages/fontutils.scm            |   1 -
 gnu/packages/geo.scm                  |   9 +-
 gnu/packages/gettext.scm              |   4 -
 gnu/packages/gpodder.scm              |   3 +-
 gnu/packages/graph.scm                |   6 +-
 gnu/packages/graphviz.scm             |   5 -
 gnu/packages/jupyter.scm              |   8 +-
 gnu/packages/logging.scm              |   2 +-
 gnu/packages/machine-learning.scm     |  64 +---
 gnu/packages/mail.scm                 |   3 +-
 gnu/packages/mastodon.scm             |   1 -
 gnu/packages/messaging.scm            |   6 +-
 gnu/packages/music.scm                |  23 +-
 gnu/packages/package-management.scm   |   7 +-
 gnu/packages/patchutils.scm           |   2 +-
 gnu/packages/pdf.scm                  |   6 +-
 gnu/packages/potassco.scm             |   3 +-
 gnu/packages/protobuf.scm             |   4 +-
 gnu/packages/python-check.scm         |  29 +-
 gnu/packages/python-compression.scm   |  21 +-
 gnu/packages/python-crypto.scm        |   4 +-
 gnu/packages/python-science.scm       |  21 +-
 gnu/packages/python-web.scm           | 175 +++--------
 gnu/packages/python-xyz.scm           | 414 +++++++-------------------
 gnu/packages/radio.scm                |   3 +-
 gnu/packages/serialization.scm        |   1 -
 gnu/packages/simulation.scm           |   2 -
 gnu/packages/sphinx.scm               |   7 -
 gnu/packages/statistics.scm           |  14 +-
 gnu/packages/syndication.scm          |   8 +-
 gnu/packages/task-management.scm      |   1 -
 gnu/packages/telegram.scm             |   3 +-
 gnu/packages/terminals.scm            |  12 +-
 gnu/packages/textutils.scm            |   3 -
 gnu/packages/time.scm                 |  20 +-
 gnu/packages/version-control.scm      |   1 -
 gnu/packages/virtualization.scm       |   6 +-
 gnu/packages/vpn.scm                  |   2 -
 gnu/packages/web.scm                  |   6 +-
 gnu/packages/wm.scm                   |   2 -
 gnu/packages/xml.scm                  |   2 +-
 guix/build/pyproject-build-system.scm |  99 +++++-
 guix/import/pypi.scm                  |  21 +-
 guix/lint.scm                         |  12 +-
 tests/pypi.scm                        |   3 +-
 62 files changed, 405 insertions(+), 809 deletions(-)

-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 01/32] guix: import: pypi: Ignore pypi-ignored-inputs.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-2-ngraves@ngraves.fr

* guix/import/pypi.scm (pypi-ignored-inputs): New variable.

(compute-inputs): Use it.

* tests/pypi.scm (parse-requires.txt): Add ignored input to test the

feature.

* guix/lint.scm (check-inputs-should-be-native): Adapt list.

(check-inputs-should-not-be-an-input-at-all): Use pypi-ignored-list.

Change-Id: I774e526c5a090026e778ee44049637174a1dca95

---

guix/import/pypi.scm | 21 ++++++++++++++++++---

guix/lint.scm | 12 +++++++-----

tests/pypi.scm | 3 ++-

3 files changed, 27 insertions(+), 9 deletions(-)

Toggle diff (119 lines)diff --git a/guix/import/pypi.scm b/guix/import/pypi.scm
index 6719fde330a..d4b70061e86 100644
--- a/guix/import/pypi.scm
+++ b/guix/import/pypi.scm
@@ -14,6 +14,7 @@
 ;;; Copyright © 2022 Vivien Kraus <vivien@planete-kraus.eu>
 ;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2022 Hartmut Goebel <h.goebel@crazy-compilers.com>
+;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -61,6 +62,7 @@ (define-module (guix import pypi)
   #:use-module (guix upstream)
   #:use-module ((guix licenses) #:prefix license:)
   #:export (%pypi-base-url
+            pypi-ignored-inputs
             parse-requires.txt
             parse-wheel-metadata
             specification->requirement-name
@@ -77,6 +79,18 @@ (define %pypi-base-url
   ;; Base URL of the PyPI API.
   (make-parameter "https://pypi.org/pypi/"))
 
+(define pypi-ignored-inputs
+  ;; This list contains packages that are useful for development or quality
+  ;; testing, but that most of the time are not necessary to have as an input.
+  (list "argparse"  ; native
+        "tox" ; test wrapper for other environments
+        "codecov" "coverage"  ; coverage
+        "black" "isort" "pycodestyle" "pep8"  ; style
+        "pyflakes" "flake8" "pylint" "mypy"  ; style+lint
+        "coveralls" "twine"  ; upload integration tools
+        "pytest-isort" "pytest-flake8" "pytest-cov" "pytest-black"
+        "pytest-pep8" "pytest-mypy" "pytest-pep8" "pre-commit"))  ; variants
+
 (define non-empty-string-or-false
   (match-lambda
     ("" #f)
@@ -424,9 +438,10 @@ (define (compute-inputs source-url wheel-url archive)
   "Given the SOURCE-URL and WHEEL-URL of an already downloaded ARCHIVE, return
 the corresponding list of <upstream-input> records."
   (define (requirements->upstream-inputs deps type)
-    (filter-map (match-lambda
-                  ("argparse" #f)
-                  (name (upstream-input
+    (filter-map (lambda (name)
+                  (if (member name pypi-ignored-inputs)
+                      #f
+                      (upstream-input
                          (name name)
                          (downstream-name (python->package-name name))
                          (type type))))
diff --git a/guix/lint.scm b/guix/lint.scm
index 68d532968de..f689cc2a2a8 100644
--- a/guix/lint.scm
+++ b/guix/lint.scm
@@ -71,6 +71,7 @@ (define-module (guix lint)
                                     hg-reference-url)
   #:autoload   (guix bzr-download) (bzr-reference?
                                     bzr-reference-url)
+  #:use-module ((guix import pypi) #:select (pypi-ignored-inputs))
   #:use-module (guix import stackage)
   #:use-module (ice-9 match)
   #:use-module (ice-9 regex)
@@ -557,14 +558,12 @@ (define (check-inputs-should-be-native package)
             "m4"
             "qttools-5"
             "yasm" "nasm" "fasm"
-            "python-coverage"
             "python-cython"
             "python-docutils"
             "python-mock"
             "python-nose"
             "python-pbr"
             "python-pytest"
-            "python-pytest-cov"
             "python-setuptools-scm"
             "python-sphinx"
             "scdoc"
@@ -586,9 +585,12 @@ (define (check-inputs-should-be-native package)
 (define (check-inputs-should-not-be-an-input-at-all package)
   ;; Emit a warning if some inputs of PACKAGE are likely to should not be
   ;; an input at all.
-  (let ((input-names '("python-setuptools"
-                       "python-pip"
-                       "python-pre-commit")))
+  (let ((input-names (append
+                      '("python-setuptools"
+                        "python-pip"
+                        "pre-commit")
+                      (map (cut string-append "python-" <>)
+                           pypi-ignored-inputs))))
     (map (lambda (input)
            (make-warning
             package
diff --git a/tests/pypi.scm b/tests/pypi.scm
index 42b39cde730..fe01ab3beb3 100644
--- a/tests/pypi.scm
+++ b/tests/pypi.scm
@@ -97,6 +97,7 @@ (define test-requires.txt "\
 
 [test]
 pytest (>=2.5.0)
+pytest-cov  # read but ignored
 ")
 
 ;; Beaker contains only optional dependencies.
@@ -244,7 +245,7 @@ (define-syntax-rule (with-pypi responses body ...)
   (map specification->requirement-name test-specifications))
 
 (test-equal "parse-requires.txt"
-  (list '("foo" "bar") '("pytest"))
+  (list '("foo" "bar") '("pytest" "pytest-cov"))
   (mock ((ice-9 ports) call-with-input-file
          call-with-input-string)
         (parse-requires.txt test-requires.txt)))
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 02/32] build-system/pyproject: Ignore unwanted pytest flags.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-3-ngraves@ngraves.fr

* guix/build/pyproject-build-system.scm : Ignore unwanted pytest flags.

Change-Id: Ib9f1602e5af11227e5b7ce124f0f9be4fa2b78e4

---

guix/build/pyproject-build-system.scm | 99 ++++++++++++++++++++++++++-

1 file changed, 96 insertions(+), 3 deletions(-)

Toggle diff (137 lines)diff --git a/guix/build/pyproject-build-system.scm b/guix/build/pyproject-build-system.scm
index 947d240114a..2df9f2f4798 100644
--- a/guix/build/pyproject-build-system.scm
+++ b/guix/build/pyproject-build-system.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2021 Lars-Dominik Braun <lars@6xq.net>
 ;;; Copyright © 2022 Marius Bakke <marius@gnu.org>
+;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -35,7 +36,8 @@ (define-module (guix build pyproject-build-system)
             add-installed-pythonpath
             site-packages
             python-version
-            pyproject-build))
+            pyproject-build
+            with-guix-pytest-plugin))
 
 ;;; Commentary:
 ;;;
@@ -142,7 +144,94 @@ (define* (build #:key outputs build-backend backend-path configure-flags #:allow
      wheel-dir
      config-settings)))
 
-(define* (check #:key tests? test-backend test-flags #:allow-other-keys)
+(define pytest-default-ignore-alist
+  '(("cov" . ("--cov" "--cov-reset" "--cov-report" "--cov-config"
+              "--no-cov-on-fail" "--no-cov" "--cov-fail-under"
+              "--cov-append" "--cov-branch" "--cov-context"))
+    ("mypy" . ("--mypy" "--mypy-config-file" "--mypy-ignore-missing-imports"))
+    ("isort" . ("--isort"))
+    ("flake8" . ("--flake8"))
+    ("black" . ("--black"))
+    ("flakes" . ("--flakes"))
+    ("pep8" . ("--pep8"))))
+
+(define (pytest-ignore-flags-plugin flags)
+  "This function converts an list of flags into a string that can
+  be instantiated as a python pytest plugin."
+  (format #f "\
+import pytest
+
+def pytest_addoption(parser):
+    group = parser.getgroup('guix','Guix ignored options')
+    options = [~{~s, ~}]
+    for option in options:
+        group.addoption(option, action='append', nargs='?')"
+          flags))
+
+(define (call-with-guix-pytest-plugin inputs thunk)
+  "This function emulates command line options provided by pytest plugins in
+the absence of the plugins defining these options.
+
+This is done by selecting absent plugins, gettings their flags defined in
+PYTEST-DEFAULT-IGNORE-ALIST, and generating the plugin from there with
+PYTEST-IGNORE-FLAGS-PLUGIN."
+  (let* ((former-path (getenv "PYTHONPATH"))
+         (input-names
+          (map car
+               (filter (match-lambda
+                         ((name . _)
+                          (if (string-prefix? "python-pytest-" name)
+                              name
+                              #f))
+                         ( _ #f))
+                       inputs)))
+         (filtered-flags
+          (filter identity
+                  (append-map
+                   (match-lambda
+                     ((group . flags)
+                      (if (member (string-append "python-pytest-" group)
+                                  input-names)
+                          (list #f)
+                          flags))
+                     (_ (list #f)))
+                   pytest-default-ignore-alist)))
+         (dir (string-append
+               (if (access? (dirname (getcwd)) W_OK)
+                   (dirname (getcwd))
+                   ;; fallback if we're already out-of-source
+                   (getcwd))
+               "/.guix-pytest")))
+    (dynamic-wind
+      (lambda ()
+        (setenv "PYTHONPATH"
+                (string-append
+                 (if former-path
+                     (string-append former-path ":")
+                     "")
+                 dir))
+        (setenv "PYTEST_PLUGINS"
+                (string-append
+                 (if (getenv "PYTEST_PLUGINS")
+                     (string-append former-path ",")
+                     "")
+                 "pytest_guix_plugin"))
+        (mkdir-p dir)
+        (with-output-to-file (string-append dir "/__init__.py")
+          (lambda _ (display "")))
+        (with-output-to-file (string-append dir "/pytest_guix_plugin.py")
+          (lambda _
+            (display (pytest-ignore-flags-plugin filtered-flags)))))
+      thunk
+      (lambda ()
+        (setenv "PYTHONPATH" former-path)
+        (unsetenv "PYTEST_PLUGINS")))))
+
+(define-syntax-rule (with-guix-pytest-plugin inputs exp ...)
+  "Evaluate EXP in a context where the Guix pytest plugin is added."
+  (call-with-guix-pytest-plugin inputs (lambda () exp ...)))
+
+(define* (check #:key inputs tests? test-backend test-flags #:allow-other-keys)
   "Run the test suite of a given Python package."
   (if tests?
       ;; Unfortunately with PEP 517 there is no common method to specify test
@@ -165,7 +254,8 @@ (define* (check #:key tests? test-backend test-flags #:allow-other-keys)
         (format #t "Using ~a~%" use-test-backend)
         (match use-test-backend
           ('pytest
-           (apply invoke pytest "-vv" test-flags))
+           (with-guix-pytest-plugin inputs
+             (apply invoke pytest "-vv" test-flags)))
           ('nose
            (apply invoke nosetests "-v" test-flags))
           ('nose2
@@ -386,3 +476,6 @@ (define* (pyproject-build #:key inputs (phases %standard-phases)
   (apply python:python-build #:inputs inputs #:phases phases args))
 
 ;;; pyproject-build-system.scm ends here
+;;; Local Variables:
+;;; eval: (put 'with-guix-pytest-plugin 'scheme-indent-function 1)
+;;; End:
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 03/32] build-system/pyproject: Remove python-black input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-4-ngraves@ngraves.fr

* gnu/packages/bioinformatics.scm (python-doubletdetection,

python-liana-py, scvelo)[native-inputs]: Remove python-black.

* gnu/packages/databases.scm (datasette):

[arguments]<#:test-flags>: Ignore black tests.

<#:phases>: Remove parts related to black in relax-requirements

added phase.

[native-inputs]: Remove python-black.

* gnu/packages/finance.scm (python-trezor)[native-inputs]: Remove

python-black.

* gnu/packages/graph.scm (python-graphtools)[native-inputs]: Remove

python-black.

* gnu/packages/machine-learning.scm (python-funsor,

python-imbalanced-learn, python-hyperopt, python-captum,

python-pyro-ppl)[native-inputs]: Remove python-black.

* gnu/packages/python-check.scm (python-vcrpy)[native-inputs]:

Remove python-black.

* gnu/packages/python-web.scm (python-ovh, python-openai,

python-starsessions-for-pytorch-lightning)[native-inputs]: Remove

python-black.

* gnu/packages/python-xyz.scm (python-pydantic-cli, python-imageio,

python-update-checker, python-eliot, python-minikanren,

python-jupytext)[native-inputs]: Remove python-black.

(ptpython)[propagated-inputs]: Remove python-black.

* gnu/packages/virtualization.scm (python-transient)[native-inputs]:

Remove python-black.

Change-Id: Ie8098afda264bf9a5ab2cfe5d915bc7a41fdc604

---

gnu/packages/bioinformatics.scm | 11 +++--------

gnu/packages/databases.scm | 8 ++------

gnu/packages/finance.scm | 1 -

gnu/packages/graph.scm | 1 -

gnu/packages/machine-learning.scm | 11 +++--------

gnu/packages/python-check.scm | 3 +--

gnu/packages/python-web.scm | 8 +++-----

gnu/packages/python-xyz.scm | 15 +++++----------

gnu/packages/virtualization.scm | 3 +--

9 files changed, 18 insertions(+), 43 deletions(-)

Toggle diff (272 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d4a39fd3e1a..adeb7b1c3be 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2152,8 +2152,7 @@ (define-public python-doubletdetection
            python-scipy
            python-tqdm))
     (native-inputs
-     (list python-black
-           python-flake8
+     (list python-flake8
            python-poetry-core
            python-pytest))
     (home-page "https://github.com/JonathanShor/DoubletDetection")
@@ -2278,10 +2277,7 @@ (define-public python-liana-py
                              python-tqdm
                              tzdata))
     (native-inputs
-     (list python-black
-           python-poetry-core
-           python-pytest
-           python-pytest-cov))
+     (list python-poetry-core python-pytest python-pytest-cov))
     (home-page "https://github.com/saezlab/liana-py")
     (synopsis "LIANA is a ligand-receptor analysis framework")
     (description "This is a Ligand-Receptor inference framework.  The
@@ -21838,8 +21834,7 @@ (define-public scvelo
            python-umap-learn
            pybind11))
     (native-inputs
-     (list python-black
-           python-flake8
+     (list python-flake8
            python-hypothesis
            python-pytest
            python-setuptools-scm
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 67e6ced7c32..96b2c2a0437 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -5537,16 +5537,13 @@ (define-public datasette
                     " or test_custom_query_with_unicode_characters"
                     " or test_searchmode)")
               "-n" (number->string (parallel-job-count))
-              "-m" "not serial")        ;cannot run in parallel
+              "-m" "not serial"  ;cannot run in parallel
+              "--ignore=tests/test_black.py")
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'relax-requirements
             (lambda _
-              ;; The package needlessly specifies exact versions
-              ;; of dependencies, when it works fine with others.
               (substitute* "setup.py"
-                (("(black)==[0-9\\.]+" _ package)
-                 package)
                 (("click-default-group-wheel")
                  "click-default-group")))))))
     (propagated-inputs
@@ -5569,7 +5566,6 @@ (define-public datasette
            python-uvicorn))
     (native-inputs
      (list python-beautifulsoup4
-           python-black
            python-cogapp
            python-pip
            python-pytest
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index 3c32a220c4e..7d1efde8187 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -1149,7 +1149,6 @@ (define-public python-trezor
            python-typing-extensions))
     (native-inputs ; Only needed for running the tests
      (list protobuf
-           python-black
            python-isort
            python-pillow
            python-protobuf
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index eda8365a424..033027a5aa9 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -476,7 +476,6 @@ (define-public python-graphtools
     (native-inputs
      (list util-linux ;for lscpu
            python-anndata
-           python-black
            python-coverage
            python-coveralls
            python-nose
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index d5ce3bfe7de..494d7174859 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -175,8 +175,7 @@ (define-public python-funsor
     (propagated-inputs (list python-makefun python-multipledispatch
                              python-numpy python-opt-einsum
                              python-typing-extensions))
-    (native-inputs (list python-black
-                         python-flake8
+    (native-inputs (list python-flake8
                          python-isort
                          python-nbsphinx
                          python-pandas
@@ -1923,8 +1922,7 @@ (define-public python-imbalanced-learn
                               (getcwd)))))))
     (propagated-inputs (list python-joblib python-numpy python-scikit-learn
                              python-scipy python-threadpoolctl))
-    (native-inputs (list python-black
-                         python-flake8
+    (native-inputs (list python-flake8
                          python-keras
                          python-mypy
                          python-pandas
@@ -2359,8 +2357,7 @@ (define-public python-hyperopt
            python-six
            python-tqdm))
     (native-inputs
-     (list python-black
-           python-nose
+     (list python-nose
            python-pymongo
            python-pytest
            python-wheel))
@@ -4525,7 +4522,6 @@ (define-public python-captum
      (list python-matplotlib python-numpy python-pytorch python-tqdm))
     (native-inputs (list jupyter
                          python-annoy
-                         python-black
                          python-flake8
                          python-flask
                          python-flask-compress
@@ -5064,7 +5060,6 @@ (define-public python-pyro-ppl
     (native-inputs
      (list ninja
            jupyter
-           python-black
            python-flake8
            python-graphviz
            python-isort
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index e3f0499fecb..ca87289a1e1 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -411,8 +411,7 @@ (define-public python-vcrpy
     (propagated-inputs
      (list python-pyyaml python-six python-wrapt python-yarl))
     (native-inputs
-     (list python-black
-           python-coverage
+     (list python-coverage
            python-flake8
            python-flask
            python-httplib2
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index e417fc2bb47..4f5d7baab97 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -977,8 +977,7 @@ (define-public python-ovh
     (build-system pyproject-build-system)
     (arguments (list #:tests? #f))      ; XXX: tests require networking
     (propagated-inputs (list python-requests))
-    (native-inputs (list python-black
-                         python-coverage
+    (native-inputs (list python-coverage
                          python-flake8
                          python-isort
                          python-pytest
@@ -2171,7 +2170,7 @@ (define-public python-openai
  and not test_file_cli")))
     (propagated-inputs (list python-aiohttp python-requests python-tqdm
                              python-typing-extensions))
-    (native-inputs (list python-black python-pytest python-pytest-asyncio
+    (native-inputs (list python-pytest python-pytest-asyncio
                          python-pytest-mock python-setuptools python-wheel))
     (home-page "https://github.com/openai/openai-python")
     (synopsis "Python client library for the OpenAI API")
@@ -8974,8 +8973,7 @@ (define-public python-starsessions-for-pytorch-lightning
            python-itsdangerous
            python-starlette-for-fastapi-0.88))
     (native-inputs
-     (list python-black
-           python-flake8
+     (list python-flake8
            python-httpx
            python-mypy
            python-poetry-core
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index d81de891c4f..0388cefee4c 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -478,7 +478,6 @@ (define-public python-jupytext
     (native-inputs
      (list git-minimal
            python-autopep8
-           python-black
            python-flake8
            python-gitpython
            python-isort
@@ -8029,8 +8028,7 @@ (define-public python-pydantic-cli
     (propagated-inputs
      (list python-pydantic))
     (native-inputs
-     (list python-black
-           python-mypy
+     (list python-mypy
            python-pytest))
     (home-page "https://github.com/mpkocher/pydantic-cli")
     (synopsis "Turn Pydantic defined data models into CLI tools")
@@ -10812,7 +10810,7 @@ (define-public python-imageio
     (propagated-inputs
      (list python-imageio-ffmpeg python-numpy python-pillow python-tifffile python-setuptools))
     (native-inputs
-     (list python-black python-flake8 python-fsspec python-pytest
+     (list python-flake8 python-fsspec python-pytest
            python-pytest-cov python-wheel))
     (home-page "https://imageio.github.io/")
     (synopsis "Library for reading and writing a wide range of image data")
@@ -22112,8 +22110,7 @@ (define-public ptpython
     (arguments
      `(#:tests? #f)) ;there are no tests
     (propagated-inputs
-     (list python-appdirs python-black python-jedi python-prompt-toolkit
-           python-pygments))
+     (list python-appdirs python-jedi python-prompt-toolkit python-pygments))
     (home-page "https://github.com/jonathanslenders/ptpython")
     (synopsis "Python Read-Eval-Print-Loop with nice IDE-like features")
     (description
@@ -27295,7 +27292,7 @@ (define-public python-update-checker
         (base32 "04yb5a9mi45ax50m2m0ih6gdvkk1j7gfmy83dd58i1f59axlabba"))))
     (build-system python-build-system)
     (propagated-inputs (list python-requests))
-    (native-inputs (list python-black python-flake8 python-pytest))
+    (native-inputs (list python-flake8 python-pytest))
     (home-page "https://github.com/bboe/update_checker")
     (synopsis "Python module that will check for package updates")
     (description "This package provides a Python module that will check for
@@ -31409,8 +31406,7 @@ (define-public python-eliot
      (list python-boltons python-pyrsistent python-six
            python-zope-interface))
     (native-inputs
-     (list python-black
-           python-coverage
+     (list python-coverage
            python-dask
            python-flake8
            python-hypothesis
@@ -34165,7 +34161,6 @@ (define-public python-minikanren
            python-pytest
            python-pytest-cov
            python-pylint
-           python-black
            python-sympy
            python-versioneer
            python-coverage))
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index 6d28b32c863..85ad5031059 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -2809,8 +2809,7 @@ (define-public python-transient
            python-requests
            python-toml))
     (native-inputs
-     (list python-black
-           python-mypy
+     (list python-mypy
            python-pyhamcrest
            python-setuptools
            python-twine
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 04/32] build-system/pyproject: Remove python-pylint native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-5-ngraves@ngraves.fr

* gnu/packages/potassco.scm (python-clingraph):

[native-inputs]: Remove python-pylint.

* gnu/packages/python-xyz.scm (python-mediapy, python-fastjsonschema,

python-trio)[native-inputs]: Remove python-pylint.

* gnu/packages/syndication.scm (rtv, tuir)[native-inputs]: Remove

python-pylint.

* gnu/packages/terminals.scm (python-halo, python-log-symbols,

python-spinners)[native-inputs]: Remove python-pylint.

Change-Id: If6a20e0b790f7157013a6868bba9e4a8d7e5ba28

---

gnu/packages/potassco.scm | 3 +--

gnu/packages/python-xyz.scm | 3 ---

gnu/packages/syndication.scm | 2 --

gnu/packages/terminals.scm | 5 ++---

4 files changed, 3 insertions(+), 10 deletions(-)

Toggle diff (94 lines)diff --git a/gnu/packages/potassco.scm b/gnu/packages/potassco.scm
index 9af307b4a90..054f9e9b180 100644
--- a/gnu/packages/potassco.scm
+++ b/gnu/packages/potassco.scm
@@ -563,8 +563,7 @@ (define-public python-clingraph
                              python-jsonschema
                              python-networkx
                              python-setuptools))
-    (native-inputs (list dot2tex graphviz python-pylint python-pytest
-                         python-wheel))
+    (native-inputs (list dot2tex graphviz python-pytest python-wheel))
     (home-page "https://github.com/potassco/clingraph")
     (synopsis "Visualizer for graphs defined as logic programs")
     (description
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 0388cefee4c..8d4ce3f9844 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4440,7 +4440,6 @@ (define-public python-mediapy
                              python-pillow))
     (native-inputs
      (list python-flit-core
-           python-pylint
            python-pytest
            python-pytest-xdist))
     (home-page "https://github.com/google/mediapy")
@@ -17189,7 +17188,6 @@ (define-public python-fastjsonschema
      (list python-colorama
            python-json-spec
            python-jsonschema
-           python-pylint
            python-pytest
            python-pytest-benchmark
            python-pytest-cache
@@ -29079,7 +29077,6 @@ (define-public python-trio
      (list python-astor
            python-ipython
            python-jedi
-           python-pylint
            python-pyopenssl
            python-pytest
            python-pytest-xdist
diff --git a/gnu/packages/syndication.scm b/gnu/packages/syndication.scm
index bbb89099b06..0f12f94d0bc 100644
--- a/gnu/packages/syndication.scm
+++ b/gnu/packages/syndication.scm
@@ -437,7 +437,6 @@ (define-public rtv
            python-coveralls
            python-coverage
            python-mock
-           python-pylint
            python-pytest
            python-vcrpy))
     (home-page "https://github.com/michael-lazar/rtv")
@@ -472,7 +471,6 @@ (define-public tuir
      (list python-coverage
            python-coveralls
            python-mock
-           python-pylint
            python-pytest
            python-setuptools
            python-vcrpy
diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index 8d9157fd949..90dc011a70e 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -1199,7 +1199,6 @@ (define-public python-halo
     (native-inputs
      (list python-coverage
            python-nose
-           python-pylint
            python-setuptools
            python-tox
            python-twine
@@ -1230,7 +1229,7 @@ (define-public python-log-symbols
                      (("(.*)==(.*)$" _ dep ver)
                       (string-append dep ">=" ver))))))))
     (propagated-inputs (list python-colorama))
-    (native-inputs (list python-coverage python-nose python-pylint
+    (native-inputs (list python-coverage python-nose
                          python-setuptools python-tox python-wheel))
     (home-page "https://github.com/manrajgrover/py-log-symbols")
     (synopsis "Python library with graphical symbols for logging on the terminal")
@@ -1258,7 +1257,7 @@ (define-public python-spinners
                    (substitute* "requirements-dev.txt"
                      (("(.*)==(.*)$" _ dep ver)
                       (string-append dep ">=" ver))))))))
-    (native-inputs (list python-coverage python-nose python-pylint
+    (native-inputs (list python-coverage python-nose
                          python-setuptools python-tox python-wheel))
     (home-page "https://github.com/manrajgrover/py-spinners")
     (synopsis "Python library with graphical spinners for the terminal")
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 05/32] build-system/pyproject: Remove python-flake8 inputs.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-6-ngraves@ngraves.fr

* gnu/packages/astronomy.scm (python-crds)[native-inputs]: Remove

python-flake8.

* gnu/packages/bioinformatics.scm (python-doubletdetection,

python-biom-format)[native-inputs]: Remove python-flake8.

* gnu/packages/ebook.scm (calibre)[native-inputs]: Remove

python-flake8.

* gnu/packages/engineering.scm (python-scikit-rf)[native-inputs]:

Remove python-flake8.

* gnu/packages/finance.scm (python-mt-940)[native-inputs]: Remove

python-flake8.

* gnu/packages/geo.scm (python-geopy)[native-inputs]: Remove

python-flake8.

* gnu/packages/gettext.scm (python-mdpo)[native-inputs]: Remove

python-flake8.

* gnu/packages/graph.scm (python-pygsp)[native-inputs]: Remove

python-flake8.

* gnu/packages/graphviz.scm (python-uqbar)[native-inputs]: Remove

python-flake8.

* gnu/packages/machine-learning.scm (python-funsor,

python-imbalanced-learn, python-captum, python-pyro-api,

python-pyro-ppl, python-linear-operator,

python-gpytorch)[native-inputs]: Remove python-flake8.

* gnu/packages/music.scm (python-mutagen):

[arguments]<#:test-flags>: Ignore flake8 quality tests.

[native-inputs]: Remove python-flake8.

* gnu/packages/protobuf.scm (python-pure-protobuf):

[arguments]<#:phases>: Remove flake8 invocation from check phase.

[native-inputs]: Remove python-flake8.

* gnu/packages/python-web.scm (python-ovh, python-furl,

python-httplib2, python-http-ece, python-woob,

python-starsessions-for-pytorch-lightning)[native-inputs]: Remove

python-flake8.

* gnu/packages/python-xyz.scm (python-apispec,

python-apispec-webframeworks, python-apprise, python-colorful,

python-pymd4c, python-pyls-black, python-docx, python-flasgger,

python-imageio, python-importlib-ressources, python-jaraco-test,

python-seaborn, python-progressbar2, python-inflect,

python-argcomplete, python-diff-cover, python-validators,

python-marshmallow, python-marshmallow-jsonapi, python-yq,

python-update-checker, python-eliot, python-dateparser,

python-jinja2-cli, python-nikola, python-verspec, python-mike,

python-arpeggio, python-versioneer, python-codespell)[native-inputs]:

Remove python-flake8.

* gnu/packages/simulation.scm (python-dolfin-adjoint)[native-inputs]:

Remove python-flake8.

* gnu/packages/sphinx.scm (python-sphinx,

python-sphinx-5)[propagated-inputs]: Remove python-flake8.

* gnu/packages/statistics.scm (python-statsmodels)[native-inputs]:

Remove python-flake8.

* gnu/packages/vpn.scm (sshuttle)[native-inputs]: Remove

python-flake8.

* gnu/packages/wm.scm (qtile)[native-inputs]: Remove python-flake8.

* gnu/packages/textutils.scm (python-panflute)[native-inputs]: Remove

python-flake8.

Change-Id: I196a9c0b7497106c8f98598535cb8e0ea667481c

---

gnu/packages/astronomy.scm | 3 +-

gnu/packages/bioinformatics.scm | 7 +---

gnu/packages/ebook.scm | 1 -

gnu/packages/engineering.scm | 1 -

gnu/packages/finance.scm | 4 +-

gnu/packages/geo.scm | 1 -

gnu/packages/gettext.scm | 1 -

gnu/packages/graph.scm | 3 +-

gnu/packages/graphviz.scm | 1 -

gnu/packages/machine-learning.scm | 15 ++------

gnu/packages/music.scm | 4 +-

gnu/packages/protobuf.scm | 4 +-

gnu/packages/python-web.scm | 12 ++----

gnu/packages/python-xyz.scm | 62 +++++++++++--------------------

gnu/packages/simulation.scm | 1 -

gnu/packages/sphinx.scm | 2 -

gnu/packages/statistics.scm | 1 -

gnu/packages/textutils.scm | 1 -

gnu/packages/vpn.scm | 1 -

gnu/packages/wm.scm | 1 -

20 files changed, 36 insertions(+), 90 deletions(-)

Toggle diff (407 lines)diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index c05f8e51885..02d0726b9be 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2188,8 +2188,7 @@ (define-public python-crds
                              python-roman-datamodels
                              python-stsynphot
                              python-requests))
-    (native-inputs (list python-flake8
-                         python-ipython
+    (native-inputs (list python-ipython
                          python-lockfile
                          python-mock
                          python-nose
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index adeb7b1c3be..aa7f2988191 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2152,8 +2152,7 @@ (define-public python-doubletdetection
            python-scipy
            python-tqdm))
     (native-inputs
-     (list python-flake8
-           python-poetry-core
+     (list python-poetry-core
            python-pytest))
     (home-page "https://github.com/JonathanShor/DoubletDetection")
     (synopsis
@@ -3006,7 +3005,6 @@ (define-public python-biom-format
     (propagated-inputs
      (list python-anndata
            python-click
-           python-flake8
            python-future
            python-h5py
            python-numpy
@@ -21834,8 +21832,7 @@ (define-public scvelo
            python-umap-learn
            pybind11))
     (native-inputs
-     (list python-flake8
-           python-hypothesis
+     (list python-hypothesis
            python-pytest
            python-setuptools-scm
            python-wheel))
diff --git a/gnu/packages/ebook.scm b/gnu/packages/ebook.scm
index 16d4fcd6e36..3d536e59add 100644
--- a/gnu/packages/ebook.scm
+++ b/gnu/packages/ebook.scm
@@ -154,7 +154,6 @@ (define-public calibre
     (native-inputs
      (list bash-minimal
            pkg-config
-           python-flake8
            python-pyqt-builder
            qtbase-5                     ; for qmake
            xdg-utils))
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index f082f346278..610fb53087b 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -2679,7 +2679,6 @@ (define-public python-scikit-rf
                              python-qtpy
                              python-scipy))
     (native-inputs (list python-coverage
-                         python-flake8
                          python-nbval
                          python-networkx
                          python-pytest
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index 7d1efde8187..7579001dd1f 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -2307,9 +2307,7 @@ (define-public python-mt-940
                         ;; Remove custom --cov flags.
                         (delete-file "pytest.ini")
                         (invoke "pytest" "-vv")))))))
-    (native-inputs (list python-flake8
-                         python-pytest
-                         python-pyyaml))
+    (native-inputs (list python-pytest python-pyyaml))
     (home-page "https://mt940.readthedocs.io/")
     (synopsis "Python parser for MT940-encoded SWIFT data")
     (description
diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 81a854f8a2a..69cc7e6ddc5 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -3265,7 +3265,6 @@ (define-public python-geopy
     (native-inputs
      (list python-async-generator
            python-coverage
-           python-flake8
            python-isort
            python-pytest
            python-pytest-aiohttp
diff --git a/gnu/packages/gettext.scm b/gnu/packages/gettext.scm
index 1408cc4cb46..bbb19bd4cb8 100644
--- a/gnu/packages/gettext.scm
+++ b/gnu/packages/gettext.scm
@@ -214,7 +214,6 @@ (define-public mdpo
     (build-system python-build-system)
     (native-inputs
      (list python-bump2version
-           python-flake8
            python-flake8-implicit-str-concat
            python-flake8-print
            python-isort
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 033027a5aa9..eb8aa17fdfe 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -564,8 +564,7 @@ (define-public python-pygsp
                 "")))))))
     (propagated-inputs (list python-numpy python-scikit-image python-scipy))
     (native-inputs
-     (list python-coverage python-coveralls python-flake8
-           python-pytest))
+     (list python-coverage python-coveralls python-pytest))
     (home-page "https://github.com/epfl-lts2/pygsp")
     (synopsis "Graph Signal Processing in Python")
     (description "The PyGSP is a Python package to ease signal processing on
diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm
index db40b99928a..b396a97c0bc 100644
--- a/gnu/packages/graphviz.scm
+++ b/gnu/packages/graphviz.scm
@@ -217,7 +217,6 @@ (define-public python-uqbar
 and not test_sphinx_book_text_broken_strict")))
     (native-inputs
      (list graphviz
-           python-flake8
            python-isort
            python-mypy
            python-pytest
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 494d7174859..bf09c9ec4c1 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -175,8 +175,7 @@ (define-public python-funsor
     (propagated-inputs (list python-makefun python-multipledispatch
                              python-numpy python-opt-einsum
                              python-typing-extensions))
-    (native-inputs (list python-flake8
-                         python-isort
+    (native-inputs (list python-isort
                          python-nbsphinx
                          python-pandas
                          python-pillow
@@ -1922,8 +1921,7 @@ (define-public python-imbalanced-learn
                               (getcwd)))))))
     (propagated-inputs (list python-joblib python-numpy python-scikit-learn
                              python-scipy python-threadpoolctl))
-    (native-inputs (list python-flake8
-                         python-keras
+    (native-inputs (list python-keras
                          python-mypy
                          python-pandas
                          python-pytest
@@ -4522,7 +4520,6 @@ (define-public python-captum
      (list python-matplotlib python-numpy python-pytorch python-tqdm))
     (native-inputs (list jupyter
                          python-annoy
-                         python-flake8
                          python-flask
                          python-flask-compress
                          python-ipython
@@ -5010,8 +5007,7 @@ (define-public python-pyro-api
     (build-system python-build-system)
     (arguments '(#:tests? #false)) ;requires pyro
     (native-inputs
-     (list python-flake8
-           python-ipython
+     (list python-ipython
            python-pytest
            python-sphinx
            python-sphinx-rtd-theme))
@@ -5060,7 +5056,6 @@ (define-public python-pyro-ppl
     (native-inputs
      (list ninja
            jupyter
-           python-flake8
            python-graphviz
            python-isort
            python-lap
@@ -5107,8 +5102,7 @@ (define-public python-linear-operator
                              python-pytorch
                              python-scipy
                              python-typeguard))
-    (native-inputs (list python-flake8
-                         python-flake8-print
+    (native-inputs (list python-flake8-print
                          python-pytest
                          python-setuptools
                          python-setuptools-scm
@@ -5139,7 +5133,6 @@ (define-public python-gpytorch
                                        " and not test_t_matmul_matrix"))))
     (propagated-inputs (list python-linear-operator python-scikit-learn))
     (native-inputs (list python-coverage
-                         python-flake8
                          python-flake8-print
                          python-nbval
                          python-pytest
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index ab3fe970997..ad026f5d359 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -3968,6 +3968,7 @@ (define-public python-mutagen
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags '(list "--ignore=tests/quality/test_flake8.py")
        #:phases
        #~(modify-phases %standard-phases
            (add-before 'check 'remove-hypothesis-deadlines
@@ -3978,8 +3979,7 @@ (define-public python-mutagen
                  (("( +)@given" all spaces)
                   (string-append spaces "@settings(deadline=None)\n" all))))))))
     (native-inputs
-     (list python-flake8
-           python-hypothesis
+     (list python-hypothesis
            python-pytest
            python-setuptools
            python-wheel))
diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm
index 8ca730df3c3..502ad09a3a6 100644
--- a/gnu/packages/protobuf.scm
+++ b/gnu/packages/protobuf.scm
@@ -469,7 +469,7 @@ (define-public python-pure-protobuf
         (base32 "15dp5pvazd0jx4wzzh79080ah7hkpd3axh40al9vhzs2hf3v90hx"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-flake8 python-pytest python-pytest-cov python-isort))
+     (list python-pytest python-pytest-cov python-isort))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
@@ -477,8 +477,6 @@ (define-public python-pure-protobuf
            (lambda _
              (invoke "pytest" "--cov-report" "term-missing" "--cov"
                      "pure_protobuf")
-             (invoke "flake8" "pure_protobuf" "tests"
-                     "--ignore=F541")
              (invoke "isort" "-rc" "-c" "pure_protobuf" "tests"))))))
     (home-page "https://pypi.org/project/pure-protobuf/")
     (synopsis "Protobuf implementation using dataclasses")
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 4f5d7baab97..ba378088cf8 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -978,7 +978,6 @@ (define-public python-ovh
     (arguments (list #:tests? #f))      ; XXX: tests require networking
     (propagated-inputs (list python-requests))
     (native-inputs (list python-coverage
-                         python-flake8
                          python-isort
                          python-pytest
                          python-pytest-cov
@@ -1240,8 +1239,6 @@ (define-public python-furl
     (build-system python-build-system)
     (propagated-inputs
      (list python-six python-orderedmultidict))
-    (native-inputs
-     (list python-flake8))
     (home-page "https://github.com/gruns/furl")
     (synopsis "URL manipulation in Python")
     (description "Furl provides an easy-to-use alternative to the
@@ -1274,7 +1271,6 @@ (define-public python-httplib2
                  (("==") ">=")))))))
     (native-inputs
      (list python-cryptography
-           python-flake8
            python-future
            python-mock
            python-pytest
@@ -7313,7 +7309,7 @@ (define-public python-http-ece
     (propagated-inputs
      (list python-cryptography))
     (native-inputs
-     (list python-coverage python-flake8 python-mock python-nose))
+     (list python-coverage python-mock python-nose))
     (home-page "https://github.com/web-push-libs/encrypted-content-encoding")
     (synopsis "Encrypted Content Encoding for HTTP")
     (description
@@ -8333,8 +8329,7 @@ (define-public python-woob
            python-six
            python-unidecode))
     (native-inputs
-     (list python-coverage python-flake8 python-nose python-selenium
-           python-xunitparser))
+     (list python-coverage python-nose python-selenium python-xunitparser))
     (home-page "https://woob.tech/")
     (synopsis "Woob, Web Outside Of Browsers")
     (description "Woob is a collection of applications able to interact with
@@ -8973,8 +8968,7 @@ (define-public python-starsessions-for-pytorch-lightning
            python-itsdangerous
            python-starlette-for-fastapi-0.88))
     (native-inputs
-     (list python-flake8
-           python-httpx
+     (list python-httpx
            python-mypy
            python-poetry-core
            python-pytest
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 8d4ce3f9844..3ca12d05ee5 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -320,7 +320,6 @@ (define-public python-apprise
     (native-inputs (list python-babel
                          python-coverage
                          python-cryptography
-                         python-flake8
                          python-paho-mqtt
                          python-pytest
                          python-pytest-cov
@@ -1183,8 +1182,7 @@ (define-public python-colorful
         (base32 "0kyy9qhvrb5m9h8xmri7c88i0k1g5qc7017anw39gx44an7mn33y"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage python-flake8 python-pytest python-setuptools
-           python-wheel))
+     (list python-coverage python-pytest python-setuptools python-wheel))
     (propagated-inputs
      (list python-colorama))
     (home-page "http://github.com/timofurrer/colorful")
@@ -2370,7 +2368,7 @@ (define-public python-pymd4c
     (inputs
      (list md4c))
     (native-inputs
-     (list python-flake8 python-pkgconfig pkg-config))
+     (list python-pkgconfig pkg-config))
     (home-page "https://github.com/dominickpastore/pymd4c")
     (synopsis "Python bindings for MD4C")
     (description
@@ -3028,7 +3026,7 @@ (define-public python-pyls-black
     (propagated-inputs
      (list python-black python-lsp-server python-toml python-tomli))
     (native-inputs
-     (list python-flake8 python-isort python-mypy python-pytest
+     (list python-isort python-mypy python-pytest
            python-pytest-runner python-setuptools python-wheel))
     (home-page "https://github.com/rupert/pyls-black")
     (synopsis "Black plugin for the Python Language Server")
@@ -7006,7 +7004,6 @@ (define-public python-docx
     (build-system pyproject-build-system)
     (native-inputs
      (list behave
-           python-flake8
            python-mock
            python-pyparsing
            python-pytest
@@ -10809,7 +10806,7 @@ (define-public python-imageio
     (propagated-inputs
      (list python-imageio-ffmpeg python-numpy python-pillow python-tifffile python-setuptools))
     (native-inputs
-     (list python-flake8 python-fsspec python-pytest
+     (list python-fsspec python-pytest
            python-pytest-cov python-wheel))
     (home-page "https://imageio.github.io/")
     (synopsis "Library for reading and writing a wide range of image data")
@@ -11587,8 +11584,7 @@ (define-public python-importlib-resources
              (setenv "PYTHONPATH"
                      (string-append (getcwd) "/_custom_build")))))))
     (native-inputs
-     (list python-flake8
-           python-pytest
+     (list python-pytest
            python-pytest-black
            python-pytest-checkdocs
            python-pytest-cov
@@ -11910,8 +11906,7 @@ (define-public python-jaraco-test
     (arguments
      (list #:test-flags '(list "-k" "http")))
     (propagated-inputs (list python-jaraco-context python-jaraco-functools))
-    (native-inputs (list python-flake8
-                         python-pytest
+    (native-inputs (list python-pytest
                          python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-cov
@@ -13710,8 +13705,7 @@ (define-public python-seaborn
            python-scipy
            python-statsmodels))
     (native-inputs
-     (list python-flake8
-           python-flit-core
+     (list python-flit-core
            python-ipykernel
            python-nbconvert
            python-numpydoc
@@ -18695,8 +18689,7 @@ (define-public python-progressbar2
     (propagated-inputs
      (list python-six python-utils))
     (native-inputs
-     (list python-flake8
-           python-freezegun
+     (list python-freezegun
            python-pycodestyle
            python-pytest
            python-pytest-cache
@@ -20052,8 +20045,7 @@ (define-public python-codespell
     (inputs
       (list python-chardet))
     (native-inputs
-      (l

This message was truncated. Download the full message here.

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 06/32] build-system/pyproject: Remove python-coverage input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-7-ngraves@ngraves.fr

* gnu/packages/android.scm (python-androguard):

[native-inputs]: Remove python-coverage.

[arguments]<#:phases>: Adapt 'check phase replacement.

* gnu/packages/astronomy.scm (python-asdf-astropy, python-astropy,

python-poliastro)[native-inputs]: Remove python-coverage.

* gnu/packages/bioinformatics.scm (python-ega-download-client,

python-scikit-bio, python-cooler)[native-inputs]: Remove

python-coverage.

* gnu/packages/check.scm (python-pytest-randomly,

python-pytest-flakes, python-aiounittest)[native-inputs]: Remove

python-coverage.

* gnu/packages/cpp.scm (cpplint)[native-inputs]: Remove

python-coverage.

* gnu/packages/diffoscope.scm (reprotest)[native-inputs]: Remove

python-coverage.

* gnu/packages/django.scm (python-django-haystack)[native-inputs]:

Remove python-coverage.

* gnu/packages/engineering.scm (python-scikit-rf)[native-inputs]:

Remove python-coverage.

* gnu/packages/geo.scm (python-geopy)[native-inputs]: Remove

python-coverage.

* gnu/packages/gpodder.scm (gpodder)[native-inputs]: Remove

python-coverage.

* gnu/packages/graph.scm (python-graphtools,

python-pygsp)[native-inputs]: Remove python-coverage.

* gnu/packages/jupyter.scm (python-jupyter-packaging)[native-inputs]:

Remove python-coverage.

* gnu/packages/machine-learning.scm (onnx, onnx-optimizer,

python-lightning-utilities, python-pytorch-lightning,

python-torchmetrics, python-gpytorch)[native-inputs]: Remove

python-coverage.

* gnu/packages/music.scm (python-pylast)[native-inputs]: Remove

python-coverage.

* gnu/packages/package-management.scm (python-anaconda-client,

conda)[native-inputs]: Remove python-coverage.

* gnu/packages/python-check.scm (python-vcrpy,

python-re-assert)[native-inputs]: Remove python-coverage.

* gnu/packages/python-compression.scm (python-multivolumefile,

python-pybcj, python-bcj-cffi, python-pyppmd, python-ppmd-cffi,

python-py7zr)[native-inputs]: Remove python-coverage.

* gnu/packages/python-web.scm (python-ovh, python-flask-misaka,

python-zope-interface, python-zope-hookable, python-url,

python-transaction, python-sanic, python-woob,

python-flask-combo-jsonapi)[native-inputs]: Remove python-coverage.

* gnu/packages/python-xyz.scm (python-apprise, python-arpeggio,

python-affine, python-colorful, python-lunr, python-mdit-py-plugins,

python-bidict, python-sh, python-cftime, python-can,

python-jsonargparse, python-extension-helpers, python-pyjwt,

python-virtualenv-clone, python-lsp-server, python-pikepdf,

python-tasklogger, python-notebook, python-structlog, binwalk,

python-argcomplete, python-attrs, python-yq, python-stone,

python-identify, python-nodeenv, python-anyio, python-forbiddenfruit,

python-watchgod, python-eliot, python-pem, python-scikit-build,

python-minikanren, nikola, python-verspec, python-mike)

[native-inputs]: Remove python-coverage.

* gnu/packages/simulation.scm (python-dolfin-adjoint)[native-inputs]:

Remove python-coverage.

* gnu/packages/statistics.scm (python-emcee,

python-rpy2)[native-inputs]: Remove python-coverage.

* gnu/packages/syndication.scm (rtv, tuir)[native-inputs]: Remove

python-coverage.

* gnu/packages/terminals.scm (python-halo, python-log-symbols,

python-spinners)[native-inputs]: Remove python-coverage.

* gnu/packages/textutils.scm (python-panflute)[native-inputs]: Remove

python-coverage.

* gnu/packages/version-control.scm (pre-commit)[native-inputs]: Remove

python-coverage.

* gnu/packages/web.scm (python-httpretty)[native-inputs]: Remove

python-coverage.

* gnu/packages/xml.scm (python-xmltodict)[native-inputs]: Remove

python-coverage.

Change-Id: I66b28e624aac94f1a2f6e4fae5cdb444193cd8d9

---

gnu/packages/android.scm | 6 +--

gnu/packages/astronomy.scm | 7 +--

gnu/packages/bioinformatics.scm | 8 ++--

gnu/packages/check.scm | 7 ++-

gnu/packages/cpp.scm | 3 +-

gnu/packages/diffoscope.scm | 1 -

gnu/packages/django.scm | 1 -

gnu/packages/engineering.scm | 3 +-

gnu/packages/geo.scm | 1 -

gnu/packages/gpodder.scm | 3 +-

gnu/packages/graph.scm | 3 +-

gnu/packages/jupyter.scm | 2 +-

gnu/packages/machine-learning.scm | 10 +---

gnu/packages/music.scm | 3 +-

gnu/packages/package-management.scm | 6 +--

gnu/packages/python-check.scm | 5 +-

gnu/packages/python-compression.scm | 12 ++---

gnu/packages/python-web.scm | 20 ++++----

gnu/packages/python-xyz.scm | 72 +++++++++--------------------

gnu/packages/simulation.scm | 1 -

gnu/packages/statistics.scm | 6 +--

gnu/packages/syndication.scm | 4 +-

gnu/packages/terminals.scm | 9 ++--

gnu/packages/textutils.scm | 1 -

gnu/packages/version-control.scm | 1 -

gnu/packages/web.scm | 3 +-

gnu/packages/xml.scm | 2 +-

27 files changed, 63 insertions(+), 137 deletions(-)

Toggle diff (383 lines)diff --git a/gnu/packages/android.scm b/gnu/packages/android.scm
index cbfbd6522f4..ab42f2be980 100644
--- a/gnu/packages/android.scm
+++ b/gnu/packages/android.scm
@@ -1072,11 +1072,9 @@ (define-public python-androguard
          (replace 'check
            ;; Adapted from .travis.yml
            (lambda _
-             (invoke "nosetests" "--with-coverage" "--with-timer"
-                     "--timer-top-n" "50"))))))
+             (invoke "nosetests" "--with-timer" "--timer-top-n" "50"))))))
     (native-inputs
-     (list python-codecov python-coverage python-mock python-nose
-           python-nose-timer))
+     (list python-codecov python-mock python-nose python-nose-timer))
     (propagated-inputs
      (list python-asn1crypto
            python-colorama
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 02d0726b9be..7589ecbb8ae 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1678,7 +1678,6 @@ (define-public python-astropy
     (native-inputs
      (list pkg-config
            python-colorlog
-           python-coverage
            python-cython-3
            python-extension-helpers
            python-h5py
@@ -2606,8 +2605,7 @@ (define-public python-poliastro
             (lambda _
               (setenv "HOME" "/tmp"))))))
     (native-inputs
-     (list python-coverage
-           python-hypothesis
+     (list python-hypothesis
            python-mypy
            python-flit-core
            python-pytest
@@ -4955,8 +4953,7 @@ (define-public python-asdf-astropy
                    (add-before 'check 'set-home-env
                      (lambda _ (setenv "HOME" "/tmp"))))))
     (native-inputs
-     (list python-coverage
-           python-h5py
+     (list python-h5py
            python-pandas
            python-pytest
            python-pytest-astropy
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index aa7f2988191..d8994cf65fa 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2767,8 +2767,7 @@ (define-public python-ega-download-client
     (propagated-inputs (list python-htsget python-psutil python-requests
                              python-tqdm python-urllib3))
     (native-inputs
-     (list python-coverage
-           python-mock
+     (list python-mock
            python-pyfakefs
            python-pytest
            python-responses
@@ -5360,7 +5359,7 @@ (define-public python-scikit-bio
            python-requests
            python-scipy))
     (native-inputs
-     (list python-coverage python-pytest))
+     (list python-pytest))
     (home-page "https://scikit-bio.org")
     (synopsis "Data structures, algorithms and educational resources for bioinformatics")
     (description
@@ -17972,8 +17971,7 @@ (define-public python-cooler
            python-scipy
            python-simplejson))
     (native-inputs
-     (list python-coverage
-           python-hatchling
+     (list python-hatchling
            python-isort
            python-pytest
            python-pytest-cov))
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 880d3cb46f3..b7116b3f0e2 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -1617,8 +1617,7 @@ (define-public python-pytest-randomly
                          "not reordered "
                          "and not test_it_runs_before_stepwise "
                          "and not test_entrypoint_injection"))))))))
-    (native-inputs (list python-coverage
-                         python-factory-boy
+    (native-inputs (list python-factory-boy
                          python-faker
                          python-numpy
                          python-pytest-xdist))
@@ -2715,7 +2714,7 @@ (define-public python-pytest-flakes
              (add-installed-pythonpath inputs outputs)
              (invoke "py.test" "-vv" "-k" "not test_syntax_error"))))))
     (native-inputs
-     (list python-coverage python-pytest python-pytest-pep8))
+     (list python-pytest python-pytest-pep8))
     (propagated-inputs
      (list python-pyflakes))
     (home-page "https://github.com/fschulze/pytest-flakes")
@@ -3568,7 +3567,7 @@ (define-public python-aiounittest
                       #t)))))
     (propagated-inputs (list python-wrapt))
     (native-inputs
-     (list python-coverage python-nose))
+     (list python-nose))
     (home-page
      "https://github.com/kwarunek/aiounittest")
     (synopsis "Test asyncio code more easily")
diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index 8a0bd62d6b6..ba2698056da 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -1189,8 +1189,7 @@ (define-public cpplint
                    (setenv "GUIX_PYTHONPATH"
                            (getenv "TMP_PYTHONPATH")))))))
     (native-inputs
-     (list python-coverage
-           python-pytest
+     (list python-pytest
            python-pytest-cov
            python-pytest-runner
            python-testfixtures))
diff --git a/gnu/packages/diffoscope.scm b/gnu/packages/diffoscope.scm
index fd2146456d6..67567a6b310 100644
--- a/gnu/packages/diffoscope.scm
+++ b/gnu/packages/diffoscope.scm
@@ -269,7 +269,6 @@ (define-public reprotest
      `(("diffoscope" ,diffoscope)
        ("help2man" ,help2man)
        ("libfaketime" ,libfaketime)
-       ("python-coverage" ,python-coverage)
        ("python-docutils" ,python-docutils)
        ("python-magic " ,python-magic)
        ("python-pytest " ,python-pytest)
diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index 4a271eaf0b5..298968d37c6 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -495,7 +495,6 @@ (define-public python-django-haystack
      (list python-django))
     (native-inputs
      (list gdal
-           python-coverage
            python-dateutil
            python-geopy
            python-mock
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index 610fb53087b..2620d5272b6 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -2678,8 +2678,7 @@ (define-public python-scikit-rf
                              python-pyqtgraph
                              python-qtpy
                              python-scipy))
-    (native-inputs (list python-coverage
-                         python-nbval
+    (native-inputs (list python-nbval
                          python-networkx
                          python-pytest
                          python-pytest-cov
diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 69cc7e6ddc5..806120e939d 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -3264,7 +3264,6 @@ (define-public python-geopy
      (list python-geographiclib))
     (native-inputs
      (list python-async-generator
-           python-coverage
            python-isort
            python-pytest
            python-pytest-aiohttp
diff --git a/gnu/packages/gpodder.scm b/gnu/packages/gpodder.scm
index f9102d3a447..0786010471f 100644
--- a/gnu/packages/gpodder.scm
+++ b/gnu/packages/gpodder.scm
@@ -64,7 +64,6 @@ (define-public gpodder
     (build-system python-build-system)
     (native-inputs
      (list intltool
-           python-coverage
            python-minimock
            python-pytest
            python-pytest-cov
@@ -173,7 +172,7 @@ (define-public python-mygpoclient
          "1fi5x6k1mngr0iviw2s4n1f3y2x7pwqy5ivkcrjdprzvwr37f0mh"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-coverage python-minimock python-nose))
+     (list python-minimock python-nose))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index eb8aa17fdfe..f83a23dd0be 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -476,7 +476,6 @@ (define-public python-graphtools
     (native-inputs
      (list util-linux ;for lscpu
            python-anndata
-           python-coverage
            python-coveralls
            python-nose
            python-nose2
@@ -564,7 +563,7 @@ (define-public python-pygsp
                 "")))))))
     (propagated-inputs (list python-numpy python-scikit-image python-scipy))
     (native-inputs
-     (list python-coverage python-coveralls python-pytest))
+     (list python-coveralls python-pytest))
     (home-page "https://github.com/epfl-lts2/pygsp")
     (synopsis "Graph Signal Processing in Python")
     (description "The PyGSP is a Python package to ease signal processing on
diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm
index 9175780b748..6600aab6c6b 100644
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -512,7 +512,7 @@ (define-public python-jupyter-packaging
      (list python-deprecation python-packaging python-setuptools
            python-tomlkit python-wheel))
     (native-inputs
-     (list python-pypa-build python-coverage python-pytest
+     (list python-pypa-build python-pytest
            python-pytest-cov python-pytest-mock))
     (home-page "https://jupyter.org")
     (synopsis "Jupyter packaging utilities")
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index bf09c9ec4c1..19f73d562e7 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1364,7 +1364,6 @@ (define args
      (list cmake
            googletest
            pybind11
-           python-coverage
            python-nbval
            python-pytest
            python-pytest-runner))
@@ -1443,8 +1442,7 @@ (define-public onnx-optimizer
         #~(modify-phases #$phases
             (delete 'relax-requirements)))))
     (native-inputs
-     (list cmake python-pytest python-pytest-runner python-nbval
-           python-coverage))
+     (list cmake python-pytest python-pytest-runner python-nbval))
     (inputs
      (list onnx protobuf pybind11))
     (propagated-inputs
@@ -4487,7 +4485,6 @@ (define-public python-lightning-utilities
     (build-system python-build-system)
     (propagated-inputs (list python-importlib-metadata python-packaging
                              python-typing-extensions))
-    (native-inputs (list python-coverage))
     (home-page "https://github.com/Lightning-AI/utilities")
     (synopsis "PyTorch Lightning sample project")
     (description "This package provides common Python utilities and GitHub
@@ -4701,7 +4698,6 @@ (define-public python-pytorch-lightning
     (native-inputs
      (list python-aiohttp
            python-cloudpickle
-           python-coverage
            python-flaky
            python-pympler
            python-pytest
@@ -4731,7 +4727,6 @@ (define-public python-torchmetrics
            python-typing-extensions))
     (native-inputs
      (list python-cloudpickle
-           python-coverage
            python-fire
            python-mir-eval
            python-mypy
@@ -5132,8 +5127,7 @@ (define-public python-gpytorch
            #~(list "-k" (string-append "not test_deprecated_methods"
                                        " and not test_t_matmul_matrix"))))
     (propagated-inputs (list python-linear-operator python-scikit-learn))
-    (native-inputs (list python-coverage
-                         python-flake8-print
+    (native-inputs (list python-flake8-print
                          python-nbval
                          python-pytest
                          python-setuptools
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index ad026f5d359..fb9ff038de5 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -4072,8 +4072,7 @@ (define-public python-pylast
     ;; https://github.com/pylast/pylast/issues/105
     (arguments '(#:tests? #f))
     (native-inputs
-     (list python-coverage python-pytest python-flaky python-pyyaml
-           python-setuptools-scm))
+     (list python-pytest python-flaky python-pyyaml python-setuptools-scm))
     (home-page "https://github.com/pylast/pylast")
     (synopsis "Python interface to Last.fm and Libre.fm")
     (description "A Python interface to Last.fm and other API-compatible
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index feed16ebcef..4e7e46bf1b3 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -1100,8 +1100,7 @@ (define-public python-anaconda-client
      (list python-clyent python-nbformat python-pyyaml python-requests
            python-setuptools))
     (native-inputs
-     (list python-coverage
-           python-dateutil
+     (list python-dateutil
            python-freezegun
            python-mock
            python-pillow
@@ -1286,8 +1285,7 @@ (define-public conda
            ;; XXX: This is dragged in by libarchive and is needed at runtime.
            zstd))
     (native-inputs
-     (list python-coverage
-           python-flaky
+     (list python-flaky
            python-pytest-timeout
            python-pytest-xprocess
            python-wheel))
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index ca87289a1e1..eb48ae3fadf 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -411,8 +411,7 @@ (define-public python-vcrpy
     (propagated-inputs
      (list python-pyyaml python-six python-wrapt python-yarl))
     (native-inputs
-     (list python-coverage
-           python-flake8
+     (list python-flake8
            python-flask
            python-httplib2
            python-ipaddress
@@ -1145,7 +1144,7 @@ (define-public python-re-assert
            (lambda _
              (invoke "pytest" "-vv"))))))
     (native-inputs
-     (list python-covdefaults python-coverage python-pytest))
+     (list python-covdefaults python-pytest))
     (propagated-inputs
      (list python-regex))
     (home-page "https://github.com/asottile/re-assert")
diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm
index 34a9cd73a20..b2d789c92d0 100644
--- a/gnu/packages/python-compression.scm
+++ b/gnu/packages/python-compression.scm
@@ -109,7 +109,6 @@ (define-public python-multivolumefile
     (build-system pyproject-build-system)
     (native-inputs
      (list python-setuptools-scm
-           python-coverage
            python-coveralls
            python-hypothesis
            python-pyannotate
@@ -247,8 +246,7 @@ (define-public python-pybcj
     (build-system pyproject-build-system)
     (propagated-inputs (list python-importlib-metadata))
     (native-inputs
-     (list python-coverage
-           python-hypothesis
+     (list python-hypothesis
            python-pytest
            python-pytest-cov
            python-setuptools-scm
@@ -281,8 +279,7 @@ (define-public python-bcj-cffi
     (propagated-inputs
      (list python-cffi python-toml python-setuptools-scm))
     (native-inputs
-     (list python-setuptools python-coverage python-pytest
-           python-pytest-cov))
+     (list python-setuptools python-pytest python-pytest-cov))
     (home-page "https://github.com/miurahr/bcj-cffi")
     (synopsis "Branch / Call /Jump CFFI library in Python")
     (

This message was truncated. Download the full message here.

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 07/32] gnu: python-cram: Remove python-coverage native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-8-ngraves@ngraves.fr

* gnu/packages/python-xyz.scm (python-cram):
  [native-inputs]: Remove python-coverage.
  [build-system]: Move to pyproject-build-system.
  [arguments]<#:phases>: Adapt check and patch-source phases
  to coverage removal.

Change-Id: I83fafcdcfbc977f9d3e3411d01d23d9a0e120ec6
---
 gnu/packages/python-xyz.scm | 16 ++++------------
 1 file changed, 4 insertions(+), 12 deletions(-)

Toggle diff (36 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index b849f6fdaa2..f45f375f38e 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -15086,25 +15086,17 @@ (define-public python-cram
                ;; causes the line showing the default shell to break into two
                ;; lines, but the test expects a single line...
                (("env\\['COLUMNS'\\] = '80'")
-                "env['COLUMNS'] = '160'"))
-
-             (substitute* "Makefile"
-               ;; Recent versions of python-coverage have caused the test
-               ;; coverage to decrease (as of version 0.7).  Allow that.
-               (("--fail-under=100")
-                "--fail-under=90"))
-
-             #t))
+                "env['COLUMNS'] = '160'"))))
          (replace 'check
            ;; The test phase uses the built library and executable.
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (add-installed-pythonpath inputs outputs)
              (setenv "PATH" (string-append (getenv "PATH") ":"
                                            (assoc-ref outputs "out") "/bin"))
-             (invoke "make" "test"))))))
-    (build-system python-build-system)
+             (invoke "make" "quicktest"))))))
+    (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage python-setuptools python-wheel which))
+     (list python-setuptools python-wheel which))
     (synopsis "Simple testing framework for command line applications")
     (description
      "Cram is a functional testing framework for command line applications.
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 08/32] gnu: u-boot-tools: Remove python-coverage native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-9-ngraves@ngraves.fr

* gnu/packages/bootloaders.scm (u-boot-tools):

[native-inputs]: Remove python-coverage.

[arguments]<#:phases>: Adapt patch phase.

Change-Id: I94394544079197b4a3f8c53cc0b3d78d1f5dc8be

---

gnu/packages/bootloaders.scm | 17 ++++-------------

1 file changed, 4 insertions(+), 13 deletions(-)

Toggle diff (44 lines)diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm
index 0e7bc66bd75..cf568b2bd6a 100644
--- a/gnu/packages/bootloaders.scm
+++ b/gnu/packages/bootloaders.scm
@@ -802,8 +802,7 @@ (define-public u-boot-tools
     (name "u-boot-tools")
     (native-inputs
      (modify-inputs (package-native-inputs u-boot)
-       (prepend python-coverage
-                python-filelock
+       (prepend python-filelock
                 python-pycryptodomex
                 python-pytest
                 python-pytest-xdist
@@ -820,14 +819,6 @@ (define-public u-boot-tools
                (("/bin/false") (which "false")))
              (substitute* "tools/dtoc/fdt_util.py"
                (("'cc'") "'gcc'"))
-             (substitute* "tools/u_boot_pylib/test_util.py"
-               ;; python3-coverage is simply called coverage in guix.
-               (("python3-coverage") "coverage")
-
-               ;; Don't require 100% coverage since it's brittle and can
-               ;; fail with newer versions of coverage or dependencies.
-               (("raise ValueError\\('Test coverage failure'\\)")
-                "print('Continuing anyway since Guix does not care :O')"))
              (substitute* "test/run"
                ;; Make it easier to find test failures.
                (("#!/bin/bash") "#!/bin/bash -x")
@@ -838,9 +829,9 @@ (define-public u-boot-tools
                ;; FIXME: test_spl fails, needs further investiation
                (("test_ofplatdata or test_handoff or test_spl")
                 "test_ofplatdata or test_handoff")
-               ;; FIXME: code coverage not working
-               (("run_test \"binman code coverage\"")
-                "# run_test \"binman code coverage\"")
+               ;; Disable code coverage tests.
+               (("run_test \"(\\w+) code coverage\"" all)
+                (string-append "# " all))
                ;; This test would require internet access.
                (("\\./tools/buildman/buildman") (which "true")))
              (substitute* "test/py/tests/test_sandbox_exit.py"
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 10/32] gnu: python-openid: Remove python-coverage native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-11-ngraves@ngraves.fr

* gnu/packages/python-web.scm (python-openid):

[native-inputs]: Remove python-coverage.

[arguments]<#:phases>: Rewrite check phase.

Change-Id: Id4ea5abc531f5fd84b60ff22407eb608f1e6ac29

---

gnu/packages/python-web.scm | 17 +++++++++--------

1 file changed, 9 insertions(+), 8 deletions(-)

Toggle diff (33 lines)diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index ffac7968e02..5e585d7b60d 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -2338,17 +2338,18 @@ (define-public python-openid
          "1bxf9a3ny1js422j962zfzl4a9dhj192pvai05whn7j0iy9gdyrk"))))
     (build-system python-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-        (replace 'check
-          (lambda* (#:key tests? #:allow-other-keys)
-            (when tests?
-              (invoke "coverage" "run" "-m"
-                      "unittest" "openid.test.test_suite")))))))
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (if tests?
+                  (invoke "python" "-m" "unittest" "openid.test.test_suite")
+                  (format #t "test suite not run~%")))))))
     (propagated-inputs
      (list python-defusedxml))
     (native-inputs
-     (list python-coverage python-psycopg2 python-django))
+     (list python-psycopg2 python-django))
     (home-page "https://github.com/necaris/python3-openid")
     (synopsis "OpenID support for servers and consumers")
     (description "This library provides OpenID authentication for Python, both
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 09/32] gnu: python-aiosqlite: Remove python-coverage native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-10-ngraves@ngraves.fr

* gnu/packages/databases.scm (python-aiosqlite):

[arguments]<#:phases>: Adapt check phase.

[native-inputs]: Remove python-coverage.

Change-Id: I165d174426022f0603223e3def91ffe280f15899

---

gnu/packages/databases.scm | 5 +----

1 file changed, 1 insertion(+), 4 deletions(-)

Toggle diff (19 lines)diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 96b2c2a0437..f9202639c53 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -3935,11 +3935,8 @@ (define-public python-aiosqlite
                         (replace 'check
                           (lambda* (#:key tests? #:allow-other-keys)
                             (when tests?
-                              (invoke "python" "-m" "coverage" "run" "-m"
-                                      "aiosqlite.tests")
-                              (invoke "python" "-m" "coverage" "report")))))))
+                              (invoke "python" "-m" "aiosqlite.tests")))))))
     (native-inputs (list python-flit-core
-                         python-coverage
                          python-mypy))
     (home-page "https://github.com/jreese/aiosqlite")
     (synopsis
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 11/32] build-system/pyproject: Remove python-coveralls native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-12-ngraves@ngraves.fr

* gnu/packages/geo.scm (python-cartopy)[native-inputs]: Remove

python-coveralls.

* gnu/packages/graph.scm (python-graphtools,

python-pygsp)[native-inputs]: Remove python-coveralls.

* gnu/packages/python-compression.scm (python-multivolumefile,

python-py7zr)[native-inputs]: Remove python-coveralls.

* gnu/packages/python-science.scm (python-trimesh)[native-inputs]:

Remove python-coveralls.

* gnu/packages/python-web.scm (python-flask-combo-jsonapi)

[native-inputs]: Remove python-coveralls.

* gnu/packages/python-xyz.scm (python-affine, python-cftime,

python-ddlparse, python-tasklogger, python-minikanren,

python-arpeggio)[native-inputs]: Remove python-coveralls.

* gnu/packages/syndication.scm (rtv, tuir)[native-inputs]: Remove

python-coveralls.

* gnu/packages/telegram.scm (tgcli)[native-inputs]: Remove

python-coveralls.

Change-Id: I47b3c21f985175876618f1457b242e6841eb6d3b

---

gnu/packages/geo.scm | 3 +--

gnu/packages/graph.scm | 3 +--

gnu/packages/python-compression.scm | 2 --

gnu/packages/python-science.scm | 3 +--

gnu/packages/python-web.scm | 3 +--

gnu/packages/python-xyz.scm | 12 ++++--------

gnu/packages/syndication.scm | 4 +---

gnu/packages/telegram.scm | 3 +--

8 files changed, 10 insertions(+), 23 deletions(-)

Toggle diff (179 lines)diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 806120e939d..be96e6800a3 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -1479,8 +1479,7 @@ (define-public python-cartopy
     (inputs
      (list geos))
     (native-inputs
-     (list python-coveralls
-           python-cython
+     (list python-cython
            python-pytest
            python-pytest-cov
            python-pytest-mpl
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index f83a23dd0be..d66a3676fd2 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -476,7 +476,6 @@ (define-public python-graphtools
     (native-inputs
      (list util-linux ;for lscpu
            python-anndata
-           python-coveralls
            python-nose
            python-nose2
            python-pandas
@@ -563,7 +562,7 @@ (define-public python-pygsp
                 "")))))))
     (propagated-inputs (list python-numpy python-scikit-image python-scipy))
     (native-inputs
-     (list python-coveralls python-pytest))
+     (list python-pytest))
     (home-page "https://github.com/epfl-lts2/pygsp")
     (synopsis "Graph Signal Processing in Python")
     (description "The PyGSP is a Python package to ease signal processing on
diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm
index b2d789c92d0..5faf7b2a3cb 100644
--- a/gnu/packages/python-compression.scm
+++ b/gnu/packages/python-compression.scm
@@ -109,7 +109,6 @@ (define-public python-multivolumefile
     (build-system pyproject-build-system)
     (native-inputs
      (list python-setuptools-scm
-           python-coveralls
            python-hypothesis
            python-pyannotate
            python-pytest
@@ -474,7 +473,6 @@ (define-public python-py7zr
      (list python-setuptools
            python-wheel
            python-setuptools-scm
-           python-coveralls
            python-libarchive-c
            python-py-cpuinfo
            python-pyannotate
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index f82feab0963..9301e82bb60 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -653,8 +653,7 @@ (define-public python-trimesh
                 (("\\$MESH_PRE")
                  "'$MESH_PRE'")))))))
     (native-inputs
-     (list python-coveralls
-           python-pyinstrument
+     (list python-pyinstrument
            python-pytest
            python-pytest-cov))
     (propagated-inputs
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 5e585d7b60d..8265ef41aff 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -8376,8 +8376,7 @@ (define-public python-flask-combo-jsonapi
            python-simplejson
            python-six))
     (native-inputs
-     (list python-coveralls
-           python-pytest
+     (list python-pytest
            python-pytest-runner))
     (home-page "https://github.com/AdCombo/flask-combo-jsonapi")
     (synopsis "Flask extension to quickly create JSON:API 1.0 REST Web APIs")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f45f375f38e..b2a5d234eab 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1019,7 +1019,7 @@ (define-public python-affine
                (base32
                 "1shyvajayyzbkp9dihb4mz835jnkp0kqqbyjfqci6v43da6q2kd2"))))
     (build-system pyproject-build-system)
-    (propagated-inputs (list python-coveralls python-pydocstyle
+    (propagated-inputs (list python-pydocstyle
                              python-pytest python-pytest-cov))
     (native-inputs (list python-flit-core))
     (home-page "https://github.com/rasterio/affine")
@@ -3070,7 +3070,6 @@ (define-public python-cftime
      (list python-numpy))
     (native-inputs
      (list python-check-manifest
-           python-coveralls
            python-cython
            python-pytest-cov
            python-sphinx
@@ -5678,7 +5677,6 @@ (define-public python-ddlparse
     (build-system pyproject-build-system)
     (native-inputs
      (list python-codecov
-           python-coveralls
            python-pytest
            python-pytest-cov
            python-setuptools
@@ -16027,7 +16025,7 @@ (define-public python-tasklogger
         (base32 "1901mibcp6aiyjy8afnybrxnb0dkbdxlbvjqbr3gginlw7dr18xh"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-deprecated))
-    (native-inputs (list python-coveralls python-nose2
+    (native-inputs (list python-nose2
                          python-numpy python-setuptools python-wheel))
     (home-page "https://github.com/scottgigante/tasklogger")
     (synopsis "Extension to the core Python logging library")
@@ -34103,8 +34101,7 @@ (define-public python-minikanren
                         (invoke "python" "-m" "pytest" "-v" "tests/" "kanren/"))
                       #t)))))
     (native-inputs
-     (list python-coveralls
-           python-pydocstyle
+     (list python-pydocstyle
            python-pytest
            python-pytest-cov
            python-pylint
@@ -35943,8 +35940,7 @@ (define-public python-arpeggio
                (base32
                 "0ggdsck1wpladd5bh9drhkmm86bblgk2wagrhn3sdf4v04wkic6n"))))
     (build-system python-build-system)
-    (native-inputs (list python-coveralls
-                         python-mike
+    (native-inputs (list python-mike
                          python-mkdocs
                          python-pytest
                          python-pytest-runner
diff --git a/gnu/packages/syndication.scm b/gnu/packages/syndication.scm
index 397a477972e..d102548bb9c 100644
--- a/gnu/packages/syndication.scm
+++ b/gnu/packages/syndication.scm
@@ -434,7 +434,6 @@ (define-public rtv
            python-requests python-six))
     (native-inputs
      (list ncurses
-           python-coveralls
            python-mock
            python-pytest
            python-vcrpy))
@@ -467,8 +466,7 @@ (define-public tuir
      (list python-beautifulsoup4 python-decorator python-kitchen
            python-requests python-six))
     (native-inputs
-     (list python-coveralls
-           python-mock
+     (list python-mock
            python-pytest
            python-setuptools
            python-vcrpy
diff --git a/gnu/packages/telegram.scm b/gnu/packages/telegram.scm
index 358374a5bb7..c5930180e6a 100644
--- a/gnu/packages/telegram.scm
+++ b/gnu/packages/telegram.scm
@@ -790,8 +790,7 @@ (define-public tgcli
                (add-installed-pythonpath inputs outputs)
                (invoke "pytest" "tests")))))))
     (native-inputs
-     `(("coveralls" ,python-coveralls)
-       ("pytest" ,python-pytest)
+     `(("pytest" ,python-pytest)
        ("pytest-click" ,python-pytest-click)
        ("pytest-cov" ,python-pytest-cov)
        ("mkdocs" ,python-mkdocs)
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 12/32] build-system/pyproject: Remove python-pycodestyle native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-13-ngraves@ngraves.fr

* gnu/packages/python-science.scm (python-scipy):

[native-inputs]: Remove python-pycodestyle.

* gnu/packages/python-xyz.scm (python-jsonargparse, python-lsp-server,

python-orderedmultidict, python-progressbar2, python-stem)

[native-inputs]: Remove python-pycodestyle.

Change-Id: I4518bae13aa0e688bc6e0bb40c07082414e8130f

---

gnu/packages/python-science.scm | 1 -

gnu/packages/python-xyz.scm | 7 ++-----

2 files changed, 2 insertions(+), 6 deletions(-)

Toggle diff (60 lines)diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 9301e82bb60..e20cb56db9c 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -296,7 +296,6 @@ (define-public python-scipy
            python-doit
            python-hypothesis
            python-pooch
-           python-pycodestyle
            python-pydevtool
            python-pytest
            python-pytest-cov
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index b2a5d234eab..0b618024383 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4510,7 +4510,6 @@ (define-public python-jsonargparse
            python-typeshed-client))
     (native-inputs
      (list python-attrs
-           python-pycodestyle
            python-pydantic
            python-pytest
            python-pytest-subtests
@@ -8180,7 +8179,6 @@ (define-public python-lsp-server
            python-jedi
            python-lsp-jsonrpc
            python-pluggy
-           python-pycodestyle
            python-pydocstyle
            python-ujson
            python-whatthepatch
@@ -9925,7 +9923,7 @@ (define-public python-orderedmultidict
     (propagated-inputs
      (list python-six))
     (native-inputs
-     (list python-flake8 python-pycodestyle python-setuptools python-wheel))
+     (list python-flake8 python-setuptools python-wheel))
     (home-page "https://github.com/gruns/orderedmultidict")
     (synopsis "Python Ordered Multivalue Dictionary - omdict")
     (description "This package contains a library for ordered multivalue
@@ -18664,7 +18662,6 @@ (define-public python-progressbar2
      (list python-six python-utils))
     (native-inputs
      (list python-freezegun
-           python-pycodestyle
            python-pytest
            python-pytest-cache
            python-pytest-cov
@@ -22178,7 +22175,7 @@ (define-public python-stem
              (invoke "./run_tests.py" "--unit")
              #t)))))
     (native-inputs
-     (list python-mock python-pycodestyle python-pyflakes))
+     (list python-mock python-pyflakes))
     (home-page "https://stem.torproject.org/")
     (synopsis
      "Python controller library that allows applications to interact with Tor")
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 13/32] gnu: python-versioneer: Remove python-pycodestyle native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-14-ngraves@ngraves.fr

* gnu/packages/python-xyz.scm (python-versioneer):

[arguments]<#:phases>: Remove pycodestyle invocation in check phase.

[native-inputs]: Remove python-pycodestyle.

Change-Id: Ida3fd1e16cb8656be2af666203a82cb9f6d65f75

---

gnu/packages/python-xyz.scm | 6 ++----

1 file changed, 2 insertions(+), 4 deletions(-)

Toggle diff (20 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 0b618024383..3f5cac16d45 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -32668,11 +32668,9 @@ (define-public python-versioneer
                 (invoke "python" "setup.py" "make_long_version_py_git")
                 (invoke "pyflakes" "setup.py" "versioneer.py" "git_version.py")
                 (invoke "python" "test/run_pyflakes_src.py")
-                (invoke "pyflakes" "test")
-                (invoke "pycodestyle" "--max-line-length=88"
-                        "git_version.py" "versioneer.py")))))))
+                (invoke "pyflakes" "test")))))))
     (native-inputs
-     (list git-minimal python-pycodestyle python-pyflakes
+     (list git-minimal python-pyflakes
            python-pypa-build python-setuptools python-wheel))
     (propagated-inputs
      (list python-tomli))
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 14/32] gnu: python-versioneer: Remove python-pyflakes native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-15-ngraves@ngraves.fr

* gnu/packages/python-xyz.scm (python-versioneer):

[arguments]<#:phases>: Remove pyflakes tests.

[native-inputs]: Remove python-pyflakes.

Change-Id: If2b8ab397f2ad25f73c434d28d8382f13d417f94

---

gnu/packages/python-xyz.scm | 8 ++------

1 file changed, 2 insertions(+), 6 deletions(-)

Toggle diff (22 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 3f5cac16d45..b6260c13f65 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -32665,13 +32665,9 @@ (define-public python-versioneer
                 (invoke "python" "test/git/test_git.py" "-v")
                 ;; Some invocation tests require the network.
                 ;;(invoke "python" "test/git/test_invocations.py" "-v")
-                (invoke "python" "setup.py" "make_long_version_py_git")
-                (invoke "pyflakes" "setup.py" "versioneer.py" "git_version.py")
-                (invoke "python" "test/run_pyflakes_src.py")
-                (invoke "pyflakes" "test")))))))
+                (invoke "python" "setup.py" "make_long_version_py_git")))))))
     (native-inputs
-     (list git-minimal python-pyflakes
-           python-pypa-build python-setuptools python-wheel))
+     (list git-minimal python-pypa-build python-setuptools python-wheel))
     (propagated-inputs
      (list python-tomli))
     (home-page "https://github.com/python-versioneer/python-versioneer")
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 15/32] gnu: python-re-assert: Remove python-covdefaults native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-16-ngraves@ngraves.fr

* gnu/packages/python-check.scm (python-re-assert):

[native-inputs]: Remove python-covdefaults.

Change-Id: Ib30c58b69aef7f255e5893ae6f9a33bdf41ac85d

---

gnu/packages/python-check.scm | 2 +-

1 file changed, 1 insertion(+), 1 deletion(-)

Toggle diff (15 lines)diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index eb48ae3fadf..b7ea36cbea7 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -1144,7 +1144,7 @@ (define-public python-re-assert
            (lambda _
              (invoke "pytest" "-vv"))))))
     (native-inputs
-     (list python-covdefaults python-pytest))
+     (list python-pytest))
     (propagated-inputs
      (list python-regex))
     (home-page "https://github.com/asottile/re-assert")
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 16/32] build-system/pyproject: Remove python-codecov native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-17-ngraves@ngraves.fr

* gnu/packages/android.scm (python-androguard)[native-inputs]: Remove

python-codecov.

* gnu/packages/astronomy.scm (python-wiimatch, python-tweakwcs)

[native-inputs]: Remove python-codecov.

* gnu/packages/python-check.scm (python-pytest-trio):

[arguments]<#:test-flags>: Remove --cov flag.

[native-inputs]: Remove python-pytest-cov.

* gnu/packages/python-xyz.scm (python-can,

python-ddlparse)[native-inputs]: Remove python-codecov.

Change-Id: Ic7d3789b3b30d3263f61442bb4e55fd332a4d2f6

---

gnu/packages/android.scm | 2 +-

gnu/packages/astronomy.scm | 8 +++-----

gnu/packages/python-check.scm | 3 +--

gnu/packages/python-xyz.scm | 4 +---

4 files changed, 6 insertions(+), 11 deletions(-)

Toggle diff (84 lines)diff --git a/gnu/packages/android.scm b/gnu/packages/android.scm
index ab42f2be980..7cc1fa4ef05 100644
--- a/gnu/packages/android.scm
+++ b/gnu/packages/android.scm
@@ -1074,7 +1074,7 @@ (define-public python-androguard
            (lambda _
              (invoke "nosetests" "--with-timer" "--timer-top-n" "50"))))))
     (native-inputs
-     (list python-codecov python-mock python-nose python-nose-timer))
+     (list python-mock python-nose python-nose-timer))
     (propagated-inputs
      (list python-asn1crypto
            python-colorama
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 7589ecbb8ae..32fc07d8d86 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4607,8 +4607,7 @@ (define-public python-tweakwcs
            python-stsci-imagestats
            python-stsci-stimage))
     (native-inputs
-     (list python-codecov
-           python-pytest
+     (list python-pytest
            python-pytest-cov
            python-scipy
            python-setuptools
@@ -5274,9 +5273,8 @@ (define-public python-wiimatch
                 "15kq7z30m9i286ncs9xvpaq3dq1p5fa47jz21prq146qwr7j6dm8"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-numpy python-scipy python-setuptools))
-    (native-inputs (list python-codecov python-pytest python-pytest-cov
-                         python-pytest-doctestplus python-setuptools-scm
-                         python-wheel))
+    (native-inputs (list python-pytest python-pytest-cov python-wheel
+                         python-pytest-doctestplus python-setuptools-scm))
     (home-page "https://github.com/spacetelescope/wiimatch")
     (synopsis
      "Optimal matching of weighted N-dimensional image intensity data")
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index b7ea36cbea7..ed3625421ae 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -1194,7 +1194,7 @@ (define-public python-pytest-trio
     (arguments
      (list
       #:test-flags '(list "-W" "error" "-ra" "-v" "--pyargs"
-                          "pytest_trio" "--verbose" "--cov" "-k"
+                          "pytest_trio" "--verbose" "-k"
                           (string-append
                            ;; Needs network
                            "not test_async_yield_fixture_with_nursery"
@@ -1204,7 +1204,6 @@ (define-public python-pytest-trio
     (native-inputs
      (list python-hypothesis
            python-pytest
-           python-pytest-cov
            python-setuptools
            python-wheel))
     (propagated-inputs
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index b6260c13f65..446326afc74 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3572,7 +3572,6 @@ (define-public python-can
            python-setuptools))
     (native-inputs
      (list ;; python-canalystii ; Not packed yet
-           python-codecov
            python-future
            python-hypothesis
            python-mock
@@ -5675,8 +5674,7 @@ (define-public python-ddlparse
         (base32 "1nh8m6rxslwk05daxshxmgk41qfp18yynydba49b13l4m8dnh634"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-codecov
-           python-pytest
+     (list python-pytest
            python-pytest-cov
            python-setuptools
            python-tox
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 17/32] build-system/pyproject: Remove python-tox native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-18-ngraves@ngraves.fr

* gnu/packages/check.scm (python-pytest-regressions)[native-inputs]:

Remove python-tox.

* gnu/packages/diffoscope.scm (reprotest)[native-inputs]: Remove

python-tox.

* gnu/packages/django.scm (python-django-extensions)[native-inputs]:

Remove python-tox.

* gnu/packages/logging.scm (tailon)[native-inputs]: Remove python-tox.

* gnu/packages/messaging.scm (python-harmony)[native-inputs]: Remove

python-tox.

* gnu/packages/python-check.scm (python-vcrpy)[native-inputs]: Remove

python-tox.

* gnu/packages/python-web.scm (python-omnipath,

python-sanic)[native-inputs]: Remove python-tox.

* gnu/packages/python-xyz.scm (python-lunr, python-bidict,

python-jsonargparse, python-ddlparse, python-virtualenv-clone,

python-honcho, python-pdfminer-six, python-shshsh,

python-marshmallow-jsonapi, python-apispec-webframeworks, bpython,

python-loguru, python-ansicolors)[native-inputs]: Remove python-tox.

* gnu/packages/radio.scm (chirp)[native-inputs]: Remove python-tox.

* gnu/packages/terminals.scm (python-halo, python-log-symbols,

python-spinners)[native-inputs]: Remove python-tox.

Change-Id: I39dadb40a73ad1c64ba8b9ef9d1b3fe7d1498b5a

---

gnu/packages/check.scm | 1 -

gnu/packages/diffoscope.scm | 1 -

gnu/packages/django.scm | 1 -

gnu/packages/logging.scm | 2 +-

gnu/packages/messaging.scm | 2 --

gnu/packages/python-check.scm | 1 -

gnu/packages/python-web.scm | 2 --

gnu/packages/python-xyz.scm | 27 ++++++++-------------------

gnu/packages/radio.scm | 3 +--

gnu/packages/terminals.scm | 5 ++---

10 files changed, 12 insertions(+), 33 deletions(-)

Toggle diff (262 lines)diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index b7116b3f0e2..6042f763f15 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -3675,7 +3675,6 @@ (define-public python-pytest-regressions
            python-pandas
            python-pillow
            python-restructuredtext-lint
-           python-tox
            python-setuptools-scm
            python-pytest))
     (home-page "https://github.com/ESSS/pytest-regressions")
diff --git a/gnu/packages/diffoscope.scm b/gnu/packages/diffoscope.scm
index 67567a6b310..bfe4ce99fdc 100644
--- a/gnu/packages/diffoscope.scm
+++ b/gnu/packages/diffoscope.scm
@@ -273,7 +273,6 @@ (define-public reprotest
        ("python-magic " ,python-magic)
        ("python-pytest " ,python-pytest)
        ("python-tlsh" ,python-tlsh)
-       ("python-tox" ,python-tox)
        ("unzip" ,unzip)
        ("xxd" ,xxd)))
     (build-system python-build-system)
diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index 298968d37c6..f5b1e0462bb 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -260,7 +260,6 @@ (define-public python-django-extensions
     (native-inputs
      (list python-mock
            python-factory-boy
-           python-tox
            python-pytest
            python-pytest-cov
            python-pytest-django
diff --git a/gnu/packages/logging.scm b/gnu/packages/logging.scm
index a757c22154f..3c593001d00 100644
--- a/gnu/packages/logging.scm
+++ b/gnu/packages/logging.scm
@@ -134,7 +134,7 @@ (define-public tailon
          "0xkmrivzilsc9wqr8ms67v7399gxnh7pv5687k4rdpdgz4309fwc"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-tox python-wheel))
+     (list python-wheel))
     (inputs
      (list python-pyyaml-5 python-sockjs-tornado python-tornado-http-auth
            python-tornado python-deepmerge))
diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index cb72bfb3e25..35ff807e12c 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -3504,8 +3504,6 @@ (define-public python-harmony
                (base32
                 "1bm9xcnzpnpj6rlhbrnl2abwclzl7ivgh1vb5644y9mnhcs489js"))))
     (build-system python-build-system)
-    (native-inputs
-     (list python-tox))
     (inputs
      (list python-librecaptcha python-keyring python-requests))
     (synopsis "Discord account management")
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index ed3625421ae..8fd3a8924f1 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -419,7 +419,6 @@ (define-public python-vcrpy
            python-pytest
            python-pytest-cov
            python-pytest-httpbin
-           python-tox
            python-urllib3))
     (home-page "https://github.com/kevin1024/vcrpy")
     (synopsis "Automatically mock your HTTP interactions")
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 8265ef41aff..51753adae77 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -2134,7 +2134,6 @@ (define-public python-omnipath
            python-pytest-socket
            python-requests-mock
            python-setuptools-scm
-           python-tox
            python-setuptools
            python-wheel))
     (home-page "https://omnipathdb.org/")
@@ -7640,7 +7639,6 @@ (define-public python-sanic
            python-setuptools
            python-slotscheck
            python-towncrier
-           python-tox
            python-types-ujson
            python-uvicorn
            python-wheel))
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 446326afc74..c83146372bf 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1308,8 +1308,7 @@ (define-public python-lunr
      (list python-hatch-fancy-pypi-readme
            python-hatchling
            python-pytest
-           python-pytest-timeout
-           python-tox))
+           python-pytest-timeout))
     (propagated-inputs
      (list python-importlib-metadata python-typing-extensions))
     (home-page
@@ -2695,8 +2694,7 @@ (define-public python-bidict
            python-sortedcollections
            python-sortedcontainers
            python-sphinx
-           python-sphinx-autodoc-typehints
-           python-tox))
+           python-sphinx-autodoc-typehints))
     (arguments
      `(#:phases (modify-phases %standard-phases
                   (add-after 'unpack 'relax-reqs
@@ -4513,7 +4511,6 @@ (define-public python-jsonargparse
            python-pytest
            python-pytest-subtests
            python-responses
-           python-tox
            python-types-requests
            python-setuptools
            python-wheel))
@@ -5677,7 +5674,6 @@ (define-public python-ddlparse
      (list python-pytest
            python-pytest-cov
            python-setuptools
-           python-tox
            python-wheel))
     (propagated-inputs (list python-pyparsing))
     (home-page "https://github.com/shinichi-takii/ddlparse")
@@ -6219,7 +6215,6 @@ (define-public python-virtualenv-clone
                               (delete-file "tox.ini")
                               (invoke "pytest" "-vvv" "tests")))))))
     (native-inputs (list python-pytest
-                         python-tox
                          python-virtualenv
                          python-wheel
                          python-tomli
@@ -11342,7 +11337,7 @@ (define-public python-honcho
         (base32 "1y0r8dw4pqcq7r4n58ixjdg1iy60lp0gxsd7d2jmhals16ij71rj"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-pytest python-mock python-tox which)) ;for tests
+     (list python-pytest python-mock which)) ;for tests
     (propagated-inputs
      (list python-jinja2))
     (arguments
@@ -20129,7 +20124,7 @@ (define-public python-pdfminer-six
     (propagated-inputs
      (list python-chardet python-cryptography python-sortedcontainers))
     (native-inputs
-     (list python-nose python-tox))
+     (list python-nose))
     (home-page "https://github.com/pdfminer/pdfminer.six")
     (synopsis "PDF parser and analyzer")
     (description "@code{pdfminer.six} is a community maintained fork of
@@ -21276,9 +21271,7 @@ (define-public python-shshsh
          "1wzqyj1a6jj6cyv5ymzy834qm2lyq80yy1kfz0q0zayq9gm1cj7f"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-poetry-core
-           python-pytest
-           python-tox))
+     (list python-poetry-core python-pytest))
     (home-page "https://github.com/zqqqqz2000/shshsh")
     (synopsis "Write Shell commands simply and safely within Python")
     (description "This package provides a way to write Shell commands from
@@ -25144,8 +25137,7 @@ (define-public python-marshmallow-jsonapi
            python-flake8-bugbear
            python-flask
            python-mock
-           python-pytest
-           python-tox))
+           python-pytest))
     (home-page "https://github.com/marshmallow-code/marshmallow-jsonapi")
     (synopsis "JSON:API 1.0 formatting with Marshmallow")
     (description
@@ -25209,7 +25201,6 @@ (define-public python-apispec-webframeworks
            python-pytest
            python-pyyaml
            python-tornado
-           python-tox
            python-wheel))
     (home-page "https://github.com/marshmallow-code/apispec-webframeworks")
     (synopsis "Web framework plugins for apispec")
@@ -26667,7 +26658,7 @@ (define-public bpython
            python-watchdog
            python-jedi))
     (native-inputs
-     (list python-sphinx python-mock python-tox python-wheel))
+     (list python-sphinx python-mock python-wheel))
     (home-page "https://bpython-interpreter.org/")
     (synopsis "Fancy interface to the Python interpreter")
     (description "Bpython is a fancy interface to the Python
@@ -32933,7 +32924,6 @@ (define-public python-loguru
                          python-sphinx
                          python-sphinx-autobuild
                          python-sphinx-rtd-theme
-                         python-tox
                          python-setuptools
                          python-wheel))
     (home-page "https://github.com/Delgan/loguru")
@@ -35290,8 +35280,7 @@ (define-public python-ansicolors
         (base32 "1q3jqglkq4z0f6nkkn8bswcwqg012i2grrc27kabr8286dg4zycr"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-tox
-           python-pytest-cov
+     (list python-pytest-cov
            unzip))
     (home-page "https://github.com/jonathaneunice/colors/")
     (synopsis "ANSI colors for Python")
diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index 56e674a8edc..bfd601564d8 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -3171,8 +3171,7 @@ (define-public chirp
              python-pep8
              python-pytest
              python-pytest-mock
-             python-pyyaml
-             python-tox))
+             python-pyyaml))
       (inputs
        (list python-future
              python-importlib-resources
diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index e424e41a222..d61dc6cb3c7 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -1199,7 +1199,6 @@ (define-public python-halo
     (native-inputs
      (list python-nose
            python-setuptools
-           python-tox
            python-twine
            python-wheel))
     (home-page "https://github.com/manrajgrover/halo")
@@ -1228,7 +1227,7 @@ (define-public python-log-symbols
                      (("(.*)==(.*)$" _ dep ver)
                       (string-append dep ">=" ver))))))))
     (propagated-inputs (list python-colorama))
-    (native-inputs (list python-nose python-setuptools python-tox python-wheel))
+    (native-inputs (list python-nose python-setuptools python-wheel))
     (home-page "https://github.com/manrajgrover/py-log-symbols")
     (synopsis "Python library with graphical symbols for logging on the terminal")
     (description "This package provides a Python library with graphical symbols
@@ -1255,7 +1254,7 @@ (define-public python-spinners
                    (substitute* "requirements-dev.txt"
                      (("(.*)==(.*)$" _ dep ver)
                       (string-append dep ">=" ver))))))))
-    (native-inputs (list python-nose python-setuptools python-tox python-wheel))
+    (native-inputs (list python-nose python-setuptools python-wheel))
     (home-page "https://github.com/manrajgrover/py-spinners")
     (synopsis "Python library with graphical spinners for the terminal")
     (description "Spinners is a Python library that contains graphical spinners
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 18/32] build-system/pyproject: Remove python-mypy native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-19-ngraves@ngraves.fr

* gnu/packages/astronomy.scm (python-poliastro)[native-inputs]: Remove

python-mypy.

* gnu/packages/databases.scm (python-psycopg2)[native-inputs]: Remove

python-mypy.

* gnu/packages/engineering.scm (uranium, cura)[native-inputs]: Remove

python-mypy.

* gnu/packages/graphviz.scm (python-uqbar)[native-inputs]: Remove

python-mypy.

* gnu/packages/machine-learning.scm (python-imbalanced-learn,

python-captum, python-torchmetrics, python-pyro-ppl)[native-inputs]:

Remove python-mypy.

* gnu/packages/python-science.scm (python-scipy)[native-inputs]:

Remove python-mypy.

* gnu/packages/python-web.scm (python-huggingface-hub, python-asgiref,

python-starsessions-for-pytorch-lightning,

python-fastapi)[native-inputs]: Remove python-mypy.

* gnu/packages/python-xyz.scm (python-pyls-black, kalamine,

python-pydantic-cli, python-marshmallow, python-apispec,

python-typeguard, python-trio-typing, python-verspec,

python-catalogue, python-duckdb)[native-inputs]: Remove python-mypy.

* gnu/packages/serialization.scm (python-msgspec)[native-inputs]: Remove

python-mypy.

* gnu/packages/virtualization.scm (python-transient)[native-inputs]:

Remove python-mypy.

Change-Id: I947656750aa0c7732291d826641736aaefab274e

---

gnu/packages/astronomy.scm | 1 -

gnu/packages/databases.scm | 1 -

gnu/packages/engineering.scm | 2 --

gnu/packages/graphviz.scm | 1 -

gnu/packages/machine-learning.scm | 4 ----

gnu/packages/python-science.scm | 1 -

gnu/packages/python-web.scm | 5 +----

gnu/packages/python-xyz.scm | 22 +++++++++-------------

gnu/packages/serialization.scm | 1 -

gnu/packages/virtualization.scm | 3 +--

10 files changed, 11 insertions(+), 30 deletions(-)

Toggle diff (272 lines)diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 32fc07d8d86..77bf41b68b9 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2606,7 +2606,6 @@ (define-public python-poliastro
               (setenv "HOME" "/tmp"))))))
     (native-inputs
      (list python-hypothesis
-           python-mypy
            python-flit-core
            python-pytest
            python-pytest-cov
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index f9202639c53..ad27ec621ca 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -4112,7 +4112,6 @@ (define-public python-psycopg
                (delete 'sanity-check))))
     (native-inputs
      (list python-cython-3
-           python-mypy
            python-psycopg-pool
            python-pytest
            python-pytest-asyncio
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index 2620d5272b6..af79172e53b 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -3923,7 +3923,6 @@ (define-public uranium
            graphviz
            pkg-config
            python-pytest
-           python-mypy
            python-certifi
            python-twisted))
     (propagated-inputs
@@ -4126,7 +4125,6 @@ (define-public cura
     (build-system qt-build-system)
     (native-inputs
      (list python-certifi
-           python-mypy
            python-pytest
            python-requests))
     (inputs
diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm
index b396a97c0bc..ecc2dc2bb4c 100644
--- a/gnu/packages/graphviz.scm
+++ b/gnu/packages/graphviz.scm
@@ -218,7 +218,6 @@ (define-public python-uqbar
     (native-inputs
      (list graphviz
            python-isort
-           python-mypy
            python-pytest
            python-pytest-cov
            python-setuptools
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 19f73d562e7..686cd726e37 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1920,7 +1920,6 @@ (define-public python-imbalanced-learn
     (propagated-inputs (list python-joblib python-numpy python-scikit-learn
                              python-scipy python-threadpoolctl))
     (native-inputs (list python-keras
-                         python-mypy
                          python-pandas
                          python-pytest
                          python-pytest-cov
@@ -4521,7 +4520,6 @@ (define-public python-captum
                          python-flask-compress
                          python-ipython
                          python-ipywidgets
-                         python-mypy
                          python-parameterized
                          python-pytest
                          python-pytest-cov
@@ -4729,7 +4727,6 @@ (define-public python-torchmetrics
      (list python-cloudpickle
            python-fire
            python-mir-eval
-           python-mypy
            python-pandas
            python-psutil
            python-pytest
@@ -5055,7 +5052,6 @@ (define-public python-pyro-ppl
            python-isort
            python-lap
            python-matplotlib
-           python-mypy
            python-nbformat
            python-nbsphinx
            python-nbstripout
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index e20cb56db9c..567fa5d1559 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -273,7 +273,6 @@ (define-public python-scipy
            '())
        (list python-matplotlib
              python-mpmath
-             python-mypy
              python-numpy
              python-numpydoc
              python-pydata-sphinx-theme
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 51753adae77..db815812299 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -196,7 +196,6 @@ (define-public python-huggingface-hub
            python-fastapi
            python-jedi
            python-jinja2
-           python-mypy
            python-numpy
            python-pillow
            python-pydantic
@@ -717,7 +716,7 @@ (define-public python-asgiref
              (when tests?
                (invoke "pytest" "-vv")))))))
     (native-inputs
-     (list python-mypy python-pytest python-pytest-asyncio))
+     (list python-pytest python-pytest-asyncio))
     (propagated-inputs
      (list python-typing-extensions))
     (home-page "https://github.com/django/asgiref/")
@@ -8963,7 +8962,6 @@ (define-public python-starsessions-for-pytorch-lightning
            python-starlette-for-fastapi-0.88))
     (native-inputs
      (list python-httpx
-           python-mypy
            python-poetry-core
            python-pytest
            python-pytest-asyncio
@@ -9009,7 +9007,6 @@ (define-public python-fastapi
                          python-hatchling
                          python-isort
                          python-jose
-                         python-mypy
                          python-passlib
                          python-peewee
                          python-pytest
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index c83146372bf..963747bb06a 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3020,7 +3020,7 @@ (define-public python-pyls-black
     (propagated-inputs
      (list python-black python-lsp-server python-toml python-tomli))
     (native-inputs
-     (list python-isort python-mypy python-pytest
+     (list python-isort python-pytest
            python-pytest-runner python-setuptools python-wheel))
     (home-page "https://github.com/rupert/pyls-black")
     (synopsis "Black plugin for the Python Language Server")
@@ -6785,7 +6785,7 @@ (define-public kalamine
     ;; TODO: Add python-pytest-ruff to native-inputs once it has been
     ;; packaged.
     (native-inputs
-     (list python-hatchling python-mypy python-pytest))
+     (list python-hatchling python-pytest))
     (home-page "https://github.com/OneDeadKey/kalamine")
     (synopsis "Keyboard layout maker")
     (description
@@ -8002,8 +8002,7 @@ (define-public python-pydantic-cli
     (propagated-inputs
      (list python-pydantic))
     (native-inputs
-     (list python-mypy
-           python-pytest))
+     (list python-pytest))
     (home-page "https://github.com/mpkocher/pydantic-cli")
     (synopsis "Turn Pydantic defined data models into CLI tools")
     (description
@@ -23461,6 +23460,8 @@ (define-public python-duckdb
      (list
       #:test-flags
       '(list "--ignore=tests/slow/test_h2oai_arrow.py"
+             ;; stubs require mypy and don't actually check functionality.
+             "--ignore=tests/stubs/test_stubs.py"
              ;; Don't install anything, thank you.
              "-k" "not test_install_non_existent_extension")
       #:phases
@@ -23485,7 +23486,6 @@ (define-public python-duckdb
      (list pybind11
            python-fsspec
            python-google-cloud-storage
-           python-mypy
            python-numpy
            python-pandas
            python-psutil
@@ -25107,7 +25107,6 @@ (define-public python-marshmallow
      (list python-packaging))
     (native-inputs
      (list python-flake8-bugbear
-           python-mypy
            python-pytest
            python-pytz
            python-simplejson
@@ -25169,7 +25168,6 @@ (define-public python-apispec
     (native-inputs
      (list python-flake8-bugbear
            python-marshmallow
-           python-mypy
            python-pytest
            python-pyyaml
            python-setuptools
@@ -26586,8 +26584,7 @@ (define-public python-typeguard
                         ;; XXX: These fail when installed as a library:
                         ;; https://github.com/agronholm/typeguard/issues/176
                         "not usefixtures and not test_cached_module")))))))
-    (native-inputs (list python-mypy
-                         python-pytest
+    (native-inputs (list python-pytest
                          python-setuptools-scm
                          python-typing-extensions))
     (home-page "https://github.com/agronholm/typeguard")
@@ -29057,8 +29054,7 @@ (define-public python-trio-typing
     (native-inputs (list python-attrs python-pytest python-setuptools
                          python-wheel))
     (propagated-inputs
-     (list python-mypy python-mypy-extensions python-trio
-           python-typing-extensions))
+     (list python-mypy-extensions python-trio python-typing-extensions))
     (home-page "https://github.com/python-trio/trio-typing")
     (synopsis "Static type checking support for Trio and related projects")
     (description
@@ -35498,7 +35494,7 @@ (define-public python-verspec
                (base32
                 "07n06wv85fm4vl1ird2mja0823js3x322wgs9gdnq1djjyk4ql64"))))
     (build-system python-build-system)
-    (native-inputs (list python-mypy python-pretend python-pytest))
+    (native-inputs (list python-pretend python-pytest))
     (arguments
      `(#:phases (modify-phases %standard-phases
                   (replace 'check
@@ -36245,7 +36241,7 @@ (define-public python-catalogue
                 "0srdxiil2xys8q1gpc1nvzhvis3a33d8a7amk2i1rlpbg6p36pak"))))
     (build-system python-build-system)
     (native-inputs (list python-pytest))
-    (inputs (list python python-zipp python-typing-extensions python-mypy))
+    (inputs (list python python-zipp python-typing-extensions))
     (home-page "https://github.com/explosion/catalogue")
     (synopsis "Lightweight function registries for your library")
     (description
diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index 728d6404bb9..b39ce176502 100644
--- a/gnu/packages/serialization.scm
+++ b/gnu/packages/serialization.scm
@@ -719,7 +719,6 @@ (define-public python-msgspec
     (native-inputs (list python-attrs
                          python-gcovr
                          python-msgpack
-                         python-mypy
                          python-pytest
                          python-setuptools-scm
                          python-versioneer
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index 85ad5031059..1a75ae0a09e 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -2809,8 +2809,7 @@ (define-public python-transient
            python-requests
            python-toml))
     (native-inputs
-     (list python-mypy
-           python-pyhamcrest
+     (list python-pyhamcrest
            python-setuptools
            python-twine
            python-wheel))
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 19/32] gnu: python-immutables: Remove python-mypy native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-20-ngraves@ngraves.fr

* gnu/packages/python-xyz.scm (python-immutables):
  [origin]: Use git-fetch to use upstream test-data directory.
  [build-system]: Move to pyrpoject-build-system.
  [native-inputs]: Remove python-mypy.
  [arguments]<#:phases>: Add phase to remove python-mypy native-input.

Change-Id: Ie67f634ffecbc3711f354e915b2fab54a1639925
---
 gnu/packages/python-xyz.scm | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

Toggle diff (33 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 963747bb06a..180158e3b64 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -15824,13 +15824,22 @@ (define-public python-immutables
     (version "0.18")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "immutables" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/MagicStack/immutables")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "1x4cinh0xbl6p6p2yfm2s07mxxy3lf0zzai9gqpydk4482bwfdjk"))))
+        (base32 "1xjbkgls0dqrvpg4yzkdzz6aayizxcv5chjc5gyynk196wyshw4m"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list #:phases #~(modify-phases %standard-phases
+                        (add-after 'unpack 'remove-mypy-dependency
+                          (lambda _
+                            (delete-file "tests/test_mypy.py")
+                            (delete-file "tests/conftest.py"))))))
     (native-inputs
-     (list python-mypy python-pytest python-setuptools python-wheel))
+     (list python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/MagicStack/immutables")
     (synopsis "High-performance immutable mapping type for Python")
     (description
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 20/32] build-system/pyproject: Remove python-isort native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-21-ngraves@ngraves.fr

* gnu/packages/bioinformatics.scm (python-cooler,

scvelo)[native-inputs]: Remove python-isort.

* gnu/packages/databases.scm (aerich)[native-inputs]: Remove

python-isort.

* gnu/packages/django.scm (python-django-taggit)[native-inputs]:

Remove python-isort.

* gnu/packages/finance.scm (python-trezor)[native-inputs]: Remove

python-isort.

* gnu/packages/geo.scm (python-geopy)[native-inputs]: Remove

python-isort.

* gnu/packages/gettext.scm (mdpo)[native-inputs]: Remove python-isort.

* gnu/packages/graphviz.scm (python-uqbar)[native-inputs]: Remove

python-isort.

* gnu/packages/machine-learning.scm (python-funsor,

python-pyro-ppl)[native-inputs]: Remove python-isort.

* gnu/packages/mail.scm (python-hyperkitty, postorius)[native-inputs]:

Remove python-isort.

* gnu/packages/protobuf.scm (python-pure-protobuf)[native-inputs]:

Remove python-isort.

* gnu/packages/python-check.scm (python-pytest-toolbox)

[native-inputs]: Remove python-pytest-isort.

* gnu/packages/python-web.scm (python-ovh, python-tinycss2,

python-fastapi)[native-inputs]: Remove python-isort.

* gnu/packages/python-xyz.scm (python-jupytext, python-pyls-black,

python-eventlet, python-textdistance,

python-validators)[native-inputs]: Remove python-isort.

* gnu/packages/sphinx.scm (python-sphinx,

python-sphinx-5)[native-inputs]: Remove python-isort.

* gnu/packages/statistics.scm (python-statsmodels)[native-inputs]:

Remove python-isort.

* gnu/packages/virtualization.scm (python-qemu-qmp)[native-inputs]:

Remove python-isort.

Change-Id: I6dc9a49cdbb10ddd33ea32854f891312d3a29e53

---

gnu/packages/bioinformatics.scm | 2 --

gnu/packages/databases.scm | 1 -

gnu/packages/django.scm | 2 +-

gnu/packages/finance.scm | 1 -

gnu/packages/geo.scm | 1 -

gnu/packages/gettext.scm | 1 -

gnu/packages/graphviz.scm | 1 -

gnu/packages/machine-learning.scm | 4 +---

gnu/packages/mail.scm | 3 +--

gnu/packages/protobuf.scm | 2 +-

gnu/packages/python-check.scm | 1 -

gnu/packages/python-web.scm | 4 +---

gnu/packages/python-xyz.scm | 7 ++-----

gnu/packages/sphinx.scm | 2 --

gnu/packages/statistics.scm | 1 -

gnu/packages/virtualization.scm | 1 -

16 files changed, 7 insertions(+), 27 deletions(-)

Toggle diff (275 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d8994cf65fa..366caec31fd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -17972,7 +17972,6 @@ (define-public python-cooler
            python-simplejson))
     (native-inputs
      (list python-hatchling
-           python-isort
            python-pytest
            python-pytest-cov))
     ;; Almost all the projects of the Mirnylab are moved under Open2C umbrella
@@ -21816,7 +21815,6 @@ (define-public scvelo
     (propagated-inputs
      (list python-anndata
            python-hnswlib
-           python-isort
            python-igraph
            python-loompy
            python-louvain
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index ad27ec621ca..9ec7855109c 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -3251,7 +3251,6 @@ (define-public aerich
      (list poetry
            python-bandit
            python-cryptography
-           python-isort
            python-pydantic
            python-pytest
            python-pytest-asyncio
diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index f5b1e0462bb..48b1b38a97f 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -387,7 +387,7 @@ (define-public python-django-taggit
            (lambda _
              (invoke "python3" "-m" "django" "test" "--settings=tests.settings"))))))
     (propagated-inputs
-     (list python-django python-isort))
+     (list python-django))
     (native-inputs
      (list python-pytest python-mock))
     (home-page
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index 7579001dd1f..6f70d61f700 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -1149,7 +1149,6 @@ (define-public python-trezor
            python-typing-extensions))
     (native-inputs ; Only needed for running the tests
      (list protobuf
-           python-isort
            python-pillow
            python-protobuf
            python-pyqt
diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index be96e6800a3..73644ab2bb4 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -3263,7 +3263,6 @@ (define-public python-geopy
      (list python-geographiclib))
     (native-inputs
      (list python-async-generator
-           python-isort
            python-pytest
            python-pytest-aiohttp
            python-readme-renderer
diff --git a/gnu/packages/gettext.scm b/gnu/packages/gettext.scm
index bbb19bd4cb8..39215a0ccb6 100644
--- a/gnu/packages/gettext.scm
+++ b/gnu/packages/gettext.scm
@@ -216,7 +216,6 @@ (define-public mdpo
      (list python-bump2version
            python-flake8-implicit-str-concat
            python-flake8-print
-           python-isort
            python-pytest
            python-pytest-cov
            python-sphinx
diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm
index ecc2dc2bb4c..f6a58943ecb 100644
--- a/gnu/packages/graphviz.scm
+++ b/gnu/packages/graphviz.scm
@@ -217,7 +217,6 @@ (define-public python-uqbar
 and not test_sphinx_book_text_broken_strict")))
     (native-inputs
      (list graphviz
-           python-isort
            python-pytest
            python-pytest-cov
            python-setuptools
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 686cd726e37..bec948a4bfd 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -175,8 +175,7 @@ (define-public python-funsor
     (propagated-inputs (list python-makefun python-multipledispatch
                              python-numpy python-opt-einsum
                              python-typing-extensions))
-    (native-inputs (list python-isort
-                         python-nbsphinx
+    (native-inputs (list python-nbsphinx
                          python-pandas
                          python-pillow
                          python-pyro-api
@@ -5049,7 +5048,6 @@ (define-public python-pyro-ppl
      (list ninja
            jupyter
            python-graphviz
-           python-isort
            python-lap
            python-matplotlib
            python-nbformat
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 5743558e76b..7c4b6f2cb26 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -3724,7 +3724,6 @@ (define-public python-hyperkitty
     (native-inputs
      (list python-beautifulsoup4
            python-elasticsearch
-           python-isort
            python-lxml
            python-mock
            python-whoosh))
@@ -3763,7 +3762,7 @@ (define-public postorius
      (list python-readme-renderer python-mailmanclient
            python-django python-django-mailman3))
     (native-inputs
-     (list python-beautifulsoup4 python-isort python-mock python-vcrpy))
+     (list python-beautifulsoup4 python-mock python-vcrpy))
     (home-page "https://gitlab.com/mailman/postorius")
     (synopsis "Web user interface for GNU Mailman")
     (description
diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm
index 502ad09a3a6..9c4d56bd384 100644
--- a/gnu/packages/protobuf.scm
+++ b/gnu/packages/protobuf.scm
@@ -469,7 +469,7 @@ (define-public python-pure-protobuf
         (base32 "15dp5pvazd0jx4wzzh79080ah7hkpd3axh40al9vhzs2hf3v90hx"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-pytest python-pytest-cov python-isort))
+     (list python-pytest python-pytest-cov))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 8fd3a8924f1..1087f7b9168 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -1495,7 +1495,6 @@ (define-public python-pytest-toolbox
     (native-inputs
      (list python-pydantic
            python-pytest
-           python-pytest-isort
            python-setuptools
            python-wheel))
     (home-page "https://github.com/samuelcolvin/pytest-toolbox")
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index db815812299..a040eb81448 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -976,8 +976,7 @@ (define-public python-ovh
     (build-system pyproject-build-system)
     (arguments (list #:tests? #f))      ; XXX: tests require networking
     (propagated-inputs (list python-requests))
-    (native-inputs (list python-isort
-                         python-pytest
+    (native-inputs (list python-pytest
                          python-pytest-cov
                          python-setuptools
                          python-sphinx
@@ -9005,7 +9004,6 @@ (define-public python-fastapi
     (native-inputs (list python-databases
                          python-flask
                          python-hatchling
-                         python-isort
                          python-jose
                          python-passlib
                          python-peewee
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 180158e3b64..4538dccd84c 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -478,7 +478,6 @@ (define-public python-jupytext
            python-autopep8
            python-flake8
            python-gitpython
-           python-isort
            python-ipython-genutils
            python-jupyter-server
            python-pyaml
@@ -3020,7 +3019,7 @@ (define-public python-pyls-black
     (propagated-inputs
      (list python-black python-lsp-server python-toml python-tomli))
     (native-inputs
-     (list python-isort python-pytest
+     (list python-pytest
            python-pytest-runner python-setuptools python-wheel))
     (home-page "https://github.com/rupert/pyls-black")
     (synopsis "Black plugin for the Python Language Server")
@@ -4242,7 +4241,6 @@ (define-public python-eventlet
            python-hatchling
            python-hatch-vcs
            python-pytest
-           python-isort
            python-twine))
     (arguments
      (list
@@ -12914,7 +12912,6 @@ (define-public python-textdistance
              #t)))))
     (native-inputs
      (list python-hypothesis
-           python-isort
            python-numpy
            python-pytest
            python-pytest-runner
@@ -25046,7 +25043,7 @@ (define-public python-validators
     (propagated-inputs
      (list python-decorator python-six))
     (native-inputs
-     (list python-isort python-pytest))
+     (list python-pytest))
     (home-page "https://github.com/kvesteri/validators")
     (synopsis "Data validation library")
     (description
diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index ed3fba059d8..26ee93b3aaf 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -93,7 +93,6 @@ (define-public python-sphinx
            python-html5lib
            python-imagesize
            python-importlib-metadata
-           python-isort
            python-jinja2
            python-mypy
            python-packaging
@@ -196,7 +195,6 @@ (define-public python-sphinx-5
            python-html5lib
            python-imagesize
            python-importlib-metadata
-           python-isort
            python-jinja2
            python-mypy
            python-packaging
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index bfc69062587..de4fb6e3aa7 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2446,7 +2446,6 @@ (define-public python-statsmodels
     (native-inputs
      (list python-colorama
            python-cython
-           python-isort
            python-joblib
            python-matplotlib
            python-pytest
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index 1a75ae0a09e..b0b71cceaf5 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -2031,7 +2031,6 @@ (define-public python-qemu-qmp
     (native-inputs
      (list python-avocado-framework
            python-flake8
-           python-isort
            python-pylint
            python-setuptools
            python-setuptools-scm
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 21/32] build-system/pyproject: Remove python-twine native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-22-ngraves@ngraves.fr

* gnu/packages/gettext.scm (mdpo)[native-inputs]: Remove python-twine.

* gnu/packages/machine-learning.scm (python-linear-operator,

python-gpytorch)[native-inputs]: Remove python-twine.

* gnu/packages/python-check.scm (python-testfixtures)[native-inputs]:

Remove python-twine.

* gnu/packages/python-web.scm (python-translation-finder)

[native-inputs]: Remove python-twine.

* gnu/packages/python-xyz.scm (python-cftime, python-eventlet,

python-eliot, python-arpeggio)[native-inputs]: Remove python-twine.

* gnu/packages/terminals.scm (python-halo)[native-inputs]: Remove

python-twine.

* gnu/packages/virtualization.scm (python-transient)[native-inputs]:

Remove python-twine.

Change-Id: Ie9ff17126810dc3e2b17ad42a1f765361401eae7

---

gnu/packages/gettext.scm | 1 -

gnu/packages/machine-learning.scm | 6 ++----

gnu/packages/python-check.scm | 2 +-

gnu/packages/python-web.scm | 2 +-

gnu/packages/python-xyz.scm | 6 +-----

gnu/packages/terminals.scm | 1 -

gnu/packages/virtualization.scm | 1 -

7 files changed, 5 insertions(+), 14 deletions(-)

Toggle diff (126 lines)diff --git a/gnu/packages/gettext.scm b/gnu/packages/gettext.scm
index 39215a0ccb6..b3c807c6774 100644
--- a/gnu/packages/gettext.scm
+++ b/gnu/packages/gettext.scm
@@ -221,7 +221,6 @@ (define-public mdpo
            python-sphinx
            python-sphinx-argparse
            python-sphinx-rtd-theme
-           python-twine
            python-yamllint))
     (propagated-inputs
      (list python-polib python-pymd4c))
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index bec948a4bfd..27749093ee5 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -5094,8 +5094,7 @@ (define-public python-linear-operator
     (native-inputs (list python-flake8-print
                          python-pytest
                          python-setuptools
-                         python-setuptools-scm
-                         python-twine))
+                         python-setuptools-scm))
     (home-page "https://github.com/cornellius-gp/linear_operator/")
     (synopsis "Linear operator implementation")
     (description "LinearOperator is a PyTorch package for abstracting away the
@@ -5124,8 +5123,7 @@ (define-public python-gpytorch
     (native-inputs (list python-flake8-print
                          python-nbval
                          python-pytest
-                         python-setuptools
-                         python-twine))
+                         python-setuptools))
     (home-page "https://gpytorch.ai")
     (synopsis "Implementation of Gaussian Processes in PyTorch")
     (description
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 1087f7b9168..d2618807bc7 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -245,7 +245,7 @@ (define-public python-testfixtures
     (native-inputs
      (list python-pytest python-pytest-cov
            ;;("python-pytest-django" ,python-pytest-django)
-           python-twine python-wheel))
+           python-wheel))
     (synopsis "Tests components for Python")
     (description "Testfixtures is a collection of helpers and mock objects that
 are useful when writing automated tests in Python.")
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index a040eb81448..08be81ad1c5 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -6224,7 +6224,7 @@ (define-public python-translation-finder
      (list python-chardet python-pathlib2 python-ruamel.yaml python-six))
     (native-inputs
      (list python-codecov python-codacy-coverage python-pytest-cov
-           python-pytest-runner python-twine))
+           python-pytest-runner))
     (home-page "https://weblate.org/")
     (synopsis "Translation file finder for Weblate")
     (description "This package provides a function to find translation file in
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 4538dccd84c..9396290401d 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3070,7 +3070,6 @@ (define-public python-cftime
            python-cython
            python-pytest-cov
            python-sphinx
-           python-twine
            python-wheel))
     (home-page "https://unidata.github.io/cftime/")
     (synopsis "Library for time handling")
@@ -4240,8 +4239,7 @@ (define-public python-eventlet
      (list python-black
            python-hatchling
            python-hatch-vcs
-           python-pytest
-           python-twine))
+           python-pytest))
     (arguments
      (list
       #:test-flags
@@ -31351,7 +31349,6 @@ (define-public python-eliot
            python-sphinx
            python-sphinx-rtd-theme
            python-testtools
-           python-twine
            python-twisted))
     (home-page "https://github.com/itamarst/eliot/")
     (synopsis "Eliot: the logging system that tells you why it happened")
@@ -35924,7 +35921,6 @@ (define-public python-arpeggio
                          python-mkdocs
                          python-pytest
                          python-pytest-runner
-                         python-twine
                          python-wheel))
     (home-page "https://github.com/textX/Arpeggio")
     (synopsis "Packrat parser interpreter for Python")
diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index d61dc6cb3c7..d39d1347a2c 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -1199,7 +1199,6 @@ (define-public python-halo
     (native-inputs
      (list python-nose
            python-setuptools
-           python-twine
            python-wheel))
     (home-page "https://github.com/manrajgrover/halo")
     (synopsis "Python library to display graphical spinners in the terminal")
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index b0b71cceaf5..16919ccee51 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -2810,7 +2810,6 @@ (define-public python-transient
     (native-inputs
      (list python-pyhamcrest
            python-setuptools
-           python-twine
            python-wheel))
     (home-page "https://github.com/ALSchwalm/transient")
     (synopsis "QEMU Wrapper written in Python")
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 23/32] gnu: python-tinycss2: Remove python-pytest-cov native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-24-ngraves@ngraves.fr

* gnu/packages/python-web.scm (python-tinycss2):

[arguments]<#:phases>: Add phase remove-unwanted-dependency to

ignore coverage options.

[native-inputs]: Remove python-pytest-cov.

Change-Id: I853fe3371be84be1655db0ee8d1dca8d23c50ef9

---

gnu/packages/python-web.scm | 11 +++++++++--

1 file changed, 9 insertions(+), 2 deletions(-)

Toggle diff (27 lines)diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index c1f803cb131..707bf903bd1 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -5897,11 +5897,18 @@ (define-public python-tinycss2
        (sha256
         (base32 "0zyc48vbmczpqj7f3f0d7zb3bz29fyj50dg0m6bbwbr5i88kq3sq"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'remove-unwanted-dependencies
+            (lambda _
+              (substitute* "pyproject.toml"
+                (("^addopts.*") "")))))))
     (propagated-inputs
      (list python-webencodings))
     (native-inputs
-     (list python-flit python-pytest python-pytest-cov
-           python-pytest-flake8 python-pytest-isort))
+     (list python-flit python-pytest python-pytest-flake8 python-pytest-isort))
     (home-page "https://tinycss2.readthedocs.io/")
     (synopsis "Low-level CSS parser for Python")
     (description "@code{tinycss2} can parse strings, return Python objects
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 24/32] gnu: python-django-contact-form: Remove python-pytest-cov native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-25-ngraves@ngraves.fr

* gnu/packages/django.scm (python-django-contact-form):

[native-inputs]: Remove python-pytest-cov.

[build-system]: Upgrade to pyproject-build-system.

[arguments]<#:phases>: Remove coverage tests for check phase.

Change-Id: I4d0fc406401b7e923f7efa084dbe8ea3753e50fc

---

gnu/packages/django.scm | 7 ++-----

1 file changed, 2 insertions(+), 5 deletions(-)

Toggle diff (25 lines)diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index 3ab2bc139d1..726dd77639e 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -838,16 +838,13 @@ (define-public python-django-contact-form
               (sha256
                (base32
                 "1my9hkrylckp5vfqg9b0kncrdlxjnwxll56sdciqn4v19i4wbq1y"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
          (replace 'check
            (lambda _
-             (invoke "coverage" "run" "--source" "contact_form"
-                     "runtests.py"))))))
-    (native-inputs
-     (list python-coverage))
+             (invoke "python" "runtests.py"))))))
     (propagated-inputs
      (list python-django))
     (home-page "https://github.com/ubernostrum/django-contact-form")
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 25/32] gnu: python-dateutil: Remove python-pytest-cov native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-26-ngraves@ngraves.fr

* gnu/packages/time.scm (python-dateutil):

[native-inputs]: Remove python-pytest-cov.

[arguments]<#:phases>: Add remove-pytest-cov-dep phase.

Change-Id: Id82a147d6e40383ecc2661ac896b65b858c181e0

---

gnu/packages/time.scm | 18 ++++++++++++------

1 file changed, 12 insertions(+), 6 deletions(-)

Toggle diff (33 lines)diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm
index 6e34f80a79d..99cf7ceb6a6 100644
--- a/gnu/packages/time.scm
+++ b/gnu/packages/time.scm
@@ -246,14 +246,20 @@ (define-public python-dateutil
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags '(list  ; avoid freezegun dependency
-                     "--ignore=dateutil/test/test_utils.py"
-                     "--ignore=dateutil/test/test_rrule.py"
-                     ;; XXX: Fails to get timezone from /etc/localtime.
-                     "--ignore=dateutil/test/test_tz.py")))
+      #:test-flags '(list "dateutil/test" "docs"
+                          ;; avoid freezegun dependency
+                          "--ignore=dateutil/test/test_utils.py"
+                          "--ignore=dateutil/test/test_rrule.py"
+                          ;; XXX: Fails to get timezone from /etc/localtime.
+                          "--ignore=dateutil/test/test_tz.py")
+      #:phases #~(modify-phases %standard-phases
+                   (add-after 'unpack 'remove-pytest-cov-dep
+                     (lambda _
+                       (substitute* "dateutil/test/conftest.py"
+                         (("item\\.add_marker\\(pytest\\.mark\\.no_cover\\)")
+                          "pass")))))))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-setuptools
            python-setuptools-scm
            python-wheel))
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 26/32] build-system/pyproject: Remove python-pytest-isort native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-27-ngraves@ngraves.fr

* gnu/packages/dav.scm (radicale):

[native-inputs]: Remove python-pytest-isort.

* gnu/packages/python-web.scm (python-tinycss):

[arguments]<#:test-flags>: Ignore isort tests.

[native-inputs]: Remove python-pytest-isort.

Change-Id: I706e8c310adbeda49b91c6815d299172ce05df22

---

gnu/packages/dav.scm | 1 -

gnu/packages/python-web.scm | 3 +--

2 files changed, 1 insertion(+), 3 deletions(-)

Toggle diff (30 lines)diff --git a/gnu/packages/dav.scm b/gnu/packages/dav.scm
index 0612a72c831..99284220846 100644
--- a/gnu/packages/dav.scm
+++ b/gnu/packages/dav.scm
@@ -59,7 +59,6 @@ (define-public radicale
     (native-inputs
      (list python-pytest
            python-pytest-flake8
-           python-pytest-isort
            python-pytest-runner
            python-waitress))
     (propagated-inputs
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 707bf903bd1..0b794590620 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -5861,10 +5861,9 @@ (define-public python-tinycss
     (build-system pyproject-build-system)
     (arguments
      (list #:test-flags
-           '(list "-k" "not test_speedups")))
+           '(list "-k" "not ISORT and not test_speedups")))
     (native-inputs
      (list python-pytest-flake8
-           python-pytest-isort
            python-pytest-runner
            python-setuptools
            python-wheel))
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 22/32] build-system/pyproject: Remove python-pytest-cov native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-23-ngraves@ngraves.fr

* gnu/packages/astronomy.scm (python-astroml, python-casa-formats-io,

python-cdflib, python-czml3, python-poliastro, python-tweakwcs,

python-wiimatch, python-stcal)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/audio.scm (python-pysox)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/backup.scm (borgmatic)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/bioinformatics.scm (python-biom-format, python-pyfaidx,

python-cooler, python-screed)[native-inputs]: Remove python-pytest-cov.

* gnu/packages/build-tools.scm (meson-python)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/check.scm (python-pytest-nunit, python-pytest-timeout,

python-pytest-enabler, python-pytest-perf,

python-pyhamcrest)[native-inputs]: Remove python-pytest-cov.

* gnu/packages/cpp.scm (cpplint)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/databases.scm (python-alembic)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/dav.scm (vdirsyncer, radicale)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/django.scm (python-django-extensions)[native-inputs]:

Remove python-pytest-cov.

* gnu/packages/embedded.scm (mbed-tools)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/engineering.scm (python-scikit-rf)[native-inputs]:

Remove python-pytest-cov.

* gnu/packages/fontutils.scm (psautohint)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/geo.scm (python-fiona, python-cartopy)[native-inputs]:

Remove python-pytest-cov.

* gnu/packages/gettext.scm (mdpo)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/graphviz.scm (python-graphviz, python-uqbar)

[native-inputs]: Remove python-pytest-cov.

* gnu/packages/jupyter.scm (python-jupyter-packaging,

python-jupyter-server, python-jupyterlite-core, python-ipydatawidgets)

[native-inputs]: Remove python-pytest-cov.

* gnu/packages/machine-learning.scm (python-persim,

python-scikit-learn-extra, python-imbalanced-learn,

python-keras-application, python-keras-preprocessing, python-keras,

python-tensorly, python-pytorch-geometric, python-captum,

python-torchmetrics, python-pyro-ppl)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/mastodon.scm (python-mastodon-py)[native-inputs]:

Remove python-pytest-cov.

* gnu/packages/messaging.scm (zulip-term)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/package-management.scm (python-conda-package-handling):

[native-inputs]: Remove python-pytest-cov.

* gnu/packages/patchutils.scm (pwclient)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/protobuf.scm (python-pure-protobuf)[native-inputs]:

Remove python-pytest-cov.

* gnu/packages/python-check.scm (python-testfixtures, python-vcrpy,

python-pytest-filter-subpackage, python-atpublic, python-sybil,

python-vulture)[native-inputs]: Remove python-pytest-cov.

* gnu/packages/python-compression.scm (python-multivolumefile,

python-pybcj, python-bcj-cffi, python-pyppmd, python-ppmd-cffi,

python-py7zr)[native-inputs]: Remove python-pytest-cov.

* gnu/packages/python-crypto.scm (python-trustme)[native-inputs]:

Remove python-pytest-cov.

(python-certauth)[native-inputs]: Remove python-pytest-cov. Add

python-pytest.

* gnu/packages/python-science.scm (python-scipy, python-trimesh,

python-pandaparallel, python-pyts, python-usetplot, python-pingouin,

python-opt-einsum, python-salib)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/python-web.scm (python-apiron, python-huggingface-hub,

python-portend, python-aiosignal, python-aiostream, python-ovh,

python-cbor2, python-httplib2, python-cheroot, parfive, python-jose,

python-pyscss, python-mechanicalsoup, python-priority, hypercorn,

python-aioftp, python-oauthlib, python-tinycss, python-cssselect2,

python-httpcore, python-wsgiprox, python-venusian, python-cloud-init,

python-siosocks, python-zeep, gunicorn)[native-inputs]: Remove

python-pytest-cov.

(python-warcio)[native-inputs]: Remove python-pytest-cov. Add

python-pytest.

* gnu/packages/python-xyz.scm (python-apprise, python-janus,

python-logbook, python-affine, python-mdit-py-plugins, python-pint,

python-rasterio, python-bidict, python-can, dosage, python-contourpy,

python-portalocker, python-extension-helpers, python-mizani,

python-cligj, python-ddlparse, python-robotframework-pythonlibcore,

python-lsp-server, python-sparse, python-pikepdf, python-imageio,

python-manimpango, python-importlib-resources, python-jaraco-classes,

python-jaraco-collections, python-jaraco-context,

python-jaraco-functools, python-jaraco-test, python-jaraco-text,

python-ipyparallel, python-three-merge, python-seaborn,

python-sentry-sdk, python-sniffio, python-get-version,

python-legacy-api-wrap, python-path, python-pip-run, python-debugpy,

python-notebook, python-ipywidgets, python-qstylizer,

python-cookiecutter, python-pyqtgraph, python-codespell,

python-inflect, python-lazy-loader, python-pymemcache, python-natsort,

python-mwclient, python-flasgger, python-tempora, python-outcome,

python-trio, python-apscheduler, python-iocapture, python-argh,

python-flit, python-watchdog, python-watchgod, python-cmd2,

python-inform, python-qtsass, python-scikit-build, python-minikanren,

python-tablib, nikola, python-ansicolors, python-shtab, python-scooby,

dynaconf, python-pyan3, python-numpydoc, python-loguru,

python-multidict)[native-inputs]: Remove python-pytest-cov.

* gnu/packages/sphinx.scm (python-sphinx-gallery)[native-inputs]:

Remove python-pytest-cov.

* gnu/packages/statistics.scm (python-pymc, python-emcee,

python-rpy2)[native-inputs]: Remove python-pytest-cov.

* gnu/packages/task-management.scm (todoman)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/textutils.scm (python-panflute)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/time.scm (python-arrow, python-tzlocal)[native-inputs]:

Remove python-pytest-cov.

* gnu/packages/vpn.scm (sshuttle)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/web.scm (anonip, python-tibanna)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/wm.scm (qtile)[native-inputs]: Remove

python-pytest-cov. Add python-coverage.

Change-Id: Ia8c96b18a60b6ceb00b345ef06351eae1a68e070

---

gnu/packages/astronomy.scm | 10 +--

gnu/packages/audio.scm | 2 +-

gnu/packages/backup.scm | 2 +-

gnu/packages/bioinformatics.scm | 9 +--

gnu/packages/build-tools.scm | 1 -

gnu/packages/check.scm | 8 +-

gnu/packages/cpp.scm | 1 -

gnu/packages/databases.scm | 2 +-

gnu/packages/dav.scm | 2 -

gnu/packages/django.scm | 1 -

gnu/packages/embedded.scm | 1 -

gnu/packages/engineering.scm | 1 -

gnu/packages/fontutils.scm | 1 -

gnu/packages/geo.scm | 3 +-

gnu/packages/gettext.scm | 1 -

gnu/packages/graphviz.scm | 2 -

gnu/packages/jupyter.scm | 7 +-

gnu/packages/machine-learning.scm | 19 ++---

gnu/packages/mastodon.scm | 1 -

gnu/packages/messaging.scm | 4 +-

gnu/packages/package-management.scm | 1 -

gnu/packages/patchutils.scm | 2 +-

gnu/packages/protobuf.scm | 2 +-

gnu/packages/python-check.scm | 11 +--

gnu/packages/python-compression.scm | 9 +--

gnu/packages/python-crypto.scm | 3 +-

gnu/packages/python-science.scm | 16 ++--

gnu/packages/python-web.scm | 59 ++++----------

gnu/packages/python-xyz.scm | 121 +++++++---------------------

gnu/packages/sphinx.scm | 1 -

gnu/packages/statistics.scm | 6 +-

gnu/packages/task-management.scm | 1 -

gnu/packages/textutils.scm | 1 -

gnu/packages/time.scm | 2 -

gnu/packages/vpn.scm | 1 -

gnu/packages/web.scm | 3 +-

gnu/packages/wm.scm | 1 -

37 files changed, 84 insertions(+), 234 deletions(-)

Toggle diff (294 lines)diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 77bf41b68b9..1510ecab6de 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -601,7 +601,7 @@ (define-public python-astroml
              (setenv "HOME" "/tmp"))))))
     (propagated-inputs (list python-astropy python-matplotlib python-numpy
                              python-scikit-learn python-scipy))
-    (native-inputs (list python-pytest-astropy-header python-pytest-cov
+    (native-inputs (list python-pytest-astropy-header python-pytest
                          python-pytest-doctestplus python-pytest-remotedata
                          python-setuptools python-wheel))
     (home-page "https://astroml.org")
@@ -2041,7 +2041,6 @@ (define-public python-casa-formats-io
               (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-pytest-openfiles
            python-setuptools))
     (propagated-inputs
@@ -2113,7 +2112,6 @@ (define-public python-cdflib
      (list python-astropy
            python-hypothesis
            python-pytest
-           python-pytest-cov
            python-pytest-remotedata
            python-setuptools-scm
            python-xarray
@@ -2230,7 +2228,6 @@ (define-public python-czml3
     (native-inputs
      (list python-astropy
            python-pytest
-           python-pytest-cov
            python-pytest-mypy
            python-setuptools
            python-wheel))
@@ -2608,7 +2605,6 @@ (define-public python-poliastro
      (list python-hypothesis
            python-flit-core
            python-pytest
-           python-pytest-cov
            python-pytest-doctestplus
            python-pytest-mpl
            python-pytest-mypy))
@@ -3388,7 +3384,6 @@ (define-public python-stcal
      (list python-cython-3
            python-psutil
            python-pytest
-           python-pytest-cov
            python-pytest-doctestplus
            python-setuptools-scm
            python-setuptools
@@ -4607,7 +4602,6 @@ (define-public python-tweakwcs
            python-stsci-stimage))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-scipy
            python-setuptools
            python-setuptools-scm))
@@ -5272,7 +5266,7 @@ (define-public python-wiimatch
                 "15kq7z30m9i286ncs9xvpaq3dq1p5fa47jz21prq146qwr7j6dm8"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-numpy python-scipy python-setuptools))
-    (native-inputs (list python-pytest python-pytest-cov python-wheel
+    (native-inputs (list python-pytest python-wheel
                          python-pytest-doctestplus python-setuptools-scm))
     (home-page "https://github.com/spacetelescope/wiimatch")
     (synopsis
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index e6d16211fd4..724430dae36 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -6197,7 +6197,7 @@ (define-public python-pysox
       (propagated-inputs
        (list python-numpy python-typing-extensions))
       (native-inputs
-       (list sox python-pytest python-pytest-cov python-soundfile))
+       (list sox python-pytest python-soundfile))
       (home-page "https://github.com/rabitt/pysox")
       (synopsis "Python wrapper around SoX")
       (description "@code{python-pysox} is a wrapper around the @command{sox}
diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index 663eb2568fe..566ea06338b 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -1357,7 +1357,7 @@ (define-public borgmatic
                   python-jsonschema
                   python-requests
                   python-ruamel.yaml))
-    (native-inputs (list python-flexmock python-pytest python-pytest-cov))
+    (native-inputs (list python-flexmock python-pytest))
     (home-page "https://torsion.org/borgmatic/")
     (synopsis "Simple, configuration-driven backup software")
     (description
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 366caec31fd..84e03a65e1f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3011,7 +3011,7 @@ (define-public python-biom-format
            ;;python-scikit-bio ;mutually recursive dependency
            python-scipy))
     (native-inputs
-     (list python-cython python-pytest python-pytest-cov python-nose))
+     (list python-cython python-pytest python-nose))
     (home-page "https://www.biom-format.org")
     (synopsis "Biological Observation Matrix (BIOM) format utilities")
     (description
@@ -10188,7 +10188,7 @@ (define-public python-screed
         (base32 "0slva743xn93h4sl5zg2as4ricnnj5pp6nw9dm4qclk4i9xglkvk"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-pytest-cov
+     (list python-pytest
            python-pytest-runner
            python-setuptools
            python-wheel))
@@ -17921,7 +17921,6 @@ (define-public python-pyfaidx
            python-mock
            python-numpy
            python-pytest
-           python-pytest-cov
            python-wheel))
     (propagated-inputs (list python-setuptools))
     (home-page "http://mattshirley.com")
@@ -17971,9 +17970,7 @@ (define-public python-cooler
            python-scipy
            python-simplejson))
     (native-inputs
-     (list python-hatchling
-           python-pytest
-           python-pytest-cov))
+     (list python-hatchling python-pytest))
     ;; Almost all the projects of the Mirnylab are moved under Open2C umbrella
     (home-page "https://github.com/open2c/cooler")
     (synopsis "Sparse binary format for genomic interaction matrices")
diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm
index 8fec2f8e2f2..29974dfd8b6 100644
--- a/gnu/packages/build-tools.scm
+++ b/gnu/packages/build-tools.scm
@@ -376,7 +376,6 @@ (define-public meson-python
            python-cython
            python-gitpython
            python-pytest
-           python-pytest-cov
            python-pytest-mock))
     (home-page "https://github.com/mesonbuild/meson-python")
     (synopsis "Meson-based build backend for Python")
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 6042f763f15..6b16ec7711b 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -1530,7 +1530,7 @@ (define-public python-pytest-nunit
     (build-system pyproject-build-system)
     (arguments (list #:tests? #false)) ;no tests included
     (propagated-inputs (list python-attrs python-pytest))
-    (native-inputs (list python-pytest python-pytest-cov python-setuptools
+    (native-inputs (list python-pytest python-setuptools
                          python-wheel python-xmlschema))
     (home-page "https://github.com/pytest-dev/pytest-nunit")
     (synopsis "Pytest plugin for generating NUnit3 test result XML output")
@@ -1796,7 +1796,7 @@ (define-public python-pytest-timeout
                       (add-installed-pythonpath inputs outputs)
                       (invoke "pytest" "-vv"))))))
     (propagated-inputs
-     (list python-pytest python-pytest-cov))
+     (list python-pytest))
     (native-inputs
      (list python-pexpect))
     (home-page "https://github.com/pytest-dev/pytest-timeout")
@@ -2493,7 +2493,6 @@ (define-public python-pytest-enabler
     (native-inputs (list python-pytest
                          python-pytest-black
                          python-pytest-checkdocs
-                         python-pytest-cov
                          python-pytest-flake8
                          python-pytest-mypy
                          python-setuptools
@@ -2667,7 +2666,6 @@ (define-public python-pytest-perf
      (list python-pytest
            python-pytest-black
            python-pytest-checkdocs
-           python-pytest-cov
            python-pytest-enabler
            python-pytest-flake8
            python-pytest-mypy
@@ -3242,7 +3240,7 @@ (define-public python-pyhamcrest
                (base32
                 "05kdzlhs2kvj82pfca13qszszcj6dyrk4b9pbr46x06sq2s4qyls"))))
     (native-inputs                      ;all native inputs are for tests
-     (list python-pytest-cov python-mock python-pytest python-hypothesis))
+     (list python-mock python-pytest python-hypothesis))
     (build-system python-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases
diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index ba2698056da..9c693fb16c3 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -1190,7 +1190,6 @@ (define-public cpplint
                            (getenv "TMP_PYTHONPATH")))))))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-pytest-runner
            python-testfixtures))
     (home-page "https://github.com/cpplint/cpplint")
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 9ec7855109c..8abea7ec385 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -3763,7 +3763,7 @@ (define-public python-alembic
         (base32 "0lxi2g2025lz5k7k5dd5fc1lfijqi2yw6qqyjzp073z6laa8cckw"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-mock python-pytest-cov))
+     (list python-mock python-pytest))
     (propagated-inputs
      (list python-dateutil python-sqlalchemy python-mako python-editor))
     (home-page "https://bitbucket.org/zzzeek/alembic")
diff --git a/gnu/packages/dav.scm b/gnu/packages/dav.scm
index b30b1ef5a59..0612a72c831 100644
--- a/gnu/packages/dav.scm
+++ b/gnu/packages/dav.scm
@@ -58,7 +58,6 @@ (define-public radicale
     (build-system python-build-system)
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-pytest-flake8
            python-pytest-isort
            python-pytest-runner
@@ -146,7 +145,6 @@ (define-public vdirsyncer
            python-trustme
            python-pytest
            python-pytest-asyncio
-           python-pytest-cov
            python-pytest-httpserver
            radicale))
     (inputs
diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index 48b1b38a97f..3ab2bc139d1 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -261,7 +261,6 @@ (define-public python-django-extensions
      (list python-mock
            python-factory-boy
            python-pytest
-           python-pytest-cov
            python-pytest-django
            python-shortuuid))
     (home-page
diff --git a/gnu/packages/embedded.scm b/gnu/packages/embedded.scm
index 1da41415194..542895c8779 100644
--- a/gnu/packages/embedded.scm
+++ b/gnu/packages/embedded.scm
@@ -1798,7 +1798,6 @@ (define-public mbed-tools
                (invoke "pytest" "-vv")))))))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-factory-boy
            python-requests-mock
            python-semver))
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index af79172e53b..eaff8546dc4 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -2681,7 +2681,6 @@ (define-public python-scikit-rf
     (native-inputs (list python-nbval
                          python-networkx
                          python-pytest
-                         python-pytest-cov
                          python-pytest-mock
                          python-pyvisa))
     (home-page "https://scikit-rf.org/")
diff --git a/gnu/packages/fontutils.scm b/gnu/packages/fontutils.scm
index 84eb33d19bf..46b06765f0c 100644
--- a/gnu/packages/fontutils.scm
+++ b/gnu/packages/fontutils.scm
@@ -856,7 +856,6 @@ (define-public psautohint
     (native-inputs
      (list psautohint-font-data
            python-pytest
-           python-pytest-cov
            python-pytest-xdist
            python-setuptools-scm
            python-setuptools
diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 73644ab2bb4..a33de4bd669 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@

This message was truncated. Download the full message here.

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 27/32] build-system/pyproject: Remove python-pytest-black native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-28-ngraves@ngraves.fr

* gnu/packages/check.scm (python-pytest-perf, python-pytest-enabler)

[native-inputs]: Remove python-pytest-black.

* gnu/packages/python-web.scm (python-portend)[native-inputs]:

Remove python-pytest-black.

* gnu/packages/python-xyz.scm (python-importlib-resources,

python-jaraco-classes, python-jaraco-collections,

python-jaraco-context, python-jaraco-functools, python-jaraco-test,

python-jaraco-text, python-legacy-api-wrap, python-path,

python-pip-run, python-inflect, python-isort, python-tempora,

python-sparse)[native-inputs]: Remove python-pytest-black.

Change-Id: Ib46f1c4a3cc33821cda3d7b2172d36158aa812c9

---

gnu/packages/check.scm | 2 --

gnu/packages/python-web.scm | 1 -

gnu/packages/python-xyz.scm | 21 ++++-----------------

3 files changed, 4 insertions(+), 20 deletions(-)

Toggle diff (164 lines)diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 6b16ec7711b..f8ead8df4e4 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2491,7 +2491,6 @@ (define-public python-pytest-enabler
            python-jaraco-functools
            python-toml))
     (native-inputs (list python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-flake8
                          python-pytest-mypy
@@ -2664,7 +2663,6 @@ (define-public python-pytest-perf
                            "and not upstream_url"))))
     (native-inputs
      (list python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-enabler
            python-pytest-flake8
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 0b794590620..98dc11a9e48 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -311,7 +311,6 @@ (define-public python-portend
     (propagated-inputs (list python-tempora))
     ;; TODO: Add python-pytest-ruff to native-inputs once it has been packaged.
     (native-inputs (list python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-enabler
                          python-pytest-mypy
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index c8766db819b..8dd5bf2e9e3 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -8691,7 +8691,6 @@ (define-public python-sparse
      (list python-dask
            python-importlib-metadata
            python-pytest
-           python-pytest-black
            python-setuptools))
     (home-page "https://github.com/pydata/sparse/")
     (synopsis "Library for multi-dimensional sparse arrays")
@@ -11532,7 +11531,6 @@ (define-public python-importlib-resources
                      (string-append (getcwd) "/_custom_build")))))))
     (native-inputs
      (list python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-enabler
            python-pytest-flake8
@@ -11662,7 +11660,6 @@ (define-public python-jaraco-classes
       #:test-flags '(list "-k" "not project")))
     (native-inputs
      (list python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-flake8
            python-pytest-mypy
@@ -11695,7 +11692,6 @@ (define-public python-jaraco-collections
     ;; TODO: Add python-pytest-ruff to native-inputs once it has been
     ;; packaged.
     (native-inputs (list python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-enabler
                          python-pytest-mypy
@@ -11755,7 +11751,6 @@ (define-public python-jaraco-context
            #:test-flags '(list "-k" "not project")))
     (native-inputs
      (list python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-flake8
            python-pytest-mypy
@@ -11789,7 +11784,6 @@ (define-public python-jaraco-functools
     (native-inputs
      (list python-jaraco-classes
            python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-flake8
            python-pytest-mypy
@@ -11849,7 +11843,6 @@ (define-public python-jaraco-test
      (list #:test-flags '(list "-k" "http")))
     (propagated-inputs (list python-jaraco-context python-jaraco-functools))
     (native-inputs (list python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-enabler
                          python-pytest-flake8
@@ -11882,7 +11875,6 @@ (define-public python-jaraco-text
     ;; TODO: Add python-pytest-ruff to native-inputs once it has been
     ;; packaged.
     (native-inputs (list python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-enabler
                          python-pytest-mypy
@@ -16260,8 +16252,7 @@ (define-public python-legacy-api-wrap
          "06qhp0g543dy98vpa41hwdalvdbsjfc3ldk474yr9sd75mhl8jh3"))))
     (build-system python-build-system)
     (propagated-inputs
-     (list python-get-version python-pytest python-pytest-black
-           python-setuptools))
+     (list python-get-version python-pytest python-setuptools))
     (home-page "https://github.com/flying-sheep/legacy-api-wrap")
     (synopsis "Legacy API wrapper")
     (description "This module defines a decorator to wrap legacy APIs.  The
@@ -16521,7 +16512,6 @@ (define-public python-path
                python-packaging
                python-pygments
                python-pytest
-               python-pytest-black
                python-pytest-checkdocs
                python-pytest-enabler
                python-pytest-flake8
@@ -16626,7 +16616,6 @@ (define-public python-pip-run
        (append python-nbformat
                python-pygments
                python-pytest
-               python-pytest-black
                python-pytest-checkdocs
                python-pytest-enabler
                python-pytest-flake8
@@ -21062,7 +21051,6 @@ (define-public python-inflect
     (propagated-inputs (list python-pydantic))
     (native-inputs (list python-pygments
                          python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-enabler
                          python-pytest-flake8
@@ -24092,7 +24080,8 @@ (define-public python-isort
     (arguments
      (list
       #:test-flags '(list "tests/unit/" "-k" "not test_gitignore"
-                          "--ignore=tests/unit/test_deprecated_finders.py")
+                          "--ignore=tests/unit/test_deprecated_finders.py"
+                          "--ignore=tests/unit/profiles/test_black.py")
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'install 'install-example-plugins
@@ -24110,8 +24099,7 @@ (define-public python-isort
                 (apply invoke "pip" "--no-cache-dir" "--no-input"
                        "install"  "--user" "--no-deps" example-whls)))))))
     (native-inputs
-     (list python-black
-           python-colorama
+     (list python-colorama
            python-hypothesmith
            python-libcst-minimal
            python-natsort
@@ -25911,7 +25899,6 @@ (define-public python-tempora
     (native-inputs
      (list python-freezegun
            python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-enabler
            python-pytest-flake8
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 28/32] build-system/pyproject: Remove python-pytest-flake8 native-input.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-29-ngraves@ngraves.fr

* gnu/packages/check.scm (python-pytest-enabler, python-pytest-perf):

[native-inputs]: Remove python-pytest-flake8.

* gnu/packages/dav.scm (radicale)[native-inputs]: Remove

python-pytest-flake8.

* gnu/packages/jupyter.scm (python-nbstripout)[native-inputs]:

Remove python-pytest-flake8.

* gnu/packages/python-check.scm (python-pytest-csv):

[arguments]<#:test-flags>: Ignore flake8 test.

[native-inputs]: Remove python-pytest-flake8.

* gnu/packages/python-web.scm (python-mechanicalsoup,

python-tinycss2)[native-inputs]: Remove python-pytest-flake8.

(python-tinycss):

[arguments]<#:test-flags>: Ignore flake8 tests.

[native-inputs]: Remove python-pytest-flake8.

* gnu/packages/python-xyz.scm (python-importlib-resources,

python-jaraco-classes, python-jaraco-context, python-jaraco-functools,

python-jaraco-packaging, python-jaraco-test, python-path,

python-pip-run, python-inflect, python-tempora, python-cairosvg)

[native-inputs]: Remove python-pytest-flake8.

Change-Id: I60ad04391d1c4b081e3293d50b3ac93c6430c7bf

---

gnu/packages/check.scm | 2 --

gnu/packages/dav.scm | 1 -

gnu/packages/jupyter.scm | 1 -

gnu/packages/python-check.scm | 5 +++--

gnu/packages/python-web.scm | 10 ++++------

gnu/packages/python-xyz.scm | 13 +------------

6 files changed, 8 insertions(+), 24 deletions(-)

Toggle diff (193 lines)diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index f8ead8df4e4..e8f121e9fe9 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2492,7 +2492,6 @@ (define-public python-pytest-enabler
            python-toml))
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
-                         python-pytest-flake8
                          python-pytest-mypy
                          python-setuptools
                          python-setuptools-scm
@@ -2665,7 +2664,6 @@ (define-public python-pytest-perf
      (list python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools
            python-wheel))
diff --git a/gnu/packages/dav.scm b/gnu/packages/dav.scm
index 99284220846..b5a1ba749d8 100644
--- a/gnu/packages/dav.scm
+++ b/gnu/packages/dav.scm
@@ -58,7 +58,6 @@ (define-public radicale
     (build-system python-build-system)
     (native-inputs
      (list python-pytest
-           python-pytest-flake8
            python-pytest-runner
            python-waitress))
     (propagated-inputs
diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm
index 1745cd1f491..18b9c8db522 100644
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -849,7 +849,6 @@ (define-public python-nbstripout
     (native-inputs
      (list python-pytest
            python-pytest-cram
-           python-pytest-flake8
            python-pytest-runner
            python-setuptools
            python-wheel))
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 4643ce91e2e..e9903c89166 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -214,9 +214,10 @@ (define-public python-pytest-csv
         (base32
          "17518f2fn5l98lyk9p8r7215c1whi61imzrh6ahrmcksr8w0zz04"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list #:test-flags '(list "--ignore=tests/test_flake8.py")))
     (native-inputs
-     (list python-pytest-flake8
-           python-pytest-xdist
+     (list python-pytest-xdist
            python-setuptools
            python-tabulate
            python-wheel))
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 98dc11a9e48..93f8394ee98 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1579,8 +1579,7 @@ (define-public python-mechanicalsoup
     (propagated-inputs
      (list python-beautifulsoup4 python-lxml python-requests python-six))
     (native-inputs
-     (list python-pytest-flake8
-           python-pytest-httpbin
+     (list python-pytest-httpbin
            python-pytest-mock
            python-pytest-runner
            python-requests-mock
@@ -5860,10 +5859,9 @@ (define-public python-tinycss
     (build-system pyproject-build-system)
     (arguments
      (list #:test-flags
-           '(list "-k" "not ISORT and not test_speedups")))
+           '(list "-k" "not ISORT and not FLAKE8 and not test_speedups")))
     (native-inputs
-     (list python-pytest-flake8
-           python-pytest-runner
+     (list python-pytest-runner
            python-setuptools
            python-wheel))
     (home-page "https://tinycss.readthedocs.io/")
@@ -5906,7 +5904,7 @@ (define-public python-tinycss2
     (propagated-inputs
      (list python-webencodings))
     (native-inputs
-     (list python-flit python-pytest python-pytest-flake8 python-pytest-isort))
+     (list python-flit python-pytest python-pytest-isort))
     (home-page "https://tinycss2.readthedocs.io/")
     (synopsis "Low-level CSS parser for Python")
     (description "@code{tinycss2} can parse strings, return Python objects
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 8dd5bf2e9e3..88bea23d3b3 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -11533,7 +11533,6 @@ (define-public python-importlib-resources
      (list python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools-57
            python-setuptools-scm))
@@ -11661,7 +11660,6 @@ (define-public python-jaraco-classes
     (native-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools
            python-setuptools-scm
@@ -11752,7 +11750,6 @@ (define-public python-jaraco-context
     (native-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools
            python-setuptools-scm
@@ -11785,7 +11782,6 @@ (define-public python-jaraco-functools
      (list python-jaraco-classes
            python-pytest
            python-pytest-checkdocs
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools
            python-setuptools-scm
@@ -11815,7 +11811,6 @@ (define-public python-jaraco-packaging
     (propagated-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-flake8
            python-rst.linker
            python-setuptools
            python-setuptools-scm
@@ -11845,7 +11840,6 @@ (define-public python-jaraco-test
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-flake8
                          python-pytest-mypy
                          python-setuptools
                          python-wheel))
@@ -16514,7 +16508,6 @@ (define-public python-path
                python-pytest
                python-pytest-checkdocs
                python-pytest-enabler
-               python-pytest-flake8
                python-pytest-mypy)))
     (properties (alist-delete 'hidden?
                               (package-properties
@@ -16618,7 +16611,6 @@ (define-public python-pip-run
                python-pytest
                python-pytest-checkdocs
                python-pytest-enabler
-               python-pytest-flake8
                python-pytest-mypy)))
     (properties (alist-delete 'hidden? (package-properties
                                         python-pip-run-bootstrap)))))
@@ -21053,7 +21045,6 @@ (define-public python-inflect
                          python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-flake8
                          python-pytest-mypy
                          ;; For the version number
                          python-setuptools-scm
@@ -25901,7 +25892,6 @@ (define-public python-tempora
            python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-flake8
            python-pytest-freezegun
            python-pytest-mypy
            python-setuptools-scm
@@ -29574,8 +29564,7 @@ (define-public python-cairosvg
      (list python-cairocffi python-cssselect2 python-defusedxml
            python-pillow python-tinycss2))
     (native-inputs
-     (list python-pytest-flake8
-           python-pytest-isort
+     (list python-pytest-isort
            python-pytest-runner
            python-setuptools
            python-wheel))
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 29/32] build-system/pyproject: Remove python-pytest-mypy inputs.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-30-ngraves@ngraves.fr

* gnu/packages/astronomy.scm (python-czml3, python-poliastro)

[native-inputs]: Remove python-pytest-mypy.

* gnu/packages/check.scm (python-pytest-perf)[native-inputs]: Remove

python-pytest-mypy.

* gnu/packages/python-web.scm (python-portend)[native-inputs]: Remove

python-pytest-mypy.

* gnu/packages/python-xyz.scm (python-importlib-resources,

python-jaraco-classes, python-jaraco-collections,

python-jaraco-context, python-jaraco-functools, python-jaraco-test,

python-jaraco-text, python-path, python-pip-run, python-inflect,

python-tempora, python-loguru, python-portalocker)[native-inputs]: Remove

python-pytest-mypy.

* gnu/packages/sphinx.scm (python-sphinx, python-sphinx-5):

[propagated-inputs]: Remove python-mypy.

Change-Id: Ia36ca82e0327a886f9c5317e9ef4ffc35dc8ac9d

---

gnu/packages/astronomy.scm | 4 +---

gnu/packages/check.scm | 1 -

gnu/packages/python-web.scm | 1 -

gnu/packages/python-xyz.scm | 17 ++---------------

gnu/packages/sphinx.scm | 2 --

5 files changed, 3 insertions(+), 22 deletions(-)

Toggle diff (180 lines)diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 1510ecab6de..a670f3b12d9 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2228,7 +2228,6 @@ (define-public python-czml3
     (native-inputs
      (list python-astropy
            python-pytest
-           python-pytest-mypy
            python-setuptools
            python-wheel))
     (home-page "https://github.com/poliastro/czml3")
@@ -2606,8 +2605,7 @@ (define-public python-poliastro
            python-flit-core
            python-pytest
            python-pytest-doctestplus
-           python-pytest-mpl
-           python-pytest-mypy))
+           python-pytest-mpl))
     (propagated-inputs
      (list python-astropy
            python-astroquery
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index e8f121e9fe9..8eac2b13563 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2664,7 +2664,6 @@ (define-public python-pytest-perf
      (list python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-mypy
            python-setuptools
            python-wheel))
     (propagated-inputs
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 93f8394ee98..f956ad5b0c2 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -313,7 +313,6 @@ (define-public python-portend
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-mypy
                          python-setuptools
                          python-wheel))
     (home-page "https://github.com/jaraco/portend")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 88bea23d3b3..1069f6292f8 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4928,7 +4928,6 @@ (define-public python-portalocker
                 "0lawjm736vs86wlnxc3qqh37l11z0yx81xq3dmrw33m86kaq2bh3"))))
     (build-system pyproject-build-system)
     (native-inputs (list python-pytest
-                         python-pytest-mypy
                          python-pytest-timeout
                          python-redis
                          python-setuptools
@@ -11533,7 +11532,6 @@ (define-public python-importlib-resources
      (list python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-mypy
            python-setuptools-57
            python-setuptools-scm))
     (propagated-inputs
@@ -11660,7 +11658,6 @@ (define-public python-jaraco-classes
     (native-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-mypy
            python-setuptools
            python-setuptools-scm
            python-wheel))
@@ -11692,7 +11689,6 @@ (define-public python-jaraco-collections
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-mypy
                          python-setuptools
                          python-wheel))
     (home-page "https://github.com/jaraco/jaraco.collections")
@@ -11750,7 +11746,6 @@ (define-public python-jaraco-context
     (native-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-mypy
            python-setuptools
            python-setuptools-scm
            python-wheel))
@@ -11782,7 +11777,6 @@ (define-public python-jaraco-functools
      (list python-jaraco-classes
            python-pytest
            python-pytest-checkdocs
-           python-pytest-mypy
            python-setuptools
            python-setuptools-scm
            python-wheel))
@@ -11840,7 +11834,6 @@ (define-public python-jaraco-test
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-mypy
                          python-setuptools
                          python-wheel))
     (home-page "https://github.com/jaraco/jaraco.test")
@@ -11871,7 +11864,6 @@ (define-public python-jaraco-text
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-mypy
                          python-setuptools
                          python-wheel))
     (home-page "https://github.com/jaraco/jaraco.text")
@@ -16507,8 +16499,7 @@ (define-public python-path
                python-pygments
                python-pytest
                python-pytest-checkdocs
-               python-pytest-enabler
-               python-pytest-mypy)))
+               python-pytest-enabler)))
     (properties (alist-delete 'hidden?
                               (package-properties
                                python-path-bootstrap)))))
@@ -16610,8 +16601,7 @@ (define-public python-pip-run
                python-pygments
                python-pytest
                python-pytest-checkdocs
-               python-pytest-enabler
-               python-pytest-mypy)))
+               python-pytest-enabler)))
     (properties (alist-delete 'hidden? (package-properties
                                         python-pip-run-bootstrap)))))
 
@@ -21045,7 +21035,6 @@ (define-public python-inflect
                          python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-mypy
                          ;; For the version number
                          python-setuptools-scm
                          python-setuptools
@@ -25893,7 +25882,6 @@ (define-public python-tempora
            python-pytest-checkdocs
            python-pytest-enabler
            python-pytest-freezegun
-           python-pytest-mypy
            python-setuptools-scm
            python-types-freezegun
            python-types-pytz
@@ -32835,7 +32823,6 @@ (define-public python-loguru
     (propagated-inputs (list python-colorama))
     (native-inputs (list python-colorama
                          python-freezegun
-                         python-mypy
                          python-pre-commit
                          python-pytest
                          python-pytest-mypy-plugins
diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index b977367ee35..3dbcce04b32 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -94,7 +94,6 @@ (define-public python-sphinx
            python-imagesize
            python-importlib-metadata
            python-jinja2
-           python-mypy
            python-packaging
            python-pygments
            python-requests
@@ -196,7 +195,6 @@ (define-public python-sphinx-5
            python-imagesize
            python-importlib-metadata
            python-jinja2
-           python-mypy
            python-packaging
            python-pygments
            python-requests
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 30/32] build-system/pyproject: Stop hiding options.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-31-ngraves@ngraves.fr

* gnu/packages/pdf.scm (python-pydyf, weasyprint)[arguments]
<#:test-flags>: Remove arguments hiding coverage options.

* gnu/packages/python-crypto.scm (python-keyring)
[arguments]<#:test-flags>: Remove arguments hiding coverage options.

* gnu/packages/python-web.scm (python-asgi-csrf, python-asgi-lifespan,
python-openapi-schema-validator, python-openapi-spec-validator,
python-openapi-core)[arguments]<#:test-flags>: Remove arguments hiding
coverage options.
(python-openapi-schema-validator, python-openapi-spec-validator)
[arguments]<#:phases>: Remove 'remove-coverage-pytest-options phase.
(python-cssselect2, python-tinycss2)[arguments]: Remove uneeded field.
(python-jsonpickle)[arguments]<#:test-flags>: Remove uneeded
test-flags.

* gnu/packages/python-xyz.scm (python-cattrs)
[arguments]<#:phases>: Remove arguments hiding coverage options.

Change-Id: Ibe08ecfebf8a24259c8658918d98fe9e5a8925b7
---
 gnu/packages/pdf.scm           |  6 +---
 gnu/packages/python-crypto.scm |  1 -
 gnu/packages/python-web.scm    | 51 ++++------------------------------
 gnu/packages/python-xyz.scm    |  4 +--
 4 files changed, 7 insertions(+), 55 deletions(-)

Toggle diff (164 lines)diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm
index 4e260d614de..16d4d9336e3 100644
--- a/gnu/packages/pdf.scm
+++ b/gnu/packages/pdf.scm
@@ -816,9 +816,6 @@ (define-public python-pydyf
        (sha256
         (base32 "18q43g5d9455msipcgd5fvnh8m4a2rz189slzfg80yycjw66rshs"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:test-flags #~'("-c" "/dev/null")))
     (propagated-inputs (list python-pillow))
     (native-inputs
      (list ghostscript
@@ -1635,8 +1632,7 @@ (define-public weasyprint
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags #~(list "-c" "/dev/null"
-                           "-n" (number->string (parallel-job-count)))
+      #:test-flags #~(list "-n" (number->string (parallel-job-count)))
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-library-paths
diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm
index 6965a330624..6139856a906 100644
--- a/gnu/packages/python-crypto.scm
+++ b/gnu/packages/python-crypto.scm
@@ -288,7 +288,6 @@ (define-public python-keyring
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags '(list "-c" "/dev/null") ;avoid extra test dependencies
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'check 'workaround-test-failure
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index f956ad5b0c2..ef786e59308 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -738,10 +738,7 @@ (define-public python-asgi-csrf
     (build-system pyproject-build-system)
     (arguments
      (list #:test-flags
-           ;; Provide a null config to avoid the extraneous dependency on
-           ;; python-pytest-coverage.
-           #~(list "-c" "/dev/null"
-                   ;; Disable two failing tests (see:
+           #~(list ;; Disable two failing tests (see:
                    ;; https://github.com/simonw/asgi-csrf/issues/24).
                    "-k" (string-append
                          "not (test_multipart "
@@ -780,8 +777,7 @@ (define-public python-asgi-lifespan
     (arguments
      (list
       #:test-flags
-      '(list "-c" "/dev/null"           ;ignore coverage-related options
-             "-k"
+      '(list "-k"
              (string-append
               ;; XXX: Some tests fail because of a 'lifespan.shutdown.failed'
               ;; extra event, perhaps because our version of trio is older.
@@ -1529,10 +1525,7 @@ (define-public python-jsonpickle
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags
-      ;; Prevent running the flake8 and black pytest plugins, which only tests
-      ;; style and frequently causes harmless failures.
-      '(list "-o" "addopts=''" "tests")
+      #:test-flags '(list "tests")
       #:phases
       '(modify-phases %standard-phases
          (add-before 'check 'pre-check
@@ -2175,13 +2168,7 @@ (define-public python-openapi-schema-validator
      (list
       #:test-flags
       ;; This one returns 5 instead of 4 elements
-      '(list "-k" "not test_array_prefixitems_invalid")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'remove-coverage-pytest-options
-            (lambda _
-              (substitute* "pyproject.toml"
-                (("^--cov.*") "")))))))
+      '(list "-k" "not test_array_prefixitems_invalid")))
     (native-inputs (list python-poetry-core python-pytest))
     (propagated-inputs
      (list python-isodate
@@ -2219,13 +2206,7 @@ (define-public python-openapi-spec-validator
      (list
       ;; These tests attempt to fetch resources from the Internet
       #:test-flags '(list "--ignore-glob=tests/integration/validation/**"
-                          "-k" "not example")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'remove-coverage-pytest-options
-            (lambda _
-              (substitute* "pyproject.toml"
-                (("^--cov.*") "")))))))
+                          "-k" "not example")))
     (native-inputs
      (list python-poetry-core
            python-pytest))
@@ -2264,9 +2245,6 @@ (define-public python-openapi-core
      (list
       #:test-flags
       '(list "tests/unit"
-             ;; Ignore Pytest configuration in setup.cfg that adds
-             ;; unwanted flake8 and coverage options.
-             "-c" "/dev/null"
              "-k" (string-append
                    ;; Type mismatches
                    "not TestFlaskOpenAPIRequest"
@@ -5892,14 +5870,6 @@ (define-public python-tinycss2
        (sha256
         (base32 "0zyc48vbmczpqj7f3f0d7zb3bz29fyj50dg0m6bbwbr5i88kq3sq"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'check 'remove-unwanted-dependencies
-            (lambda _
-              (substitute* "pyproject.toml"
-                (("^addopts.*") "")))))))
     (propagated-inputs
      (list python-webencodings))
     (native-inputs
@@ -5926,17 +5896,6 @@ (define-public python-cssselect2
        (sha256
         (base32 "1j2fcr217rsvkipsg6zjq03rl64rxnvb5hqqpx0dv58fhspvkywk"))))
     (build-system pyproject-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'disable-linters
-           ;; Their check fails; none of our business.
-           (lambda _
-             (substitute* '("setup.py" "pyproject.toml")
-               (("'pytest-flake8',") "")
-               (("'pytest-isort',") "")
-               (("--flake8") "")
-               (("--isort") "")))))))
     (propagated-inputs
      (list python-tinycss2))
     (native-inputs
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 1069f6292f8..7bcd4c299c3 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21318,9 +21318,7 @@ (define-public python-cattrs
               (substitute* "pyproject.toml"
                 ;; Fix version string
                 (("dynamic = \\[\"version\"\\]")
-                 (string-append "version = \"" #$version "\""))
-                ;; Just run pytest with no frills
-                (("addopts = \"-l.*") "")))))))
+                 (string-append "version = \"" #$version "\""))))))))
     (native-inputs
      (list python-hatchling
            python-hatch-vcs
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 31/32] gnu: python-linear-operator: Remove python-flake8-print native-input

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-32-ngraves@ngraves.fr

* gnu/packages/machine-learning.scm (python-linear-operator):

[native-inputs]: Remove pytest-flake8-print.

Change-Id: Iba2670b47e479c20a3f4ae1c703ad9fe815e3764

---

gnu/packages/machine-learning.scm | 3 +--

1 file changed, 1 insertion(+), 2 deletions(-)

Toggle diff (16 lines)diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index a3c598ba1c8..cc33a3e9762 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -5082,8 +5082,7 @@ (define-public python-linear-operator
                              python-pytorch
                              python-scipy
                              python-typeguard))
-    (native-inputs (list python-flake8-print
-                         python-pytest
+    (native-inputs (list python-pytest
                          python-setuptools
                          python-setuptools-scm))
     (home-page "https://github.com/cornellius-gp/linear_operator/")
-- 
2.41.0

Nicolas Graves wrote 9 months ago

[PATCH python-team v2 32/32] gnu: abjad-ext-ipython: Remove uneeded inputs.

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:20240601153854.30805-33-ngraves@ngraves.fr

* gnu/packages/music.scm (abjad-ext-ipython):
  [arguments]<#:phases>: Remove unwanted dev dependencies in phase
  losen-requirements.
  [native-inputs]: Remove python-black, python-flake8, python-isort,
  python-mypy, python-pytest-cov, python-iniconfig,
  python-pytest-helpers-namespace.
  [propagated-inputs]: Remove python-sphinx-autodoc-typehints.

Change-Id: Id337da7731bc04d69831096b31f52e0e4c6a13c0
---
 gnu/packages/music.scm | 16 +++++-----------
 1 file changed, 5 insertions(+), 11 deletions(-)

Toggle diff (37 lines)diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index fb9ff038de5..b87e6390f90 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -1790,7 +1790,9 @@ (define-public abjad-ext-ipython
              (substitute* "setup.py"
                ;; Don't require a specific version of abjad.
                (("abjad==")
-                "abjad>="))))
+                "abjad>=")
+               ;; XXX: Remove unwanted dev dependencies.
+               (("\"(black|flake8|isort|mypy|pytest)[^,]*,") ""))))
          (replace 'check
            (lambda* (#:key tests? inputs outputs #:allow-other-keys)
              (when tests?
@@ -1800,17 +1802,9 @@ (define-public abjad-ext-ipython
                (invoke "jupyter" "nbconvert" "--to=html"
                "--ExecutePreprocessor.enabled=True" "tests/test.ipynb")))))))
     (native-inputs
-     (list lilypond
-           python-black
-           python-flake8
-           python-iniconfig
-           python-isort
-           python-mypy
-           python-pytest
-           python-pytest-cov
-           python-pytest-helpers-namespace))
+     (list lilypond python-pytest))
     (propagated-inputs
-     (list abjad jupyter python-sphinx-autodoc-typehints))
+     (list abjad jupyter))
     (home-page "https://abjad.github.io")
     (synopsis "Abjad IPython Extension")
     (description
-- 
2.41.0

Nicolas Graves wrote 9 months ago

control message for bug #70858

Recipients:(address . control@debbugs.gnu.org)

Message-ID:871q5gbrgg.fsf@ngraves.fr

block 70858 by 69980

quit

Best regards,

Nicolas Graves

Nicolas Graves wrote 9 months ago

Re: [bug#70858] [PATCH python-team v2 00/32] Remove unwanted native-inputs.

Recipients:

Message-ID:87jzj3nxfd.fsf@ngraves.fr

Hi python-team,

Just to let you know, ci.guix seems to have proceeded the current

python-team mostly. There are a lot of failures due to urllib's

update, I can try and update those, though I would also love a review of

those patches now that they are done.

It can actually be split in two series, one about python-pytest-*

patches, the other about other removed native-inputs. Tell me if that's

more convenient.

Nicolas

On 2024-06-01 17:36, Nicolas Graves via Guix-patches via wrote:

Toggle quote (101 lines)> Simply rebased the v1, ontop of 69980.
>
> Nicolas Graves (32):
>   guix: import: pypi: Ignore pypi-ignored-inputs.
>   build-system/pyproject: Ignore unwanted pytest flags.
>   build-system/pyproject: Remove python-black input.
>   build-system/pyproject: Remove python-pylint native-input.
>   build-system/pyproject: Remove python-flake8 inputs.
>   build-system/pyproject: Remove python-coverage input.
>   gnu: python-cram: Remove python-coverage native-input.
>   gnu: u-boot-tools: Remove python-coverage native-input.
>   gnu: python-aiosqlite: Remove python-coverage native-input.
>   gnu: python-openid: Remove python-coverage native-input.
>   build-system/pyproject: Remove python-coveralls native-input.
>   build-system/pyproject: Remove python-pycodestyle native-input.
>   gnu: python-versioneer: Remove python-pycodestyle native-input.
>   gnu: python-versioneer: Remove python-pyflakes native-input.
>   gnu: python-re-assert: Remove python-covdefaults native-input.
>   build-system/pyproject: Remove python-codecov native-input.
>   build-system/pyproject: Remove python-tox native-input.
>   build-system/pyproject: Remove python-mypy native-input.
>   gnu: python-immutables: Remove python-mypy native-input.
>   build-system/pyproject: Remove python-isort native-input.
>   build-system/pyproject: Remove python-twine native-input.
>   build-system/pyproject: Remove python-pytest-cov native-input.
>   gnu: python-tinycss2: Remove python-pytest-cov native-input.
>   gnu: python-django-contact-form: Remove python-pytest-cov
>     native-input.
>   gnu: python-dateutil: Remove python-pytest-cov native-input.
>   build-system/pyproject: Remove python-pytest-isort native-input.
>   build-system/pyproject: Remove python-pytest-black native-input.
>   build-system/pyproject: Remove python-pytest-flake8 native-input.
>   build-system/pyproject: Remove python-pytest-mypy inputs.
>   build-system/pyproject: Stop hiding options.
>   gnu: python-linear-operator: Remove python-flake8-print native-input
>   gnu: abjad-ext-ipython: Remove uneeded inputs.
>
>  gnu/packages/android.scm              |   6 +-
>  gnu/packages/astronomy.scm            |  31 +-
>  gnu/packages/audio.scm                |   2 +-
>  gnu/packages/backup.scm               |   2 +-
>  gnu/packages/bioinformatics.scm       |  31 +-
>  gnu/packages/bootloaders.scm          |  17 +-
>  gnu/packages/build-tools.scm          |   1 -
>  gnu/packages/check.scm                |  21 +-
>  gnu/packages/cpp.scm                  |   4 +-
>  gnu/packages/databases.scm            |  17 +-
>  gnu/packages/dav.scm                  |   4 -
>  gnu/packages/diffoscope.scm           |   2 -
>  gnu/packages/django.scm               |  12 +-
>  gnu/packages/ebook.scm                |   1 -
>  gnu/packages/embedded.scm             |   1 -
>  gnu/packages/engineering.scm          |   7 +-
>  gnu/packages/finance.scm              |   6 +-
>  gnu/packages/fontutils.scm            |   1 -
>  gnu/packages/geo.scm                  |   9 +-
>  gnu/packages/gettext.scm              |   4 -
>  gnu/packages/gpodder.scm              |   3 +-
>  gnu/packages/graph.scm                |   6 +-
>  gnu/packages/graphviz.scm             |   5 -
>  gnu/packages/jupyter.scm              |   8 +-
>  gnu/packages/logging.scm              |   2 +-
>  gnu/packages/machine-learning.scm     |  64 +---
>  gnu/packages/mail.scm                 |   3 +-
>  gnu/packages/mastodon.scm             |   1 -
>  gnu/packages/messaging.scm            |   6 +-
>  gnu/packages/music.scm                |  23 +-
>  gnu/packages/package-management.scm   |   7 +-
>  gnu/packages/patchutils.scm           |   2 +-
>  gnu/packages/pdf.scm                  |   6 +-
>  gnu/packages/potassco.scm             |   3 +-
>  gnu/packages/protobuf.scm             |   4 +-
>  gnu/packages/python-check.scm         |  29 +-
>  gnu/packages/python-compression.scm   |  21 +-
>  gnu/packages/python-crypto.scm        |   4 +-
>  gnu/packages/python-science.scm       |  21 +-
>  gnu/packages/python-web.scm           | 175 +++--------
>  gnu/packages/python-xyz.scm           | 414 +++++++-------------------
>  gnu/packages/radio.scm                |   3 +-
>  gnu/packages/serialization.scm        |   1 -
>  gnu/packages/simulation.scm           |   2 -
>  gnu/packages/sphinx.scm               |   7 -
>  gnu/packages/statistics.scm           |  14 +-
>  gnu/packages/syndication.scm          |   8 +-
>  gnu/packages/task-management.scm      |   1 -
>  gnu/packages/telegram.scm             |   3 +-
>  gnu/packages/terminals.scm            |  12 +-
>  gnu/packages/textutils.scm            |   3 -
>  gnu/packages/time.scm                 |  20 +-
>  gnu/packages/version-control.scm      |   1 -
>  gnu/packages/virtualization.scm       |   6 +-
>  gnu/packages/vpn.scm                  |   2 -
>  gnu/packages/web.scm                  |   6 +-
>  gnu/packages/wm.scm                   |   2 -
>  gnu/packages/xml.scm                  |   2 +-
>  guix/build/pyproject-build-system.scm |  99 +++++-
>  guix/import/pypi.scm                  |  21 +-
>  guix/lint.scm                         |  12 +-
>  tests/pypi.scm                        |   3 +-
>  62 files changed, 405 insertions(+), 809 deletions(-)

-- 
Best regards,
Nicolas Graves

Sharlatan Hellseher wrote 1 months ago

[PATCH 00/32] python-team: Remove native inputs

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:87h65hpd04.fsf@gmail.com

Hi Nicolas,

Thank you for your work, I would like to apply it on the current

python-team branch which is about to be merged by the end of Feb.

May you check if the series is still applicable as #69980 was resolved.

Oleg

Nicolas Graves wrote 1 months ago

Recipients:

Message-ID:87y0ysclzu.fsf@ngraves.fr

On 2025-01-29 20:43, Sharlatan Hellseher wrote:

Toggle quote (8 lines)

> Hi Nicolas,

> Thank you for your work, I would like to apply it on the current

> python-team branch which is about to be merged by the end of Feb.

> May you check if the series is still applicable as #69980 was

> resolved.

Probably not applicable anymore, I'll rebase that.

Best regards,

Nicolas Graves

Nicolas Graves wrote 1 months ago

[PATCH v3 00/28] python-team: Remove native-inputs

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-1-ngraves@ngraves.fr

This is a rebase of the v2.
To note : I've rebased and updated patch commit messages. BUT:
* I've not rebuild anything locally, untested in this sense, but CI
  will do the work here.
* I've not updated in the sense of searching to remove unwanted
  native-inputs in packages added since v2.  More removing is needed
  if we want this patch series to be exhaustive.

From what was rejected and untested :
* maybe datasette will require an additional "--ignore=tests/test_black.py" flag.

From what was injected and untested :
* maybe the injected arguments in python-immutables are now unnecessary or incorrect

Nicolas Graves (28):
  guix: import: pypi: Ignore pypi-ignored-inputs.
  build-system/pyproject: Ignore unwanted pytest flags.
  build-system/pyproject: Remove python-black input.
  build-system/pyproject: Remove python-pylint native-input.
  build-system/pyproject: Remove python-flake8 inputs.
  build-system/pyproject: Remove python-coverage input.
  gnu: python-cram: Remove python-coverage native-input.
  gnu: u-boot-tools: Remove python-coverage native-input.
  gnu: python-aiosqlite: Remove python-coverage native-input.
  gnu: python-openid: Remove python-coverage native-input.
  build-system/pyproject: Remove python-coveralls native-input.
  build-system/pyproject: Remove python-pycodestyle native-input.
  gnu: python-re-assert: Remove python-covdefaults native-input.
  build-system/pyproject: Remove python-codecov native-input.
  build-system/pyproject: Remove python-tox native-input.
  build-system/pyproject: Remove python-mypy native-input.
  gnu: python-immutables: Remove python-mypy native-input.
  build-system/pyproject: Remove python-isort native-input.
  build-system/pyproject: Remove python-twine native-input.
  build-system/pyproject: Remove python-pytest-cov native-input.
  gnu: python-django-contact-form: Remove python-pytest-cov
    native-input.
  gnu: python-dateutil: Remove python-pytest-cov native-input.
  build-system/pyproject: Remove python-pytest-isort native-input.
  build-system/pyproject: Remove python-pytest-black native-input.
  build-system/pyproject: Remove python-pytest-flake8 native-input.
  build-system/pyproject: Remove python-pytest-mypy inputs.
  build-system/pyproject: Stop hiding options.
  gnu: python-linear-operator: Remove python-flake8-print native-input

 gnu/packages/android.scm              |   6 +-
 gnu/packages/astronomy.scm            |  26 +-
 gnu/packages/audio.scm                |   2 +-
 gnu/packages/backup.scm               |   1 -
 gnu/packages/bioinformatics.scm       |  31 +--
 gnu/packages/bootloaders.scm          |  17 +-
 gnu/packages/build-tools.scm          |   1 -
 gnu/packages/check.scm                | 361 +++++++++-----------------
 gnu/packages/cpp.scm                  |   4 +-
 gnu/packages/databases.scm            |   8 +-
 gnu/packages/dav.scm                  |   4 -
 gnu/packages/django.scm               |  12 +-
 gnu/packages/ebook.scm                |   1 -
 gnu/packages/embedded.scm             |   1 -
 gnu/packages/engineering.scm          |   7 +-
 gnu/packages/fediverse.scm            |   1 -
 gnu/packages/finance.scm              |   6 +-
 gnu/packages/fontutils.scm            |   1 -
 gnu/packages/geo.scm                  |   6 +-
 gnu/packages/gettext.scm              |   4 -
 gnu/packages/gpodder.scm              |   3 +-
 gnu/packages/graph.scm                |   6 +-
 gnu/packages/graphviz.scm             |   5 -
 gnu/packages/jupyter.scm              |   7 +-
 gnu/packages/logging.scm              |   2 +-
 gnu/packages/machine-learning.scm     |  61 ++---
 gnu/packages/mail.scm                 |   2 +-
 gnu/packages/messaging.scm            |   6 +-
 gnu/packages/music.scm                |   7 +-
 gnu/packages/package-management.scm   |   7 +-
 gnu/packages/patchutils.scm           |   2 +-
 gnu/packages/pdf.scm                  |   6 +-
 gnu/packages/potassco.scm             |   3 +-
 gnu/packages/protobuf.scm             |   4 +-
 gnu/packages/python-check.scm         |  17 +-
 gnu/packages/python-compression.scm   |  23 +-
 gnu/packages/python-crypto.scm        |   4 +-
 gnu/packages/python-science.scm       |  21 +-
 gnu/packages/python-web.scm           | 156 ++++-------
 gnu/packages/python-xyz.scm           | 329 ++++++++---------------
 gnu/packages/radio.scm                |   3 +-
 gnu/packages/serialization.scm        |   1 -
 gnu/packages/simulation.scm           |   2 -
 gnu/packages/sphinx.scm               |   1 -
 gnu/packages/statistics.scm           |  12 +-
 gnu/packages/syndication.scm          |   8 +-
 gnu/packages/task-management.scm      |   1 -
 gnu/packages/telegram.scm             |   3 +-
 gnu/packages/terminals.scm            |  16 +-
 gnu/packages/textutils.scm            |   3 -
 gnu/packages/time.scm                 |  20 +-
 gnu/packages/version-control.scm      |   1 -
 gnu/packages/virtualization.scm       |   6 +-
 gnu/packages/vpn.scm                  |   2 -
 gnu/packages/web.scm                  |   4 +-
 gnu/packages/wm.scm                   |   2 -
 gnu/packages/xml.scm                  |   2 +-
 guix/build/pyproject-build-system.scm |  99 ++++++-
 guix/import/pypi.scm                  |  21 +-
 guix/lint.scm                         |  10 +-
 tests/pypi.scm                        |   3 +-
 61 files changed, 505 insertions(+), 886 deletions(-)

-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 01/28] guix: import: pypi: Ignore pypi-ignored-inputs.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-2-ngraves@ngraves.fr

* guix/import/pypi.scm (pypi-ignored-inputs): New variable.

(compute-inputs): Use it.

* tests/pypi.scm (parse-requires.txt): Add ignored input to test the

feature.

* guix/lint.scm (check-inputs-should-be-native): Adapt list.

(check-inputs-should-not-be-an-input-at-all): Use pypi-ignored-list.

Change-Id: I774e526c5a090026e778ee44049637174a1dca95

---

guix/import/pypi.scm | 21 ++++++++++++++++++---

guix/lint.scm | 10 ++++++----

tests/pypi.scm | 3 ++-

3 files changed, 26 insertions(+), 8 deletions(-)

Toggle diff (117 lines)diff --git a/guix/import/pypi.scm b/guix/import/pypi.scm
index 4af02dd250..a49ab1e429 100644
--- a/guix/import/pypi.scm
+++ b/guix/import/pypi.scm
@@ -14,6 +14,7 @@
 ;;; Copyright © 2022 Vivien Kraus <vivien@planete-kraus.eu>
 ;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2022 Hartmut Goebel <h.goebel@crazy-compilers.com>
+;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -62,6 +63,7 @@ (define-module (guix import pypi)
   #:use-module (guix upstream)
   #:use-module ((guix licenses) #:prefix license:)
   #:export (%pypi-base-url
+            pypi-ignored-inputs
             parse-requires.txt
             parse-wheel-metadata
             specification->requirement-name
@@ -78,6 +80,18 @@ (define %pypi-base-url
   ;; Base URL of the PyPI API.
   (make-parameter "https://pypi.org/pypi/"))
 
+(define pypi-ignored-inputs
+  ;; This list contains packages that are useful for development or quality
+  ;; testing, but that most of the time are not necessary to have as an input.
+  (list "argparse"  ; native
+        "tox" ; test wrapper for other environments
+        "codecov" "coverage"  ; coverage
+        "black" "isort" "pycodestyle" "pep8"  ; style
+        "pyflakes" "flake8" "pylint" "mypy"  ; style+lint
+        "coveralls" "twine"  ; upload integration tools
+        "pytest-isort" "pytest-flake8" "pytest-cov" "pytest-black"
+        "pytest-pep8" "pytest-mypy" "pytest-pep8" "pre-commit"))  ; variants
+
 (define non-empty-string-or-false
   (match-lambda
     ("" #f)
@@ -464,9 +478,10 @@ (define (compute-inputs source-url wheel-url archive)
   "Given the SOURCE-URL and WHEEL-URL of an already downloaded ARCHIVE, return
 the corresponding list of <upstream-input> records."
   (define (requirements->upstream-inputs deps type)
-    (filter-map (match-lambda
-                  ("argparse" #f)
-                  (name (upstream-input
+    (filter-map (lambda (name)
+                  (if (member name pypi-ignored-inputs)
+                      #f
+                      (upstream-input
                          (name name)
                          (downstream-name (python->package-name name))
                          (type type))))
diff --git a/guix/lint.scm b/guix/lint.scm
index 46b2e99241..302043c929 100644
--- a/guix/lint.scm
+++ b/guix/lint.scm
@@ -73,6 +73,7 @@ (define-module (guix lint)
                                     hg-reference-url)
   #:autoload   (guix bzr-download) (bzr-reference?
                                     bzr-reference-url)
+  #:use-module ((guix import pypi) #:select (pypi-ignored-inputs))
   #:use-module (guix import stackage)
   #:use-module (ice-9 match)
   #:use-module (ice-9 regex)
@@ -582,14 +583,12 @@ (define (check-inputs-should-be-native package)
             "m4"
             "qttools-5"
             "yasm" "nasm" "fasm"
-            "python-coverage"
             "python-cython"
             "python-docutils"
             "python-mock"
             "python-nose"
             "python-pbr"
             "python-pytest"
-            "python-pytest-cov"
             "python-setuptools-scm"
             "python-sphinx"
             "scdoc"
@@ -611,8 +610,11 @@ (define (check-inputs-should-be-native package)
 (define (check-inputs-should-not-be-an-input-at-all package)
   ;; Emit a warning if some inputs of PACKAGE are likely to should not be
   ;; an input at all.
-  (let ((input-names '("python-pip"
-                       "python-pre-commit")))
+  (let ((input-names (append
+                      '("python-pip"
+                       "python-pre-commit")
+                      (map (cut string-append "python-" <>)
+                           pypi-ignored-inputs))))
     (map (lambda (input)
            (make-warning
             package
diff --git a/tests/pypi.scm b/tests/pypi.scm
index 3fbce1786f..f848325ad7 100644
--- a/tests/pypi.scm
+++ b/tests/pypi.scm
@@ -97,6 +97,7 @@ (define test-requires.txt "\
 
 [test]
 pytest (>=2.5.0)
+pytest-cov  # read but ignored
 ")
 
 ;; Beaker contains only optional dependencies.
@@ -258,7 +259,7 @@ (define-syntax-rule (with-pypi responses body ...)
   (map specification->requirement-name test-specifications))
 
 (test-equal "parse-requires.txt"
-  (list '("foo" "bar") '("pytest"))
+  (list '("foo" "bar") '("pytest" "pytest-cov"))
   (mock ((ice-9 ports) call-with-input-file
          call-with-input-string)
         (parse-requires.txt test-requires.txt)))
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 02/28] build-system/pyproject: Ignore unwanted pytest flags.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-3-ngraves@ngraves.fr

* guix/build/pyproject-build-system.scm : Ignore unwanted pytest flags.

Change-Id: Ib9f1602e5af11227e5b7ce124f0f9be4fa2b78e4

---

guix/build/pyproject-build-system.scm | 99 ++++++++++++++++++++++++++-

1 file changed, 96 insertions(+), 3 deletions(-)

Toggle diff (137 lines)diff --git a/guix/build/pyproject-build-system.scm b/guix/build/pyproject-build-system.scm
index 947d240114..2df9f2f479 100644
--- a/guix/build/pyproject-build-system.scm
+++ b/guix/build/pyproject-build-system.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2021 Lars-Dominik Braun <lars@6xq.net>
 ;;; Copyright © 2022 Marius Bakke <marius@gnu.org>
+;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -35,7 +36,8 @@ (define-module (guix build pyproject-build-system)
             add-installed-pythonpath
             site-packages
             python-version
-            pyproject-build))
+            pyproject-build
+            with-guix-pytest-plugin))
 
 ;;; Commentary:
 ;;;
@@ -142,7 +144,94 @@ (define* (build #:key outputs build-backend backend-path configure-flags #:allow
      wheel-dir
      config-settings)))
 
-(define* (check #:key tests? test-backend test-flags #:allow-other-keys)
+(define pytest-default-ignore-alist
+  '(("cov" . ("--cov" "--cov-reset" "--cov-report" "--cov-config"
+              "--no-cov-on-fail" "--no-cov" "--cov-fail-under"
+              "--cov-append" "--cov-branch" "--cov-context"))
+    ("mypy" . ("--mypy" "--mypy-config-file" "--mypy-ignore-missing-imports"))
+    ("isort" . ("--isort"))
+    ("flake8" . ("--flake8"))
+    ("black" . ("--black"))
+    ("flakes" . ("--flakes"))
+    ("pep8" . ("--pep8"))))
+
+(define (pytest-ignore-flags-plugin flags)
+  "This function converts an list of flags into a string that can
+  be instantiated as a python pytest plugin."
+  (format #f "\
+import pytest
+
+def pytest_addoption(parser):
+    group = parser.getgroup('guix','Guix ignored options')
+    options = [~{~s, ~}]
+    for option in options:
+        group.addoption(option, action='append', nargs='?')"
+          flags))
+
+(define (call-with-guix-pytest-plugin inputs thunk)
+  "This function emulates command line options provided by pytest plugins in
+the absence of the plugins defining these options.
+
+This is done by selecting absent plugins, gettings their flags defined in
+PYTEST-DEFAULT-IGNORE-ALIST, and generating the plugin from there with
+PYTEST-IGNORE-FLAGS-PLUGIN."
+  (let* ((former-path (getenv "PYTHONPATH"))
+         (input-names
+          (map car
+               (filter (match-lambda
+                         ((name . _)
+                          (if (string-prefix? "python-pytest-" name)
+                              name
+                              #f))
+                         ( _ #f))
+                       inputs)))
+         (filtered-flags
+          (filter identity
+                  (append-map
+                   (match-lambda
+                     ((group . flags)
+                      (if (member (string-append "python-pytest-" group)
+                                  input-names)
+                          (list #f)
+                          flags))
+                     (_ (list #f)))
+                   pytest-default-ignore-alist)))
+         (dir (string-append
+               (if (access? (dirname (getcwd)) W_OK)
+                   (dirname (getcwd))
+                   ;; fallback if we're already out-of-source
+                   (getcwd))
+               "/.guix-pytest")))
+    (dynamic-wind
+      (lambda ()
+        (setenv "PYTHONPATH"
+                (string-append
+                 (if former-path
+                     (string-append former-path ":")
+                     "")
+                 dir))
+        (setenv "PYTEST_PLUGINS"
+                (string-append
+                 (if (getenv "PYTEST_PLUGINS")
+                     (string-append former-path ",")
+                     "")
+                 "pytest_guix_plugin"))
+        (mkdir-p dir)
+        (with-output-to-file (string-append dir "/__init__.py")
+          (lambda _ (display "")))
+        (with-output-to-file (string-append dir "/pytest_guix_plugin.py")
+          (lambda _
+            (display (pytest-ignore-flags-plugin filtered-flags)))))
+      thunk
+      (lambda ()
+        (setenv "PYTHONPATH" former-path)
+        (unsetenv "PYTEST_PLUGINS")))))
+
+(define-syntax-rule (with-guix-pytest-plugin inputs exp ...)
+  "Evaluate EXP in a context where the Guix pytest plugin is added."
+  (call-with-guix-pytest-plugin inputs (lambda () exp ...)))
+
+(define* (check #:key inputs tests? test-backend test-flags #:allow-other-keys)
   "Run the test suite of a given Python package."
   (if tests?
       ;; Unfortunately with PEP 517 there is no common method to specify test
@@ -165,7 +254,8 @@ (define* (check #:key tests? test-backend test-flags #:allow-other-keys)
         (format #t "Using ~a~%" use-test-backend)
         (match use-test-backend
           ('pytest
-           (apply invoke pytest "-vv" test-flags))
+           (with-guix-pytest-plugin inputs
+             (apply invoke pytest "-vv" test-flags)))
           ('nose
            (apply invoke nosetests "-v" test-flags))
           ('nose2
@@ -386,3 +476,6 @@ (define* (pyproject-build #:key inputs (phases %standard-phases)
   (apply python:python-build #:inputs inputs #:phases phases args))
 
 ;;; pyproject-build-system.scm ends here
+;;; Local Variables:
+;;; eval: (put 'with-guix-pytest-plugin 'scheme-indent-function 1)
+;;; End:
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 03/28] build-system/pyproject: Remove python-black input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-4-ngraves@ngraves.fr

* gnu/packages/bioinformatics.scm (python-doubletdetection,

python-liana-py, scvelo)[native-inputs]: Remove python-black.

* gnu/packages/databases.scm (datasette):

[native-inputs]: Remove python-black.

* gnu/packages/finance.scm (python-trezor)[native-inputs]: Remove

python-black.

* gnu/packages/graph.scm (python-graphtools)[native-inputs]: Remove

python-black.

* gnu/packages/machine-learning.scm (python-funsor,

python-imbalanced-learn, python-hyperopt, python-captum)

[native-inputs]: Remove python-black.

* gnu/packages/python-check.scm (python-vcrpy)[native-inputs]:

Remove python-black.

* gnu/packages/python-web.scm (python-ovh, python-openai,

python-starsessions-for-pytorch-lightning)[native-inputs]: Remove

python-black.

* gnu/packages/python-xyz.scm (python-pydantic-cli, python-imageio,

python-update-checker, python-eliot, python-minikanren)

[native-inputs]: Remove python-black.

(ptpython)[propagated-inputs]: Remove python-black.

* gnu/packages/virtualization.scm (python-transient)[native-inputs]:

Remove python-black.

---

gnu/packages/bioinformatics.scm | 11 +++--------

gnu/packages/databases.scm | 1 -

gnu/packages/finance.scm | 1 -

gnu/packages/graph.scm | 1 -

gnu/packages/machine-learning.scm | 10 +++-------

gnu/packages/python-web.scm | 8 +++-----

gnu/packages/python-xyz.scm | 15 +++++----------

gnu/packages/virtualization.scm | 3 +--

8 files changed, 15 insertions(+), 35 deletions(-)

Toggle diff (224 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5dca1bb3d4..546aa97c71 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2765,8 +2765,7 @@ (define-public python-doubletdetection
            python-scipy
            python-tqdm))
     (native-inputs
-     (list python-black
-           python-flake8
+     (list python-flake8
            python-poetry-core
            python-pytest))
     (home-page "https://github.com/JonathanShor/DoubletDetection")
@@ -2985,10 +2984,7 @@ (define-public python-liana-py
                              python-tqdm
                              tzdata))
     (native-inputs
-     (list python-black
-           python-poetry-core
-           python-pytest
-           python-pytest-cov))
+     (list python-poetry-core python-pytest python-pytest-cov))
     (home-page "https://github.com/saezlab/liana-py")
     (synopsis "LIANA is a ligand-receptor analysis framework")
     (description "This is a Ligand-Receptor inference framework.  The
@@ -23577,8 +23573,7 @@ (define-public scvelo
            python-umap-learn
            pybind11))
     (native-inputs
-     (list python-black
-           python-flake8
+     (list python-flake8
            python-hypothesis
            python-pytest
            python-setuptools-scm
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index e7295337af..3fe9a76a0f 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -5799,7 +5799,6 @@ (define-public datasette
     (native-inputs
      (list nss-certs-for-test
            python-beautifulsoup4
-           python-black
            python-cogapp
            python-pip
            python-pytest
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index b7413063af..0bb2f46abb 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -1159,7 +1159,6 @@ (define-public python-trezor
            python-typing-extensions))
     (native-inputs ; Only needed for running the tests
      (list protobuf
-           python-black
            python-isort
            python-pillow
            python-protobuf
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index c8bd25af9c..02268f4391 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -482,7 +482,6 @@ (define-public python-graphtools
     (native-inputs
      (list util-linux ;for lscpu
            python-anndata
-           python-black
            python-coverage
            python-coveralls
            python-nose
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index d36dca2d91..439c3c9c77 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -229,8 +229,7 @@ (define-public python-funsor
     (propagated-inputs (list python-makefun python-multipledispatch
                              python-numpy python-opt-einsum
                              python-typing-extensions))
-    (native-inputs (list python-black
-                         python-flake8
+    (native-inputs (list python-flake8
                          python-isort
                          python-nbsphinx
                          python-pandas
@@ -2151,8 +2150,7 @@ (define-public python-imbalanced-learn
                               (getcwd)))))))
     (propagated-inputs (list python-joblib python-numpy python-scikit-learn
                              python-scipy python-threadpoolctl))
-    (native-inputs (list python-black
-                         python-flake8
+    (native-inputs (list python-flake8
                          python-keras
                          python-mypy
                          python-pandas
@@ -2591,8 +2589,7 @@ (define-public python-hyperopt
            python-six
            python-tqdm))
     (native-inputs
-     (list python-black
-           python-nose
+     (list python-nose
            python-pymongo
            python-pytest
            python-wheel))
@@ -5323,7 +5320,6 @@ (define-public python-captum
      (list python-matplotlib python-numpy python-pytorch python-tqdm))
     (native-inputs (list jupyter
                          python-annoy
-                         python-black
                          python-flake8
                          python-flask
                          python-flask-compress
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index d17b61f29f..25407f4d7f 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1515,8 +1515,7 @@ (define-public python-ovh
     (build-system pyproject-build-system)
     (arguments (list #:tests? #f))      ; XXX: tests require networking
     (propagated-inputs (list python-requests))
-    (native-inputs (list python-black
-                         python-coverage
+    (native-inputs (list python-coverage
                          python-flake8
                          python-isort
                          python-pytest
@@ -2925,7 +2924,7 @@ (define-public python-openai
  and not test_file_cli")))
     (propagated-inputs (list python-aiohttp python-requests python-tqdm
                              python-typing-extensions))
-    (native-inputs (list python-black python-pytest python-pytest-asyncio
+    (native-inputs (list python-pytest python-pytest-asyncio
                          python-pytest-mock python-setuptools python-wheel))
     (home-page "https://github.com/openai/openai-python")
     (synopsis "Python client library for the OpenAI API")
@@ -10211,8 +10210,7 @@ (define-public python-starsessions
            python-itsdangerous
            python-starlette))
     (native-inputs
-     (list python-black
-           python-flake8
+     (list python-flake8
            python-httpx
            python-mypy
            python-poetry-core
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index b4b233d464..6cbc2f92f5 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -8714,8 +8714,7 @@ (define-public python-pydantic-cli
     (propagated-inputs
      (list python-pydantic))
     (native-inputs
-     (list python-black
-           python-mypy
+     (list python-mypy
            python-pytest))
     (home-page "https://github.com/mpkocher/pydantic-cli")
     (synopsis "Turn Pydantic defined data models into CLI tools")
@@ -11762,8 +11761,7 @@ (define-public python-imageio
     (propagated-inputs
      (list python-imageio-ffmpeg python-numpy python-pillow python-tifffile))
     (native-inputs
-     (list python-black
-           python-flake8
+     (list python-flake8
            python-fsspec
            python-pytest
            python-pytest-cov
@@ -23623,8 +23621,7 @@ (define-public ptpython
     (arguments
      `(#:tests? #f)) ;there are no tests
     (propagated-inputs
-     (list python-appdirs python-black python-jedi python-prompt-toolkit
-           python-pygments))
+     (list python-appdirs python-jedi python-prompt-toolkit python-pygments))
     (home-page "https://github.com/jonathanslenders/ptpython")
     (synopsis "Python Read-Eval-Print-Loop with nice IDE-like features")
     (description
@@ -28962,7 +28959,7 @@ (define-public python-update-checker
         (base32 "04yb5a9mi45ax50m2m0ih6gdvkk1j7gfmy83dd58i1f59axlabba"))))
     (build-system python-build-system)
     (propagated-inputs (list python-requests))
-    (native-inputs (list python-black python-flake8 python-pytest))
+    (native-inputs (list python-flake8 python-pytest))
     (home-page "https://github.com/bboe/update_checker")
     (synopsis "Python module that will check for package updates")
     (description "This package provides a Python module that will check for
@@ -33267,8 +33264,7 @@ (define-public python-eliot
     (propagated-inputs
      (list python-boltons python-orjson python-pyrsistent python-zope-interface))
     (native-inputs
-     (list python-black
-           python-coverage
+     (list python-coverage
            python-flake8
            python-hypothesis
            python-pytest
@@ -36597,7 +36593,6 @@ (define-public python-minikanren
            python-pytest
            python-pytest-cov
            python-pylint
-           python-black
            python-sympy
            python-versioneer
            python-coverage))
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index b8819bb14d..568b50fcf9 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -2972,8 +2972,7 @@ (define-public python-transient
                         (("==")
                          ">=")))))))
     (native-inputs
-     (list python-black
-           python-mypy
+     (list python-mypy
            python-pyhamcrest
            python-setuptools
            python-twine
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 04/28] build-system/pyproject: Remove python-pylint native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-5-ngraves@ngraves.fr

* gnu/packages/potassco.scm (python-clingraph):

[native-inputs]: Remove python-pylint.

* gnu/packages/python-xyz.scm (python-mediapy) [native-inputs]: Remove

python-pylint.

* gnu/packages/syndication.scm (rtv, tuir)[native-inputs]: Remove

python-pylint.

* gnu/packages/terminals.scm (python-halo, python-log-symbols,

python-spinners)[native-inputs]: Remove python-pylint.

---

gnu/packages/potassco.scm | 3 +--

gnu/packages/python-xyz.scm | 1 -

gnu/packages/syndication.scm | 2 --

gnu/packages/terminals.scm | 3 ---

4 files changed, 1 insertion(+), 8 deletions(-)

Toggle diff (76 lines)diff --git a/gnu/packages/potassco.scm b/gnu/packages/potassco.scm
index 8330c23300..cb1364d95a 100644
--- a/gnu/packages/potassco.scm
+++ b/gnu/packages/potassco.scm
@@ -699,8 +699,7 @@ (define-public python-clingraph
                              python-jsonschema
                              python-networkx
                              python-setuptools))
-    (native-inputs (list dot2tex graphviz python-pylint python-pytest
-                         python-wheel))
+    (native-inputs (list dot2tex graphviz python-pytest python-wheel))
     (home-page "https://github.com/potassco/clingraph")
     (synopsis "Visualizer for graphs defined as logic programs")
     (description
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 6cbc2f92f5..d9a4b3340b 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4961,7 +4961,6 @@ (define-public python-mediapy
                              python-pillow))
     (native-inputs
      (list python-flit-core
-           python-pylint
            python-pytest
            python-pytest-xdist))
     (home-page "https://github.com/google/mediapy")
diff --git a/gnu/packages/syndication.scm b/gnu/packages/syndication.scm
index a84893786c..9fbccf6087 100644
--- a/gnu/packages/syndication.scm
+++ b/gnu/packages/syndication.scm
@@ -501,7 +501,6 @@ (define-public rtv
            python-coveralls
            python-coverage
            python-mock
-           python-pylint
            python-pytest
            python-vcrpy))
     (home-page "https://github.com/michael-lazar/rtv")
@@ -545,7 +544,6 @@ (define-public tuir
      (list python-coverage
            python-coveralls
            python-mock
-           python-pylint
            python-pytest
            python-setuptools
            python-vcrpy
diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index 88e84ce647..662a40c689 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -1178,7 +1178,6 @@ (define-public python-halo
     (native-inputs
      (list python-coverage
            python-nose
-           python-pylint
            python-setuptools
            python-tox
            python-twine
@@ -1211,7 +1210,6 @@ (define-public python-log-symbols
     (native-inputs
      (list python-coverage
            python-nose
-           python-pylint
            python-setuptools
            python-tox
            python-wheel))
@@ -1245,7 +1243,6 @@ (define-public python-spinners
     (native-inputs
      (list python-coverage
            python-nose
-           python-pylint
            python-setuptools
            python-tox
            python-wheel))
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 05/28] build-system/pyproject: Remove python-flake8 inputs.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-6-ngraves@ngraves.fr

* gnu/packages/bioinformatics.scm (python-doubletdetection,

python-biom-format)[native-inputs]: Remove python-flake8.

* gnu/packages/ebook.scm (calibre)[native-inputs]: Remove

python-flake8.

* gnu/packages/engineering.scm (python-scikit-rf)[native-inputs]:

Remove python-flake8.

* gnu/packages/finance.scm (python-mt-940)[native-inputs]: Remove

python-flake8.

* gnu/packages/geo.scm (python-geopy)[native-inputs]: Remove

python-flake8.

* gnu/packages/gettext.scm (python-mdpo)[native-inputs]: Remove

python-flake8.

* gnu/packages/graph.scm (python-pygsp)[native-inputs]: Remove

python-flake8.

* gnu/packages/graphviz.scm (python-uqbar)[native-inputs]: Remove

python-flake8.

* gnu/packages/machine-learning.scm (python-funsor,

python-imbalanced-learn, python-captum, python-pyro-api,

python-pyro-ppl, python-linear-operator,

python-gpytorch)[native-inputs]: Remove python-flake8.

* gnu/packages/music.scm (python-mutagen):

[arguments]<#:test-flags>: Ignore flake8 quality tests.

[native-inputs]: Remove python-flake8.

* gnu/packages/protobuf.scm (python-pure-protobuf):

[arguments]<#:phases>: Remove flake8 invocation from check phase.

[native-inputs]: Remove python-flake8.

* gnu/packages/python-web.scm (python-ovh, python-furl,

python-httplib2, python-http-ece, python-woob,

python-starsessions-for-pytorch-lightning)[native-inputs]: Remove

python-flake8.

* gnu/packages/python-xyz.scm (python-colorful, python-pymd4c,

python-flasgger, python-imageio, python-importlib-ressources,

python-seaborn, python-inflect, python-yq, python-update-checker,

python-eliot, python-dateparser, python-jinja2-cli, python-verspec,

python-mike)[native-inputs]: Remove python-flake8.

* gnu/packages/simulation.scm (python-dolfin-adjoint)[native-inputs]:

Remove python-flake8.

* gnu/packages/statistics.scm (python-statsmodels)[native-inputs]:

Remove python-flake8.

* gnu/packages/vpn.scm (sshuttle)[native-inputs]: Remove

python-flake8.

* gnu/packages/wm.scm (qtile)[native-inputs]: Remove python-flake8.

* gnu/packages/textutils.scm (python-panflute)[native-inputs]: Remove

python-flake8.

---

gnu/packages/bioinformatics.scm | 7 ++-----

gnu/packages/ebook.scm | 1 -

gnu/packages/engineering.scm | 1 -

gnu/packages/finance.scm | 4 +---

gnu/packages/gettext.scm | 1 -

gnu/packages/graph.scm | 3 +--

gnu/packages/graphviz.scm | 1 -

gnu/packages/machine-learning.scm | 14 ++++----------

gnu/packages/music.scm | 4 ++--

gnu/packages/protobuf.scm | 4 +---

gnu/packages/python-web.scm | 12 +++---------

gnu/packages/python-xyz.scm | 30 ++++++++++++------------------

gnu/packages/simulation.scm | 1 -

gnu/packages/statistics.scm | 1 -

gnu/packages/textutils.scm | 1 -

gnu/packages/vpn.scm | 1 -

gnu/packages/wm.scm | 1 -

17 files changed, 26 insertions(+), 61 deletions(-)

Toggle diff (416 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 546aa97c71..fca21ebd73 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2765,8 +2765,7 @@ (define-public python-doubletdetection
            python-scipy
            python-tqdm))
     (native-inputs
-     (list python-flake8
-           python-poetry-core
+     (list python-poetry-core
            python-pytest))
     (home-page "https://github.com/JonathanShor/DoubletDetection")
     (synopsis
@@ -3813,7 +3812,6 @@ (define-public python-biom-format
     (propagated-inputs
      (list python-anndata
            python-click
-           python-flake8
            python-future
            python-h5py
            python-numpy
@@ -23573,8 +23571,7 @@ (define-public scvelo
            python-umap-learn
            pybind11))
     (native-inputs
-     (list python-flake8
-           python-hypothesis
+     (list python-hypothesis
            python-pytest
            python-setuptools-scm
            python-wheel))
diff --git a/gnu/packages/ebook.scm b/gnu/packages/ebook.scm
index 46ec951916..75e14801dd 100644
--- a/gnu/packages/ebook.scm
+++ b/gnu/packages/ebook.scm
@@ -156,7 +156,6 @@ (define-public calibre
     (native-inputs
      (list bash-minimal
            pkg-config
-           python-flake8
            python-pyqt-builder
            qtbase-5                     ; for qmake
            xdg-utils))
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index 009629307d..d19b58b3e7 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -2828,7 +2828,6 @@ (define-public python-scikit-rf
                              python-qtpy
                              python-scipy))
     (native-inputs (list python-coverage
-                         python-flake8
                          python-nbval
                          python-networkx
                          python-pytest
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index 0bb2f46abb..5cf2db24a2 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -2309,9 +2309,7 @@ (define-public python-mt-940
                         ;; Remove custom --cov flags.
                         (delete-file "pytest.ini")
                         (invoke "pytest" "-vv")))))))
-    (native-inputs (list python-flake8
-                         python-pytest
-                         python-pyyaml))
+    (native-inputs (list python-pytest python-pyyaml))
     (home-page "https://mt940.readthedocs.io/")
     (synopsis "Python parser for MT940-encoded SWIFT data")
     (description
diff --git a/gnu/packages/gettext.scm b/gnu/packages/gettext.scm
index 7862c296bd..29cdbab915 100644
--- a/gnu/packages/gettext.scm
+++ b/gnu/packages/gettext.scm
@@ -226,7 +226,6 @@ (define-public mdpo
     (build-system python-build-system)
     (native-inputs
      (list python-bump2version
-           python-flake8
            python-flake8-implicit-str-concat
            python-flake8-print
            python-isort
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 02268f4391..85cb1d6437 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -570,8 +570,7 @@ (define-public python-pygsp
                 "")))))))
     (propagated-inputs (list python-numpy python-scikit-image python-scipy))
     (native-inputs
-     (list python-coverage python-coveralls python-flake8
-           python-pytest))
+     (list python-coverage python-coveralls python-pytest))
     (home-page "https://github.com/epfl-lts2/pygsp")
     (synopsis "Graph Signal Processing in Python")
     (description "The PyGSP is a Python package to ease signal processing on
diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm
index defd53df73..0d3db31212 100644
--- a/gnu/packages/graphviz.scm
+++ b/gnu/packages/graphviz.scm
@@ -224,7 +224,6 @@ (define-public python-uqbar
 and not test_sphinx_book_text_broken_strict")))
     (native-inputs
      (list graphviz
-           python-flake8
            python-isort
            python-mypy
            python-pytest
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 439c3c9c77..b93bfb551f 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -229,8 +229,7 @@ (define-public python-funsor
     (propagated-inputs (list python-makefun python-multipledispatch
                              python-numpy python-opt-einsum
                              python-typing-extensions))
-    (native-inputs (list python-flake8
-                         python-isort
+    (native-inputs (list python-isort
                          python-nbsphinx
                          python-pandas
                          python-pillow
@@ -2150,8 +2149,7 @@ (define-public python-imbalanced-learn
                               (getcwd)))))))
     (propagated-inputs (list python-joblib python-numpy python-scikit-learn
                              python-scipy python-threadpoolctl))
-    (native-inputs (list python-flake8
-                         python-keras
+    (native-inputs (list python-keras
                          python-mypy
                          python-pandas
                          python-pytest
@@ -5320,7 +5318,6 @@ (define-public python-captum
      (list python-matplotlib python-numpy python-pytorch python-tqdm))
     (native-inputs (list jupyter
                          python-annoy
-                         python-flake8
                          python-flask
                          python-flask-compress
                          python-ipython
@@ -5841,8 +5838,7 @@ (define-public python-pyro-api
     (build-system python-build-system)
     (arguments '(#:tests? #false)) ;requires pyro
     (native-inputs
-     (list python-flake8
-           python-ipython
+     (list python-ipython
            python-pytest
            python-sphinx
            python-sphinx-rtd-theme))
@@ -5899,8 +5895,7 @@ (define-public python-linear-operator
                              python-pytorch
                              python-scipy
                              python-typeguard))
-    (native-inputs (list python-flake8
-                         python-flake8-print
+    (native-inputs (list python-flake8-print
                          python-pytest
                          python-setuptools
                          python-setuptools-scm
@@ -5931,7 +5926,6 @@ (define-public python-gpytorch
                              python-scikit-learn
                              python-scipy))
     (native-inputs (list python-coverage
-                         python-flake8
                          python-flake8-print
                          python-nbval
                          python-pytest
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 6659dc0d53..dc82cfa570 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -4112,6 +4112,7 @@ (define-public python-mutagen
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags '(list "--ignore=tests/quality/test_flake8.py")
        #:phases
        #~(modify-phases %standard-phases
            (add-before 'check 'remove-hypothesis-deadlines
@@ -4122,8 +4123,7 @@ (define-public python-mutagen
                  (("( +)@given" all spaces)
                   (string-append spaces "@settings(deadline=None)\n" all))))))))
     (native-inputs
-     (list python-flake8
-           python-hypothesis
+     (list python-hypothesis
            python-pytest
            python-setuptools
            python-wheel))
diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm
index d4b48e585b..4f18d1e6e2 100644
--- a/gnu/packages/protobuf.scm
+++ b/gnu/packages/protobuf.scm
@@ -505,7 +505,7 @@ (define-public python-pure-protobuf
         (base32 "15dp5pvazd0jx4wzzh79080ah7hkpd3axh40al9vhzs2hf3v90hx"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-flake8 python-pytest python-pytest-cov python-isort))
+     (list python-pytest python-pytest-cov python-isort))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
@@ -513,8 +513,6 @@ (define-public python-pure-protobuf
            (lambda _
              (invoke "pytest" "--cov-report" "term-missing" "--cov"
                      "pure_protobuf")
-             (invoke "flake8" "pure_protobuf" "tests"
-                     "--ignore=F541")
              (invoke "isort" "-rc" "-c" "pure_protobuf" "tests"))))))
     (home-page "https://pypi.org/project/pure-protobuf/")
     (synopsis "Protobuf implementation using dataclasses")
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 25407f4d7f..8f88693e56 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1516,7 +1516,6 @@ (define-public python-ovh
     (arguments (list #:tests? #f))      ; XXX: tests require networking
     (propagated-inputs (list python-requests))
     (native-inputs (list python-coverage
-                         python-flake8
                          python-isort
                          python-pytest
                          python-pytest-cov
@@ -1832,8 +1831,6 @@ (define-public python-furl
     (build-system python-build-system)
     (propagated-inputs
      (list python-six python-orderedmultidict))
-    (native-inputs
-     (list python-flake8))
     (home-page "https://github.com/gruns/furl")
     (synopsis "URL manipulation in Python")
     (description "Furl provides an easy-to-use alternative to the
@@ -1866,7 +1863,6 @@ (define-public python-httplib2
                  (("==") ">=")))))))
     (native-inputs
      (list python-cryptography
-           python-flake8
            python-future
            python-mock
            python-pytest
@@ -8472,7 +8468,7 @@ (define-public python-http-ece
     (propagated-inputs
      (list python-cryptography))
     (native-inputs
-     (list python-coverage python-flake8 python-mock python-nose))
+     (list python-coverage python-mock python-nose))
     (home-page "https://github.com/web-push-libs/encrypted-content-encoding")
     (synopsis "Encrypted Content Encoding for HTTP")
     (description
@@ -9549,8 +9545,7 @@ (define-public python-woob
            python-six
            python-unidecode))
     (native-inputs
-     (list python-coverage python-flake8 python-nose python-selenium
-           python-xunitparser))
+     (list python-coverage python-nose python-selenium python-xunitparser))
     (home-page "https://woob.tech/")
     (synopsis "Woob, Web Outside Of Browsers")
     (description "Woob is a collection of applications able to interact with
@@ -10210,8 +10205,7 @@ (define-public python-starsessions
            python-itsdangerous
            python-starlette))
     (native-inputs
-     (list python-flake8
-           python-httpx
+     (list python-httpx
            python-mypy
            python-poetry-core
            python-pytest
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index d9a4b3340b..c4cd591093 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1470,8 +1470,7 @@ (define-public python-colorful
         (base32 "0kyy9qhvrb5m9h8xmri7c88i0k1g5qc7017anw39gx44an7mn33y"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage python-flake8 python-pytest python-setuptools
-           python-wheel))
+     (list python-coverage python-pytest python-setuptools python-wheel))
     (propagated-inputs
      (list python-colorama))
     (home-page "http://github.com/timofurrer/colorful")
@@ -2815,7 +2814,7 @@ (define-public python-pymd4c
     (inputs
      (list md4c))
     (native-inputs
-     (list python-flake8 python-pkgconfig pkg-config))
+     (list python-pkgconfig pkg-config))
     (home-page "https://github.com/dominickpastore/pymd4c")
     (synopsis "Python bindings for MD4C")
     (description
@@ -11760,8 +11759,7 @@ (define-public python-imageio
     (propagated-inputs
      (list python-imageio-ffmpeg python-numpy python-pillow python-tifffile))
     (native-inputs
-     (list python-flake8
-           python-fsspec
+     (list python-fsspec
            python-pytest
            python-pytest-cov
            python-setuptools
@@ -12585,8 +12583,7 @@ (define-public python-importlib-resources
              (setenv "PYTHONPATH"
                      (string-append (getcwd) "/_custom_build")))))))
     (native-inputs
-     (list python-flake8
-           python-pytest
+     (list python-pytest
            python-pytest-black
            python-pytest-checkdocs
            python-pytest-cov
@@ -14858,8 +14855,7 @@ (define-public python-seaborn
            python-scipy
            python-statsmodels))
     (native-inputs
-     (list python-flake8
-           python-flit-core
+     (list python-flit-core
            python-ipykernel
            python-nbconvert
            python-numpydoc
@@ -22488,8 +22484,7 @@ (define-public python-inflect
              (setenv "PYTHONPATH"
                      (string-append (getcwd) "/_custom_build")))))))
     (propagated-inputs (list python-pydantic))
-    (native-inputs (list python-flake8
-                         python-pygments
+    (native-inputs (list python-pygments
                          python-pytest
                          python-pytest-black
                          python-pytest-checkdocs
@@ -27950,7 +27945,7 @@ (define-public python-yq
     (inputs
      (list python-argcomplete python-pyyaml python-xmltodict python-toml jq))
     (native-inputs
-     (list python-coverage python-flake8 python-setuptools-scm python-wheel))
+     (list python-coverage python-setuptools-scm python-wheel))
     (home-page "https://github.com/kislyuk/yq")
     (synopsis "Command-line YAML/XML processor")
     (description
@@ -28958,7 +28953,7 @@ (define-public python-update-checker
         (base32 "04yb5a9mi45ax50m2m0ih6gdvkk1j7gfmy83dd58i1f59axlabba"))))
     (build-system python-build-system)
     (propagated-inputs (list python-requests))
-    (native-inputs (list python-flake8 python-pytest))
+    (native-inputs (list python-pytest))
     (home-page "https://github.com/bboe/update_checker")
     (synopsis "Python module that will check for package updates")
     (description "This package provides a Python module that will check for
@@ -33264,7 +33259,6 @@ (define-public python-eliot
      (list python-boltons python-orjson python-pyrsistent python-zope-interface))
     (native-inputs
      (list python-coverage
-           python-flake8
            python-hypothesis
            python-pytest
            python-pytest-xdist
@@ -34073,7 +34067,7 @@ (define-public python-dateparser
      (list python-dateutil python-pytz python-regex python-ruamel.yaml
            python-tzlocal))
     (native-inputs
-     (list python-flake8 python-pytest python-parameterized tzdata-for-tests
+     (list python-pytest python-parameterized tzdata-for-tests
            python-setuptools python-wheel))
     (arguments
      `(#:phases
@@ -35496,7 +35490,7 @@ (define-public python-jinja2-cli
     (propagated-inputs
       (list python-jinja2))
     (native-inputs
-      (list python-flake8 python-jinja2 python-pytest))
+      (list python-jinja2 python-pytest))
     (home-page "https://github.com/mattrobenolt/jinja2-cli")
     (synopsis "Command-line interface to Jinja2")
     (description
@@ -38051,7 +38045,7 @@ (define-public python-verspec
                (base32
                 "07n06wv85fm4vl1ird2mja0823js3x322wgs9gdnq1djjyk4ql64"))))
     (build-system python-build-system)
-    (native-inputs (list python-coverage python-flake8 python-mypy
+    (native-inputs (list python-coverage python-mypy
                          python-pretend python-pytest))
     (arguments
      `(#:phases (modify-phases %standard-phases
@@ -38451,7 +38445,7 @@ (define-public python-mike
                 "0yxp816x7s948xsd0fifvq9shg01xdxlifd9rzf5y2rd9iwz3hsn"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-coverage python-flake8 python-shtab))
+     (list python-coverage python-shtab))
     (propagated-inputs
      (list python-jinja2 python-mkdocs python-pyyaml python-verspec))
     (home-page "https://github.com/jimporter/mike")
diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index 3af29aeeaa..1eed4fd180 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -1252,7 +1252,6 @@ (define-public python-dolfin-adjoint
      (list pkg-config
            python-coverage
            python-decorator
-           python-flake8
            python-pkgconfig
            python-pytest))
     (propagated-inputs
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 0e9a07f7b8..37abd291d2 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2670,7 +2670,6 @@ (define-public python-statsmodels
     (native-inputs
      (list python-colorama

This message was truncated. Download the full message here.

Nicolas Graves wrote 1 months ago

[PATCH v3 09/28] gnu: python-aiosqlite: Remove python-coverage native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-10-ngraves@ngraves.fr

* gnu/packages/databases.scm (python-aiosqlite):

[arguments]<#:phases>: Adapt check phase.

[native-inputs]: Remove python-coverage.

Change-Id: I165d174426022f0603223e3def91ffe280f15899

---

gnu/packages/databases.scm | 5 +----

1 file changed, 1 insertion(+), 4 deletions(-)

Toggle diff (19 lines)diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 3fe9a76a0f..af5eaed244 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -4139,11 +4139,8 @@ (define-public python-aiosqlite
                         (replace 'check
                           (lambda* (#:key tests? #:allow-other-keys)
                             (when tests?
-                              (invoke "python" "-m" "coverage" "run" "-m"
-                                      "aiosqlite.tests")
-                              (invoke "python" "-m" "coverage" "report")))))))
+                              (invoke "python" "-m" "aiosqlite.tests")))))))
     (native-inputs (list python-flit-core
-                         python-coverage
                          python-mypy))
     (home-page "https://github.com/jreese/aiosqlite")
     (synopsis
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 08/28] gnu: u-boot-tools: Remove python-coverage native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-9-ngraves@ngraves.fr

* gnu/packages/bootloaders.scm (u-boot-tools):

[native-inputs]: Remove python-coverage.

[arguments]<#:phases>: Adapt patch phase.

Change-Id: I94394544079197b4a3f8c53cc0b3d78d1f5dc8be

---

gnu/packages/bootloaders.scm | 17 ++++-------------

1 file changed, 4 insertions(+), 13 deletions(-)

Toggle diff (44 lines)diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm
index b5cfacca4b..c4c585e463 100644
--- a/gnu/packages/bootloaders.scm
+++ b/gnu/packages/bootloaders.scm
@@ -825,8 +825,7 @@ (define-public u-boot-tools
     (name "u-boot-tools")
     (native-inputs
      (modify-inputs (package-native-inputs u-boot)
-       (prepend python-coverage
-                python-filelock
+       (prepend python-filelock
                 python-pycryptodomex
                 python-pytest
                 python-pytest-xdist)))
@@ -842,14 +841,6 @@ (define-public u-boot-tools
                (("/bin/false") (which "false")))
              (substitute* "tools/dtoc/fdt_util.py"
                (("'cc'") "'gcc'"))
-             (substitute* "tools/u_boot_pylib/test_util.py"
-               ;; python3-coverage is simply called coverage in guix.
-               (("python3-coverage") "coverage")
-
-               ;; Don't require 100% coverage since it's brittle and can
-               ;; fail with newer versions of coverage or dependencies.
-               (("raise ValueError\\('Test coverage failure'\\)")
-                "print('Continuing anyway since Guix does not care :O')"))
              (substitute* "test/run"
                ;; Make it easier to find test failures.
                (("#!/bin/bash") "#!/bin/bash -x")
@@ -862,9 +853,9 @@ (define-public u-boot-tools
                 "# run_test \"sandbox_noinst\"")
                (("run_test \"sandbox_vpl\"")
                 "# run_test \"sandbox_vpl\"")
-               ;; FIXME: code coverage not working
-               (("run_test \"binman code coverage\"")
-                "# run_test \"binman code coverage\"")
+               ;; Disable code coverage tests.
+               (("run_test \"(\\w+) code coverage\"" all)
+                (string-append "# " all))
                ;; This test would require internet access.
                (("\\./tools/buildman/buildman") (which "true")))
              (substitute* "test/py/tests/test_sandbox_exit.py"
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 10/28] gnu: python-openid: Remove python-coverage native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-11-ngraves@ngraves.fr

* gnu/packages/python-web.scm (python-openid):

[native-inputs]: Remove python-coverage.

[arguments]<#:phases>: Rewrite check phase.

Change-Id: Id4ea5abc531f5fd84b60ff22407eb608f1e6ac29

---

gnu/packages/python-web.scm | 17 +++++++++--------

1 file changed, 9 insertions(+), 8 deletions(-)

Toggle diff (33 lines)diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 2db955df6f..735073e96f 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -3094,17 +3094,18 @@ (define-public python-openid
          "1bxf9a3ny1js422j962zfzl4a9dhj192pvai05whn7j0iy9gdyrk"))))
     (build-system python-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-        (replace 'check
-          (lambda* (#:key tests? #:allow-other-keys)
-            (when tests?
-              (invoke "coverage" "run" "-m"
-                      "unittest" "openid.test.test_suite")))))))
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (if tests?
+                  (invoke "python" "-m" "unittest" "openid.test.test_suite")
+                  (format #t "test suite not run~%")))))))
     (propagated-inputs
      (list python-defusedxml))
     (native-inputs
-     (list python-coverage python-psycopg2 python-django))
+     (list python-psycopg2 python-django))
     (home-page "https://github.com/necaris/python3-openid")
     (synopsis "OpenID support for servers and consumers")
     (description "This library provides OpenID authentication for Python, both
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 11/28] build-system/pyproject: Remove python-coveralls native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-12-ngraves@ngraves.fr

* gnu/packages/geo.scm (python-cartopy)[native-inputs]: Remove

python-coveralls.

* gnu/packages/graph.scm (python-graphtools,

python-pygsp)[native-inputs]: Remove python-coveralls.

* gnu/packages/python-compression.scm (python-multivolumefile,

python-py7zr)[native-inputs]: Remove python-coveralls.

* gnu/packages/python-science.scm (python-trimesh)[native-inputs]:

Remove python-coveralls.

* gnu/packages/python-web.scm (python-flask-combo-jsonapi)

[native-inputs]: Remove python-coveralls.

* gnu/packages/python-xyz.scm (python-affine, python-cftime,

python-ddlparse, python-tasklogger, python-minikanren)

[native-inputs]: Remove python-coveralls.

* gnu/packages/syndication.scm (rtv, tuir)[native-inputs]: Remove

python-coveralls.

* gnu/packages/telegram.scm (tgcli)[native-inputs]: Remove

python-coveralls.

---

gnu/packages/geo.scm | 3 +--

gnu/packages/graph.scm | 3 +--

gnu/packages/python-compression.scm | 2 --

gnu/packages/python-science.scm | 3 +--

gnu/packages/python-web.scm | 3 +--

gnu/packages/python-xyz.scm | 9 +++------

gnu/packages/syndication.scm | 4 +---

gnu/packages/telegram.scm | 3 +--

8 files changed, 9 insertions(+), 21 deletions(-)

Toggle diff (169 lines)diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 3317271802..a4fa352390 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -1608,8 +1608,7 @@ (define-public python-cartopy
     (inputs
      (list geos))
     (native-inputs
-     (list python-coveralls
-           python-cython
+     (list python-cython
            python-pytest
            python-pytest-cov
            python-pytest-mpl
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 9f91d39194..3ec6180953 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -482,7 +482,6 @@ (define-public python-graphtools
     (native-inputs
      (list util-linux ;for lscpu
            python-anndata
-           python-coveralls
            python-nose
            python-nose2
            python-pandas
@@ -569,7 +568,7 @@ (define-public python-pygsp
                 "")))))))
     (propagated-inputs (list python-numpy python-scikit-image python-scipy))
     (native-inputs
-     (list python-coveralls python-pytest))
+     (list python-pytest))
     (home-page "https://github.com/epfl-lts2/pygsp")
     (synopsis "Graph Signal Processing in Python")
     (description "The PyGSP is a Python package to ease signal processing on
diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm
index dfe819733e..b2e62e1d49 100644
--- a/gnu/packages/python-compression.scm
+++ b/gnu/packages/python-compression.scm
@@ -163,7 +163,6 @@ (define-public python-multivolumefile
     (build-system pyproject-build-system)
     (native-inputs
      (list python-setuptools-scm
-           python-coveralls
            python-hypothesis
            python-pyannotate
            python-pytest
@@ -531,7 +530,6 @@ (define-public python-py7zr
            python-texttable))
     (native-inputs
      (list python-setuptools
-           python-coveralls
            python-libarchive-c
            python-py-cpuinfo
            python-pyannotate
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index fbed7ed83e..bcd0f9e550 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -934,8 +934,7 @@ (define-public python-trimesh
           ;; module 'trimesh' has no attribute '__main__'.
           (delete 'sanity-check))))
     (native-inputs
-     (list python-coveralls
-           python-pyinstrument
+     (list python-pyinstrument
            python-pytest))
     (propagated-inputs
      (list ;; python-cascadio       ; not packed yet, optional
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 735073e96f..52a63157b2 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -9592,8 +9592,7 @@ (define-public python-flask-combo-jsonapi
            python-simplejson
            python-six))
     (native-inputs
-     (list python-coveralls
-           python-pytest
+     (list python-pytest
            python-pytest-runner))
     (home-page "https://github.com/AdCombo/flask-combo-jsonapi")
     (synopsis "Flask extension to quickly create JSON:API 1.0 REST Web APIs")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 9207f479c8..eaca74f0d8 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1303,7 +1303,7 @@ (define-public python-affine
                (base32
                 "1shyvajayyzbkp9dihb4mz835jnkp0kqqbyjfqci6v43da6q2kd2"))))
     (build-system pyproject-build-system)
-    (propagated-inputs (list python-coveralls python-pydocstyle
+    (propagated-inputs (list python-pydocstyle
                              python-pytest python-pytest-cov))
     (native-inputs (list python-flit-core))
     (home-page "https://github.com/rasterio/affine")
@@ -3606,7 +3606,6 @@ (define-public python-cftime
      (list python-numpy))
     (native-inputs
      (list python-check-manifest
-           python-coveralls
            python-cython
            python-pytest-cov
            python-sphinx
@@ -6262,7 +6261,6 @@ (define-public python-ddlparse
     (build-system pyproject-build-system)
     (native-inputs
      (list python-codecov
-           python-coveralls
            python-pytest
            python-pytest-cov
            python-setuptools
@@ -17203,7 +17201,7 @@ (define-public python-tasklogger
         (base32 "1901mibcp6aiyjy8afnybrxnb0dkbdxlbvjqbr3gginlw7dr18xh"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-deprecated))
-    (native-inputs (list python-coveralls python-nose2
+    (native-inputs (list python-nose2
                          python-numpy python-setuptools python-wheel))
     (home-page "https://github.com/scottgigante/tasklogger")
     (synopsis "Extension to the core Python logging library")
@@ -36554,8 +36552,7 @@ (define-public python-minikanren
                         (invoke "python" "-m" "pytest" "-v" "tests/" "kanren/"))
                       #t)))))
     (native-inputs
-     (list python-coveralls
-           python-pydocstyle
+     (list python-pydocstyle
            python-pytest
            python-pytest-cov
            python-pylint
diff --git a/gnu/packages/syndication.scm b/gnu/packages/syndication.scm
index becb3c6bc8..cc94672e9e 100644
--- a/gnu/packages/syndication.scm
+++ b/gnu/packages/syndication.scm
@@ -498,7 +498,6 @@ (define-public rtv
            python-requests python-six))
     (native-inputs
      (list ncurses
-           python-coveralls
            python-mock
            python-pytest
            python-vcrpy))
@@ -540,8 +539,7 @@ (define-public tuir
      (list python-beautifulsoup4 python-decorator python-kitchen
            python-requests python-six))
     (native-inputs
-     (list python-coveralls
-           python-mock
+     (list python-mock
            python-pytest
            python-setuptools
            python-vcrpy
diff --git a/gnu/packages/telegram.scm b/gnu/packages/telegram.scm
index cfcd92fcbc..a4cfc6a9ef 100644
--- a/gnu/packages/telegram.scm
+++ b/gnu/packages/telegram.scm
@@ -839,8 +839,7 @@ (define-public tgcli
                (add-installed-pythonpath inputs outputs)
                (invoke "pytest" "tests")))))))
     (native-inputs
-     `(("coveralls" ,python-coveralls)
-       ("pytest" ,python-pytest)
+     `(("pytest" ,python-pytest)
        ("pytest-click" ,python-pytest-click)
        ("pytest-cov" ,python-pytest-cov)
        ("mkdocs" ,python-mkdocs)
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 06/28] build-system/pyproject: Remove python-coverage input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-7-ngraves@ngraves.fr

* gnu/packages/android.scm (python-androguard):

[native-inputs]: Remove python-coverage.

[arguments]<#:phases>: Adapt 'check phase replacement.

* gnu/packages/astronomy.scm (python-asdf-astropy,

python-poliastro)[native-inputs]: Remove python-coverage.

* gnu/packages/bioinformatics.scm (python-ega-download-client,

python-scikit-bio, python-cooler)[native-inputs]: Remove

python-coverage.

* gnu/packages/check.scm (python-pytest-randomly,

python-pytest-flakes, python-aiounittest)[native-inputs]: Remove

python-coverage.

* gnu/packages/cpp.scm (cpplint)[native-inputs]: Remove

python-coverage.

* gnu/packages/django.scm (python-django-haystack)[native-inputs]:

Remove python-coverage.

* gnu/packages/engineering.scm (python-scikit-rf)[native-inputs]:

Remove python-coverage.

* gnu/packages/geo.scm (python-geopy)[native-inputs]: Remove

python-coverage.

* gnu/packages/gpodder.scm (gpodder)[native-inputs]: Remove

python-coverage.

* gnu/packages/graph.scm (python-graphtools,

python-pygsp)[native-inputs]: Remove python-coverage.

* gnu/packages/jupyter.scm (python-jupyter-packaging)[native-inputs]:

Remove python-coverage.

* gnu/packages/machine-learning.scm (onnx, onnx-optimizer,

python-lightning-utilities, python-pytorch-lightning,

python-torchmetrics, python-gpytorch)[native-inputs]: Remove

python-coverage.

* gnu/packages/music.scm (python-pylast)[native-inputs]: Remove

python-coverage.

* gnu/packages/package-management.scm (python-anaconda-client,

conda)[native-inputs]: Remove python-coverage.

* gnu/packages/python-check.scm (python-vcrpy,

python-re-assert)[native-inputs]: Remove python-coverage.

* gnu/packages/python-compression.scm (python-multivolumefile,

python-pybcj, python-bcj-cffi, python-pyppmd, python-ppmd-cffi,

python-py7zr)[native-inputs]: Remove python-coverage.

* gnu/packages/python-web.scm (python-ovh, python-zope-interface,

python-zope-hookable, python-url, python-transaction, python-sanic,

python-woob, python-flask-combo-jsonapi)[native-inputs]: Remove

python-coverage.

* gnu/packages/python-xyz.scm (python-affine, python-colorful,

python-lunr, python-mdit-py-plugins, python-bidict, python-sh,

python-cftime, python-can, python-jsonargparse, python-pyjwt,

python-virtualenv-clone, python-pikepdf, python-tasklogger,

python-notebook, python-structlog, binwalk, python-argcomplete,

python-attrs, python-yq, python-stone, python-identify,

python-nodeenv, python-forbiddenfruit, python-watchgod, python-eliot,

python-pem, python-scikit-build, python-minikanren, python-verspec,

python-mike) [native-inputs]: Remove python-coverage.

* gnu/packages/simulation.scm (python-dolfin-adjoint)[native-inputs]:

Remove python-coverage.

* gnu/packages/statistics.scm (python-emcee,

python-rpy2)[native-inputs]: Remove python-coverage.

* gnu/packages/syndication.scm (rtv, tuir)[native-inputs]: Remove

python-coverage.

* gnu/packages/terminals.scm (python-halo, python-log-symbols,

python-spinners)[native-inputs]: Remove python-coverage.

* gnu/packages/textutils.scm (python-panflute)[native-inputs]: Remove

python-coverage.

* gnu/packages/version-control.scm (pre-commit)[native-inputs]: Remove

python-coverage.

* gnu/packages/web.scm (python-httpretty)[native-inputs]: Remove

python-coverage.

* gnu/packages/xml.scm (python-xmltodict)[native-inputs]: Remove

python-coverage.

---

gnu/packages/android.scm | 6 +--

gnu/packages/astronomy.scm | 6 +--

gnu/packages/bioinformatics.scm | 8 ++--

gnu/packages/check.scm | 7 ++--

gnu/packages/cpp.scm | 3 +-

gnu/packages/django.scm | 3 +-

gnu/packages/engineering.scm | 3 +-

gnu/packages/gpodder.scm | 3 +-

gnu/packages/graph.scm | 3 +-

gnu/packages/jupyter.scm | 2 +-

gnu/packages/machine-learning.scm | 12 ++----

gnu/packages/music.scm | 3 +-

gnu/packages/package-management.scm | 6 +--

gnu/packages/python-check.scm | 2 +-

gnu/packages/python-compression.scm | 14 ++-----

gnu/packages/python-web.scm | 18 ++++-----

gnu/packages/python-xyz.scm | 57 +++++++++--------------------

gnu/packages/simulation.scm | 1 -

gnu/packages/statistics.scm | 6 +--

gnu/packages/syndication.scm | 4 +-

gnu/packages/terminals.scm | 9 ++---

gnu/packages/textutils.scm | 1 -

gnu/packages/version-control.scm | 1 -

gnu/packages/web.scm | 1 -

gnu/packages/xml.scm | 2 +-

25 files changed, 59 insertions(+), 122 deletions(-)

Toggle diff (392 lines)diff --git a/gnu/packages/android.scm b/gnu/packages/android.scm
index 9c71a4ee47..10845bc40c 100644
--- a/gnu/packages/android.scm
+++ b/gnu/packages/android.scm
@@ -1072,11 +1072,9 @@ (define-public python-androguard
          (replace 'check
            ;; Adapted from .travis.yml
            (lambda _
-             (invoke "nosetests" "--with-coverage" "--with-timer"
-                     "--timer-top-n" "50"))))))
+             (invoke "nosetests" "--with-timer" "--timer-top-n" "50"))))))
     (native-inputs
-     (list python-codecov python-coverage python-mock python-nose
-           python-nose-timer))
+     (list python-codecov python-mock python-nose python-nose-timer))
     (propagated-inputs
      (list python-asn1crypto
            python-colorama
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index f2d5bb2fe9..fa39f3f83a 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1683,8 +1683,7 @@ (define-public python-asdf-astropy
           (add-before 'check 'set-home-env
             (lambda _ (setenv "HOME" "/tmp"))))))
     (native-inputs
-     (list python-coverage
-           python-h5py
+     (list python-h5py
            python-pandas
            python-pytest
            python-pytest-astropy
@@ -4342,8 +4341,7 @@ (define-public python-poliastro
             (lambda _
               (setenv "HOME" "/tmp"))))))
     (native-inputs
-     (list python-coverage
-           python-hypothesis
+     (list python-hypothesis
            python-mypy
            python-flit-core
            python-pytest
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fca21ebd73..0d603ca73e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3592,8 +3592,7 @@ (define-public python-ega-download-client
     (propagated-inputs (list python-htsget python-psutil python-requests
                              python-tqdm python-urllib3))
     (native-inputs
-     (list python-coverage
-           python-mock
+     (list python-mock
            python-pyfakefs
            python-pytest
            python-responses
@@ -6353,7 +6352,7 @@ (define-public python-scikit-bio
            python-requests
            python-scipy))
     (native-inputs
-     (list python-coverage python-pytest))
+     (list python-pytest))
     (home-page "https://scikit-bio.org")
     (synopsis "Data structures, algorithms and educational resources for bioinformatics")
     (description
@@ -19606,8 +19605,7 @@ (define-public python-cooler
            python-scipy
            python-simplejson))
     (native-inputs
-     (list python-coverage
-           python-hatchling
+     (list python-hatchling
            python-isort
            python-pytest
            python-pytest-cov))
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index a46062868a..e9d9b5b9e1 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -1969,8 +1969,7 @@ (define-public python-pytest-randomly
                          "not reordered "
                          "and not test_it_runs_before_stepwise "
                          "and not test_entrypoint_injection"))))))))
-    (native-inputs (list python-coverage
-                         python-factory-boy
+    (native-inputs (list python-factory-boy
                          python-faker
                          python-numpy
                          python-pytest-xdist))
@@ -3204,7 +3203,7 @@ (define-public python-pytest-flakes
              (add-installed-pythonpath inputs outputs)
              (invoke "py.test" "-vv" "-k" "not test_syntax_error"))))))
     (native-inputs
-     (list python-coverage python-pytest python-pytest-pep8))
+     (list python-pytest python-pytest-pep8))
     (propagated-inputs
      (list python-pyflakes))
     (home-page "https://github.com/fschulze/pytest-flakes")
@@ -4200,7 +4199,7 @@ (define-public python-aiounittest
                       #t)))))
     (propagated-inputs (list python-wrapt))
     (native-inputs
-     (list python-coverage python-nose))
+     (list python-nose))
     (home-page
      "https://github.com/kwarunek/aiounittest")
     (synopsis "Test asyncio code more easily")
diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index c8199af9ce..656b68e5bd 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -1347,8 +1347,7 @@ (define-public cpplint
                    (setenv "GUIX_PYTHONPATH"
                            (getenv "TMP_PYTHONPATH")))))))
     (native-inputs
-     (list python-coverage
-           python-pytest
+     (list python-pytest
            python-pytest-cov
            python-pytest-runner
            python-setuptools
diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index 7f481f785a..fcc73c6d88 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -509,8 +509,7 @@ (define-public python-django-haystack
      (list python-django python-packaging))
     ;; (inputs (list gdal)) ; it's optional, tests fail when provided
     (native-inputs
-     (list python-coverage
-           python-dateutil
+     (list python-dateutil
            python-geopy
            python-pysolr
            python-requests
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index d19b58b3e7..8bd5f155d3 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -2827,8 +2827,7 @@ (define-public python-scikit-rf
                              python-pyqtgraph
                              python-qtpy
                              python-scipy))
-    (native-inputs (list python-coverage
-                         python-nbval
+    (native-inputs (list python-nbval
                          python-networkx
                          python-pytest
                          python-pytest-cov
diff --git a/gnu/packages/gpodder.scm b/gnu/packages/gpodder.scm
index c3e1c9b496..57e14ee93f 100644
--- a/gnu/packages/gpodder.scm
+++ b/gnu/packages/gpodder.scm
@@ -65,7 +65,6 @@ (define-public gpodder
     (build-system python-build-system)
     (native-inputs
      (list intltool
-           python-coverage
            python-minimock
            python-pytest
            python-pytest-cov
@@ -169,7 +168,7 @@ (define-public python-mygpoclient
          "05hmjdb73m7vl6lzvh58bnliy4227pv8hprwfka0bg19cnvgpyf5"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-coverage python-minimock python-nose python-pytest))
+     (list python-minimock python-nose python-pytest))
     (arguments
      '(#:phases
        (modify-phases %standard-phases
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 85cb1d6437..9f91d39194 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -482,7 +482,6 @@ (define-public python-graphtools
     (native-inputs
      (list util-linux ;for lscpu
            python-anndata
-           python-coverage
            python-coveralls
            python-nose
            python-nose2
@@ -570,7 +569,7 @@ (define-public python-pygsp
                 "")))))))
     (propagated-inputs (list python-numpy python-scikit-image python-scipy))
     (native-inputs
-     (list python-coverage python-coveralls python-pytest))
+     (list python-coveralls python-pytest))
     (home-page "https://github.com/epfl-lts2/pygsp")
     (synopsis "Graph Signal Processing in Python")
     (description "The PyGSP is a Python package to ease signal processing on
diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm
index d5c298056c..5be51fc425 100644
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -519,7 +519,7 @@ (define-public python-jupyter-packaging
      (list python-deprecation python-packaging python-setuptools
            python-tomlkit python-wheel))
     (native-inputs
-     (list python-pypa-build python-coverage python-pytest
+     (list python-pypa-build python-pytest
            python-pytest-cov python-pytest-mock))
     (home-page "https://jupyter.org")
     (synopsis "Jupyter packaging utilities")
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index b93bfb551f..53eb637ce8 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1591,7 +1591,6 @@ (define args
       (list cmake-minimal
             googletest
             pybind11
-            python-coverage
             python-fb-re2
             python-parameterized
             python-pytest
@@ -1669,8 +1668,7 @@ (define-public onnx-optimizer
                              " and not test_fuse_transpose")))))))))
     (native-inputs
      (append
-      (list cmake-minimal python-pytest python-pytest-runner
-            python-coverage)
+      (list cmake-minimal python-pytest python-pytest-runner)
       (filter
        (lambda (pkg)
          (member (or (%current-target-system)
@@ -5279,8 +5277,7 @@ (define-public python-lightning-utilities
                 "016zikn39apig3y6xyipw34w0w02c73z483radddbf68ivpjgz3r"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage
-           python-setuptools
+     (list python-setuptools
            python-wheel))
     (propagated-inputs
      (list python-importlib-metadata
@@ -5471,7 +5468,6 @@ (define-public python-pytorch-lightning
       (native-inputs
        (list python-aiohttp
              python-cloudpickle
-             python-coverage
              python-flaky
              python-pympler
              python-pytest
@@ -5509,7 +5505,6 @@ (define-public python-torchmetrics
            python-lightning-utilities))
     (native-inputs
      (list python-cloudpickle
-           python-coverage
            python-fire
            python-mir-eval
            python-mypy
@@ -5925,8 +5920,7 @@ (define-public python-gpytorch
                              python-mpmath
                              python-scikit-learn
                              python-scipy))
-    (native-inputs (list python-coverage
-                         python-flake8-print
+    (native-inputs (list python-flake8-print
                          python-nbval
                          python-pytest
                          python-setuptools
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index dc82cfa570..f8c34ff529 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -4225,8 +4225,7 @@ (define-public python-pylast
     ;; https://github.com/pylast/pylast/issues/105
     (arguments '(#:tests? #f))
     (native-inputs
-     (list python-coverage python-pytest python-flaky python-pyyaml
-           python-setuptools-scm))
+     (list python-pytest python-flaky python-pyyaml python-setuptools-scm))
     (home-page "https://github.com/pylast/pylast")
     (synopsis "Python interface to Last.fm and Libre.fm")
     (description "A Python interface to Last.fm and other API-compatible
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index d06df2c55b..f42a6d002b 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -1098,8 +1098,7 @@ (define-public python-anaconda-client
            python-requests
            python-setuptools))
     (native-inputs
-     (list python-coverage
-           python-dateutil
+     (list python-dateutil
            python-freezegun
            python-mock
            python-pillow
@@ -1284,8 +1283,7 @@ (define-public conda
            ;; XXX: This is dragged in by libarchive and is needed at runtime.
            zstd))
     (native-inputs
-     (list python-coverage
-           python-flaky
+     (list python-flaky
            python-pytest-timeout
            python-pytest-xprocess
            python-wheel))
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index fae03b7606..58fc1d296a 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -1573,7 +1573,7 @@ (define-public python-re-assert
            (lambda _
              (invoke "pytest" "-vv"))))))
     (native-inputs
-     (list python-covdefaults python-coverage python-pytest))
+     (list python-covdefaults python-pytest))
     (propagated-inputs
      (list python-regex))
     (home-page "https://github.com/asottile/re-assert")
diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm
index 5b994d408f..dfe819733e 100644
--- a/gnu/packages/python-compression.scm
+++ b/gnu/packages/python-compression.scm
@@ -163,7 +163,6 @@ (define-public python-multivolumefile
     (build-system pyproject-build-system)
     (native-inputs
      (list python-setuptools-scm
-           python-coverage
            python-coveralls
            python-hypothesis
            python-pyannotate
@@ -306,8 +305,7 @@ (define-public python-pybcj
     (build-system pyproject-build-system)
     (propagated-inputs (list python-importlib-metadata))
     (native-inputs
-     (list python-coverage
-           python-hypothesis
+     (list python-hypothesis
            python-pytest
            python-pytest-cov
            python-setuptools-scm
@@ -340,8 +338,7 @@ (define-public python-bcj-cffi
     (propagated-inputs
      (list python-cffi python-toml python-setuptools-scm))
     (native-inputs
-     (list python-setuptools python-coverage python-pytest
-           python-pytest-cov))
+     (list python-setuptools python-pytest python-pytest-cov))
     (home-page "https://github.com/miurahr/bcj-cffi")
     (synopsis "Branch / Call /Jump CFFI library in Python")
     (description "This package provides an implementation of the Branch / Call /
@@ -466,8 +463,7 @@ (define-public python-pyppmd
                 "03w4x26mar0ha73c3v39psn1i0k6xrzwmaxfsxysic73jz99np07"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage
-           python-hypothesis
+     (list python-hypothesis
            python-pytest
            python-pytest-benchmark
            python-pytest-cov
@@ -500,7 +496,6 @@ (define-public python-ppmd-cffi
     (native-inputs
      (list python-hypothesis
            python-setuptools-scm
-           python-coverage
            python-pytest
            python-pytest-cov))
     (home-page "https://github.com/miurahr/ppmd")
@@ -535,8 +530,7 @@ (define-public python-py7zr
            python-pyzstd
            python-texttable))
     (native-inputs
-     (list python-coverage
-           python-setuptools
+     (list python-setuptools
            python-coveralls
            python-libarchive-c
            python-py-cpuinfo
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 8f88693e56..2db955df6f 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1515,8 +1515,7 @@ (define-public python-ovh
     (build-system pyproject-build-system)
     (arguments (list #:tests? #f))      ; XXX: tests require networking
     (propagated-inputs (list python-requests))
-    (native-inputs (list python-coverage
-                         python-isort
+    (native-inputs (list python-isort
                          python-pytest
                          python-pytest-cov
                          python-setuptools
@@ -3767,8 +3766,7 @@ (define-public python-zope-interface
     (build-system python-build-system)
     (arguments '(#:tests? #f))  ; test suite can't find python-zope-testing
     (native-inputs
-     (list python-coverage pytho

This message was truncated. Download the full message here.

Nicolas Graves wrote 1 months ago

[PATCH v3 07/28] gnu: python-cram: Remove python-coverage native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-8-ngraves@ngraves.fr

* gnu/packages/python-xyz.scm (python-cram):
  [native-inputs]: Remove python-coverage.
  [build-system]: Move to pyproject-build-system.
  [arguments]<#:phases>: Adapt check and patch-source phases
  to coverage removal.

Change-Id: I83fafcdcfbc977f9d3e3411d01d23d9a0e120ec6
---
 gnu/packages/python-xyz.scm | 16 ++++------------
 1 file changed, 4 insertions(+), 12 deletions(-)

Toggle diff (36 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 8515060e03..9207f479c8 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -16260,25 +16260,17 @@ (define-public python-cram
                ;; causes the line showing the default shell to break into two
                ;; lines, but the test expects a single line...
                (("env\\['COLUMNS'\\] = '80'")
-                "env['COLUMNS'] = '160'"))
-
-             (substitute* "Makefile"
-               ;; Recent versions of python-coverage have caused the test
-               ;; coverage to decrease (as of version 0.7).  Allow that.
-               (("--fail-under=100")
-                "--fail-under=90"))
-
-             #t))
+                "env['COLUMNS'] = '160'"))))
          (replace 'check
            ;; The test phase uses the built library and executable.
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (add-installed-pythonpath inputs outputs)
              (setenv "PATH" (string-append (getenv "PATH") ":"
                                            (assoc-ref outputs "out") "/bin"))
-             (invoke "make" "test"))))))
-    (build-system python-build-system)
+             (invoke "make" "quicktest"))))))
+    (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage python-setuptools python-wheel which))
+     (list python-setuptools python-wheel which))
     (synopsis "Simple testing framework for command line applications")
     (description
      "Cram is a functional testing framework for command line applications.
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 13/28] gnu: python-re-assert: Remove python-covdefaults native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-14-ngraves@ngraves.fr

* gnu/packages/python-check.scm (python-re-assert):

[native-inputs]: Remove python-covdefaults.

Change-Id: Ib30c58b69aef7f255e5893ae6f9a33bdf41ac85d

---

gnu/packages/python-check.scm | 2 +-

1 file changed, 1 insertion(+), 1 deletion(-)

Toggle diff (15 lines)diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 58fc1d296a..7b12c05926 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -1573,7 +1573,7 @@ (define-public python-re-assert
            (lambda _
              (invoke "pytest" "-vv"))))))
     (native-inputs
-     (list python-covdefaults python-pytest))
+     (list python-pytest))
     (propagated-inputs
      (list python-regex))
     (home-page "https://github.com/asottile/re-assert")
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 14/28] build-system/pyproject: Remove python-codecov native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-15-ngraves@ngraves.fr

* gnu/packages/android.scm (python-androguard)[native-inputs]: Remove

python-codecov.

* gnu/packages/astronomy.scm (python-wiimatch, python-tweakwcs)

[native-inputs]: Remove python-codecov.

* gnu/packages/python-xyz.scm (python-can,

python-ddlparse)[native-inputs]: Remove python-codecov.

---

gnu/packages/android.scm | 2 +-

gnu/packages/astronomy.scm | 9 +++++----

gnu/packages/python-xyz.scm | 4 +---

3 files changed, 7 insertions(+), 8 deletions(-)

Toggle diff (64 lines)diff --git a/gnu/packages/android.scm b/gnu/packages/android.scm
index 10845bc40c..1198e9591d 100644
--- a/gnu/packages/android.scm
+++ b/gnu/packages/android.scm
@@ -1074,7 +1074,7 @@ (define-public python-androguard
            (lambda _
              (invoke "nosetests" "--with-timer" "--timer-top-n" "50"))))))
     (native-inputs
-     (list python-codecov python-mock python-nose python-nose-timer))
+     (list python-mock python-nose python-nose-timer))
     (propagated-inputs
      (list python-asn1crypto
            python-colorama
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index fa39f3f83a..9c7423e521 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -6399,8 +6399,7 @@ (define-public python-tweakwcs
            python-stsci-imagestats
            python-stsci-stimage))
     (native-inputs
-     (list python-codecov
-           python-pytest
+     (list python-pytest
            python-pytest-cov
            python-scipy
            python-setuptools
@@ -6523,8 +6522,10 @@ (define-public python-wiimatch
                 "15kq7z30m9i286ncs9xvpaq3dq1p5fa47jz21prq146qwr7j6dm8"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-numpy python-scipy))
-    (native-inputs (list python-codecov python-pytest python-pytest-cov
-                         python-pytest-doctestplus python-setuptools-scm
+    (native-inputs (list python-pytest
+                         python-pytest-cov
+                         python-pytest-doctestplus
+                         python-setuptools-scm
                          python-wheel))
     (home-page "https://github.com/spacetelescope/wiimatch")
     (synopsis
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index a71eeeb645..50d073724f 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4148,7 +4148,6 @@ (define-public python-can
            python-setuptools))
     (native-inputs
      (list ;; python-canalystii ; Not packed yet
-           python-codecov
            python-future
            python-hypothesis
            python-mock
@@ -6259,8 +6258,7 @@ (define-public python-ddlparse
         (base32 "1nh8m6rxslwk05daxshxmgk41qfp18yynydba49b13l4m8dnh634"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-codecov
-           python-pytest
+     (list python-pytest
            python-pytest-cov
            python-setuptools
            python-tox
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 12/28] build-system/pyproject: Remove python-pycodestyle native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-13-ngraves@ngraves.fr

* gnu/packages/python-science.scm (python-scipy):
[native-inputs]: Remove python-pycodestyle.

* gnu/packages/python-xyz.scm (python-jsonargparse, python-lsp-server,
python-orderedmultidict, python-stem) [native-inputs]: Remove
python-pycodestyle.
---
 gnu/packages/python-science.scm | 1 -
 gnu/packages/python-xyz.scm     | 6 ++----
 2 files changed, 2 insertions(+), 5 deletions(-)

Toggle diff (52 lines)diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index bcd0f9e550..190ccd7f1d 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -416,7 +416,6 @@ (define-public python-scipy
            python-doit
            python-hypothesis
            python-pooch
-           python-pycodestyle
            python-pydevtool
            python-pytest
            python-pytest-cov
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index eaca74f0d8..a71eeeb645 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -5062,7 +5062,6 @@ (define-public python-jsonargparse
            python-typeshed-client))
     (native-inputs
      (list python-attrs
-           python-pycodestyle
            python-pydantic
            python-pytest
            python-pytest-subtests
@@ -8892,7 +8891,6 @@ (define-public python-lsp-server
            python-jedi
            python-lsp-jsonrpc
            python-pluggy
-           python-pycodestyle
            python-pydocstyle
            python-ujson
            python-whatthepatch
@@ -10767,7 +10765,7 @@ (define-public python-orderedmultidict
     (propagated-inputs
      (list python-six))
     (native-inputs
-     (list python-flake8 python-pycodestyle python-setuptools python-wheel))
+     (list python-flake8 python-setuptools python-wheel))
     (home-page "https://github.com/gruns/orderedmultidict")
     (synopsis "Python Ordered Multivalue Dictionary - omdict")
     (description "This package contains a library for ordered multivalue
@@ -23697,7 +23695,7 @@ (define-public python-stem
              (invoke "./run_tests.py" "--unit")
              #t)))))
     (native-inputs
-     (list python-mock python-pycodestyle python-pyflakes))
+     (list python-mock python-pyflakes))
     (home-page "https://stem.torproject.org/")
     (synopsis
      "Python controller library that allows applications to interact with Tor")
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 15/28] build-system/pyproject: Remove python-tox native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-16-ngraves@ngraves.fr

* gnu/packages/django.scm (python-django-extensions)[native-inputs]:

Remove python-tox.

* gnu/packages/logging.scm (tailon)[native-inputs]: Remove python-tox.

* gnu/packages/messaging.scm (python-harmony)[native-inputs]: Remove

python-tox.

* gnu/packages/python-web.scm (python-omnipath,

python-sanic)[native-inputs]: Remove python-tox.

* gnu/packages/python-xyz.scm (python-lunr, python-bidict,

python-jsonargparse, python-ddlparse, python-virtualenv-clone,

python-honcho, python-shshsh, python-ansicolors)[native-inputs]:

Remove python-tox.

* gnu/packages/radio.scm (chirp)[native-inputs]: Remove python-tox.

* gnu/packages/terminals.scm (python-halo, python-log-symbols,

python-spinners)[native-inputs]: Remove python-tox.

---

gnu/packages/django.scm | 1 -

gnu/packages/logging.scm | 2 +-

gnu/packages/messaging.scm | 2 --

gnu/packages/python-web.scm | 2 --

gnu/packages/python-xyz.scm | 18 +++++-------------

gnu/packages/radio.scm | 3 +--

gnu/packages/terminals.scm | 3 ---

7 files changed, 7 insertions(+), 24 deletions(-)

Toggle diff (180 lines)diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index fcc73c6d88..905a889de8 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -268,7 +268,6 @@ (define-public python-django-extensions
     (native-inputs
      (list python-mock
            python-factory-boy
-           python-tox
            python-pytest
            python-pytest-cov
            python-pytest-django
diff --git a/gnu/packages/logging.scm b/gnu/packages/logging.scm
index 9cc28279d7..55a1db4123 100644
--- a/gnu/packages/logging.scm
+++ b/gnu/packages/logging.scm
@@ -159,7 +159,7 @@ (define-public tailon
          "0xkmrivzilsc9wqr8ms67v7399gxnh7pv5687k4rdpdgz4309fwc"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-tox python-wheel))
+     (list python-wheel))
     (inputs
      (list python-pyyaml-5 python-sockjs-tornado python-tornado-http-auth
            python-tornado python-deepmerge))
diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index f6ac865512..e13625c64d 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -3624,8 +3624,6 @@ (define-public python-harmony
                (base32
                 "1bm9xcnzpnpj6rlhbrnl2abwclzl7ivgh1vb5644y9mnhcs489js"))))
     (build-system python-build-system)
-    (native-inputs
-     (list python-tox))
     (inputs
      (list python-librecaptcha python-keyring python-requests))
     (synopsis "Discord account management")
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 52a63157b2..1a73051889 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -2889,7 +2889,6 @@ (define-public python-omnipath
              python-requests-mock
              python-setuptools
              python-setuptools-scm
-             python-tox
              python-wheel))
       (home-page "https://omnipathdb.org/")
       (synopsis "Python client for the OmniPath web service")
@@ -8810,7 +8809,6 @@ (define-public python-sanic
            python-setuptools
            python-slotscheck
            python-towncrier
-           python-tox
            python-types-ujson
            python-uvicorn
            python-wheel))
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 50d073724f..1c0dfe8a41 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1598,8 +1598,7 @@ (define-public python-lunr
      (list python-hatch-fancy-pypi-readme
            python-hatchling
            python-pytest
-           python-pytest-timeout
-           python-tox))
+           python-pytest-timeout))
     (propagated-inputs
      (list python-importlib-metadata python-typing-extensions))
     (home-page
@@ -3234,8 +3233,7 @@ (define-public python-bidict
            python-sortedcollections
            python-sortedcontainers
            python-sphinx
-           python-sphinx-autodoc-typehints
-           python-tox))
+           python-sphinx-autodoc-typehints))
     (arguments
      `(#:phases (modify-phases %standard-phases
                   (add-after 'unpack 'relax-reqs
@@ -5065,7 +5063,6 @@ (define-public python-jsonargparse
            python-pytest
            python-pytest-subtests
            python-responses
-           python-tox
            python-types-requests
            python-setuptools
            python-wheel))
@@ -6261,7 +6258,6 @@ (define-public python-ddlparse
      (list python-pytest
            python-pytest-cov
            python-setuptools
-           python-tox
            python-wheel))
     (propagated-inputs (list python-pyparsing))
     (home-page "https://github.com/shinichi-takii/ddlparse")
@@ -6831,7 +6827,6 @@ (define-public python-virtualenv-clone
                               (delete-file "tox.ini")
                               (invoke "pytest" "-vvv" "tests")))))))
     (native-inputs (list python-pytest
-                         python-tox
                          python-virtualenv
                          python-wheel
                          python-tomli
@@ -12308,7 +12303,7 @@ (define-public python-honcho
         (base32 "1y0r8dw4pqcq7r4n58ixjdg1iy60lp0gxsd7d2jmhals16ij71rj"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-pytest python-mock python-tox which)) ;for tests
+     (list python-pytest python-mock which)) ;for tests
     (propagated-inputs
      (list python-jinja2))
     (arguments
@@ -22628,9 +22623,7 @@ (define-public python-shshsh
          "1wzqyj1a6jj6cyv5ymzy834qm2lyq80yy1kfz0q0zayq9gm1cj7f"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-poetry-core
-           python-pytest
-           python-tox))
+     (list python-poetry-core python-pytest))
     (home-page "https://github.com/zqqqqz2000/shshsh")
     (synopsis "Write Shell commands simply and safely within Python")
     (description "This package provides a way to write Shell commands from
@@ -37789,8 +37782,7 @@ (define-public python-ansicolors
         (base32 "1q3jqglkq4z0f6nkkn8bswcwqg012i2grrc27kabr8286dg4zycr"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-tox
-           python-pytest-cov
+     (list python-pytest-cov
            unzip))
     (home-page "https://github.com/jonathaneunice/colors/")
     (synopsis "ANSI colors for Python")
diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index 417c787144..c05b2b9075 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -3265,8 +3265,7 @@ (define-public chirp
              python-pep8
              python-pytest
              python-pytest-mock
-             python-pyyaml
-             python-tox))
+             python-pyyaml))
       (inputs
        (list python-future
              python-importlib-resources
diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index 590cf2a1e7..b32393c1ec 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -1178,7 +1178,6 @@ (define-public python-halo
     (native-inputs
      (list python-nose
            python-setuptools
-           python-tox
            python-twine
            python-wheel))
     (home-page "https://github.com/manrajgrover/halo")
@@ -1209,7 +1208,6 @@ (define-public python-log-symbols
     (native-inputs
      (list python-nose
            python-setuptools
-           python-tox
            python-wheel))
     (propagated-inputs (list python-colorama))
     (home-page "https://github.com/manrajgrover/py-log-symbols")
@@ -1241,7 +1239,6 @@ (define-public python-spinners
     (native-inputs
      (list python-nose
            python-setuptools
-           python-tox
            python-wheel))
     (home-page "https://github.com/manrajgrover/py-spinners")
     (synopsis "Python library with graphical spinners for the terminal")
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 16/28] build-system/pyproject: Remove python-mypy native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-17-ngraves@ngraves.fr

* gnu/packages/astronomy.scm (python-poliastro)[native-inputs]: Remove

python-mypy.

* gnu/packages/databases.scm (python-psycopg2)[native-inputs]: Remove

python-mypy.

* gnu/packages/engineering.scm (uranium, cura)[native-inputs]: Remove

python-mypy.

* gnu/packages/graphviz.scm (python-uqbar)[native-inputs]: Remove

python-mypy.

* gnu/packages/machine-learning.scm (python-imbalanced-learn,

python-captum, python-torchmetrics)[native-inputs]: Remove python-mypy.

* gnu/packages/python-science.scm (python-scipy)[native-inputs]:

Remove python-mypy.

* gnu/packages/python-web.scm (python-huggingface-hub, python-asgiref,

python-starsessions-for-pytorch-lightning)[native-inputs]:

Remove python-mypy.

* gnu/packages/python-xyz.scm (kalamine, python-pydantic-cli,

python-apispec, python-typeguard, python-verspec,

python-catalogue)[native-inputs]: Remove python-mypy.

* gnu/packages/serialization.scm (python-msgspec)[native-inputs]: Remove

python-mypy.

* gnu/packages/virtualization.scm (python-transient)[native-inputs]:

Remove python-mypy.

---

gnu/packages/astronomy.scm | 1 -

gnu/packages/databases.scm | 1 -

gnu/packages/engineering.scm | 2 --

gnu/packages/graphviz.scm | 1 -

gnu/packages/machine-learning.scm | 3 ---

gnu/packages/python-science.scm | 1 -

gnu/packages/python-web.scm | 6 +++---

gnu/packages/python-xyz.scm | 13 +++++--------

gnu/packages/serialization.scm | 1 -

gnu/packages/virtualization.scm | 3 +--

10 files changed, 9 insertions(+), 23 deletions(-)

Toggle diff (214 lines)diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 9c7423e521..ad9dcffaed 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4342,7 +4342,6 @@ (define-public python-poliastro
               (setenv "HOME" "/tmp"))))))
     (native-inputs
      (list python-hypothesis
-           python-mypy
            python-flit-core
            python-pytest
            python-pytest-cov
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index af5eaed244..24bcb35134 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -4303,7 +4303,6 @@ (define-public python-psycopg
                           "-c" "CREATE DATABASE nixbld;"))))))))
     (native-inputs
      (list python-cython-3
-           python-mypy
            python-psycopg-pool
            python-pytest
            python-pytest-asyncio
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index 8bd5f155d3..67f0d95316 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -4404,7 +4404,6 @@ (define-public uranium
            graphviz
            pkg-config
            python-pytest
-           python-mypy
            python-certifi
            python-twisted))
     (propagated-inputs
@@ -4607,7 +4606,6 @@ (define-public cura
     (build-system qt-build-system)
     (native-inputs
      (list python-certifi
-           python-mypy
            python-pytest
            python-requests))
     (inputs
diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm
index 0d3db31212..6bfe5325ac 100644
--- a/gnu/packages/graphviz.scm
+++ b/gnu/packages/graphviz.scm
@@ -225,7 +225,6 @@ (define-public python-uqbar
     (native-inputs
      (list graphviz
            python-isort
-           python-mypy
            python-pytest
            python-pytest-cov
            python-setuptools
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 53eb637ce8..5d24d3f8f0 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -2148,7 +2148,6 @@ (define-public python-imbalanced-learn
     (propagated-inputs (list python-joblib python-numpy python-scikit-learn
                              python-scipy python-threadpoolctl))
     (native-inputs (list python-keras
-                         python-mypy
                          python-pandas
                          python-pytest
                          python-pytest-cov
@@ -5319,7 +5318,6 @@ (define-public python-captum
                          python-flask-compress
                          python-ipython
                          python-ipywidgets
-                         python-mypy
                          python-parameterized
                          python-pytest
                          python-pytest-cov
@@ -5507,7 +5505,6 @@ (define-public python-torchmetrics
      (list python-cloudpickle
            python-fire
            python-mir-eval
-           python-mypy
            python-pandas
            python-psutil
            python-pytest
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 190ccd7f1d..54160f01c0 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -393,7 +393,6 @@ (define-public python-scipy
            '())
        (list python-matplotlib
              python-mpmath
-             python-mypy
              python-numpy
              python-numpydoc
              python-pydata-sphinx-theme
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 1a73051889..54a31e1bae 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -494,7 +494,6 @@ (define-public python-huggingface-hub
            python-fastapi
            python-jedi
            python-jinja2
-           python-mypy
            python-numpy
            python-pillow
            python-pydantic
@@ -1148,7 +1147,9 @@ (define-public python-asgiref
                (base32 "146mhkn3zp2bqf7j6r3chdlvfzgs5x1lrnqahsllgjdyl20bshy3"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-mypy python-pytest python-pytest-asyncio python-setuptools
+     (list python-pytest
+           python-pytest-asyncio
+           python-setuptools
            python-wheel))
     (home-page "https://github.com/django/asgiref/")
     (synopsis "ASGI specs, helper code, and adapters")
@@ -10200,7 +10201,6 @@ (define-public python-starsessions
            python-starlette))
     (native-inputs
      (list python-httpx
-           python-mypy
            python-poetry-core
            python-pytest
            python-pytest-asyncio
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 1c0dfe8a41..22b41ea4c1 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7414,7 +7414,7 @@ (define-public kalamine
     ;; TODO: Add python-pytest-ruff to native-inputs once it has been
     ;; packaged.
     (native-inputs
-     (list python-hatchling python-mypy python-pytest))
+     (list python-hatchling python-pytest))
     (home-page "https://github.com/OneDeadKey/kalamine")
     (synopsis "Keyboard layout maker")
     (description
@@ -8692,8 +8692,7 @@ (define-public python-pydantic-cli
     (propagated-inputs
      (list python-pydantic))
     (native-inputs
-     (list python-mypy
-           python-pytest))
+     (list python-pytest))
     (home-page "https://github.com/mpkocher/pydantic-cli")
     (synopsis "Turn Pydantic defined data models into CLI tools")
     (description
@@ -26878,7 +26877,6 @@ (define-public python-apispec
     (build-system pyproject-build-system)
     (native-inputs
      (list python-flit-core
-           python-mypy
            python-openapi-spec-validator
            python-pytest))
     (propagated-inputs
@@ -28262,8 +28260,7 @@ (define-public python-typeguard
         (base32 "06y22d1f5dhpyl71wbhsaibig5hvc2v44pw795yb8lxl02fsh8hd"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-mypy
-           python-pytest
+     (list python-pytest
            python-setuptools
            python-setuptools-scm
            python-typing-extensions
@@ -38002,7 +37999,7 @@ (define-public python-verspec
                (base32
                 "07n06wv85fm4vl1ird2mja0823js3x322wgs9gdnq1djjyk4ql64"))))
     (build-system python-build-system)
-    (native-inputs (list python-mypy python-pretend python-pytest))
+    (native-inputs (list python-pretend python-pytest))
     (arguments
      `(#:phases (modify-phases %standard-phases
                   (replace 'check
@@ -38749,7 +38746,7 @@ (define-public python-catalogue
                 "0srdxiil2xys8q1gpc1nvzhvis3a33d8a7amk2i1rlpbg6p36pak"))))
     (build-system python-build-system)
     (native-inputs (list python-pytest))
-    (inputs (list python python-zipp python-typing-extensions python-mypy))
+    (inputs (list python python-zipp python-typing-extensions))
     (home-page "https://github.com/explosion/catalogue")
     (synopsis "Lightweight function registries for your library")
     (description
diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index f77ae9dc16..97951cb510 100644
--- a/gnu/packages/serialization.scm
+++ b/gnu/packages/serialization.scm
@@ -762,7 +762,6 @@ (define-public python-msgspec
     (native-inputs (list python-attrs
                          python-gcovr
                          python-msgpack
-                         python-mypy
                          python-pytest
                          python-setuptools-scm
                          python-versioneer
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index 568b50fcf9..9bde297c1f 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -2972,8 +2972,7 @@ (define-public python-transient
                         (("==")
                          ">=")))))))
     (native-inputs
-     (list python-mypy
-           python-pyhamcrest
+     (list python-pyhamcrest
            python-setuptools
            python-twine
            python-wheel))
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 17/28] gnu: python-immutables: Remove python-mypy native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-18-ngraves@ngraves.fr

* gnu/packages/python-xyz.scm (python-immutables):
  [origin]: Use git-fetch to use upstream test-data directory.
  [native-inputs]: Remove python-mypy.
  [arguments]<#:phases>: Add phase to remove python-mypy native-input.
---
 gnu/packages/python-xyz.scm | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

Toggle diff (32 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 22b41ea4c1..6c1d41c39a 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -17019,13 +17019,22 @@ (define-public python-immutables
     (version "0.21")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "immutables" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/MagicStack/immutables")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32 "0jpw9nr2mbzqykigjhqa3a095bx7krwsnmjcxcpj944p8kqglpxm"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list #:phases #~(modify-phases %standard-phases
+                        (add-after 'unpack 'remove-mypy-dependency
+                          (lambda _
+                            (delete-file "tests/test_mypy.py")
+                            (delete-file "tests/conftest.py"))))))
     (native-inputs
-     (list python-mypy python-pytest python-setuptools python-wheel))
+     (list python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/MagicStack/immutables")
     (synopsis "High-performance immutable mapping type for Python")
     (description
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 18/28] build-system/pyproject: Remove python-isort native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-19-ngraves@ngraves.fr

* gnu/packages/bioinformatics.scm (python-cooler,

scvelo)[native-inputs]: Remove python-isort.

* gnu/packages/databases.scm (aerich)[native-inputs]: Remove

python-isort.

* gnu/packages/finance.scm (python-trezor)[native-inputs]: Remove

python-isort.

* gnu/packages/gettext.scm (mdpo)[native-inputs]: Remove python-isort.

* gnu/packages/graphviz.scm (python-uqbar)[native-inputs]: Remove

python-isort.

* gnu/packages/machine-learning.scm (python-funsor)

[native-inputs]: Remove python-isort.

* gnu/packages/mail.scm (postorius)[native-inputs]: Remove python-isort.

* gnu/packages/protobuf.scm (python-pure-protobuf)[native-inputs]:

Remove python-isort.

* gnu/packages/python-web.scm (python-ovh, python-tinycss2)

[native-inputs]: Remove python-isort.

* gnu/packages/statistics.scm (python-statsmodels)[native-inputs]:

Remove python-isort.

* gnu/packages/virtualization.scm (python-qemu-qmp)[native-inputs]:

Remove python-isort.

---

gnu/packages/bioinformatics.scm | 2 --

gnu/packages/databases.scm | 1 -

gnu/packages/finance.scm | 1 -

gnu/packages/gettext.scm | 1 -

gnu/packages/graphviz.scm | 1 -

gnu/packages/machine-learning.scm | 3 +--

gnu/packages/mail.scm | 2 +-

gnu/packages/protobuf.scm | 2 +-

gnu/packages/python-web.scm | 3 +--

gnu/packages/statistics.scm | 1 -

gnu/packages/virtualization.scm | 1 -

11 files changed, 4 insertions(+), 14 deletions(-)

Toggle diff (148 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0d603ca73e..11494c293a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -19606,7 +19606,6 @@ (define-public python-cooler
            python-simplejson))
     (native-inputs
      (list python-hatchling
-           python-isort
            python-pytest
            python-pytest-cov))
     ;; Almost all the projects of the Mirnylab are moved under Open2C umbrella
@@ -23555,7 +23554,6 @@ (define-public scvelo
     (propagated-inputs
      (list python-anndata
            python-hnswlib
-           python-isort
            python-igraph
            python-loompy
            python-louvain
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 24bcb35134..9f1421135d 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -3457,7 +3457,6 @@ (define-public aerich
      (list poetry
            python-bandit
            python-cryptography
-           python-isort
            python-pydantic
            python-pytest
            python-pytest-asyncio
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index 5cf2db24a2..0df0e41aab 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -1159,7 +1159,6 @@ (define-public python-trezor
            python-typing-extensions))
     (native-inputs ; Only needed for running the tests
      (list protobuf
-           python-isort
            python-pillow
            python-protobuf
            python-pyqt
diff --git a/gnu/packages/gettext.scm b/gnu/packages/gettext.scm
index 29cdbab915..841d3e0c8b 100644
--- a/gnu/packages/gettext.scm
+++ b/gnu/packages/gettext.scm
@@ -228,7 +228,6 @@ (define-public mdpo
      (list python-bump2version
            python-flake8-implicit-str-concat
            python-flake8-print
-           python-isort
            python-pytest
            python-pytest-cov
            python-sphinx
diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm
index 6bfe5325ac..33ddbeba42 100644
--- a/gnu/packages/graphviz.scm
+++ b/gnu/packages/graphviz.scm
@@ -224,7 +224,6 @@ (define-public python-uqbar
 and not test_sphinx_book_text_broken_strict")))
     (native-inputs
      (list graphviz
-           python-isort
            python-pytest
            python-pytest-cov
            python-setuptools
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 5d24d3f8f0..212a6f6288 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -229,8 +229,7 @@ (define-public python-funsor
     (propagated-inputs (list python-makefun python-multipledispatch
                              python-numpy python-opt-einsum
                              python-typing-extensions))
-    (native-inputs (list python-isort
-                         python-nbsphinx
+    (native-inputs (list python-nbsphinx
                          python-pandas
                          python-pillow
                          python-pyro-api
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 73b4c01bd7..f40724226d 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -3833,7 +3833,7 @@ (define-public postorius
      (list python-readme-renderer python-mailmanclient
            python-django python-django-mailman3))
     (native-inputs
-     (list python-beautifulsoup4 python-isort python-mock python-vcrpy))
+     (list python-beautifulsoup4 python-mock python-vcrpy))
     (home-page "https://gitlab.com/mailman/postorius")
     (synopsis "Web user interface for GNU Mailman")
     (description
diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm
index 4f18d1e6e2..b5f853c559 100644
--- a/gnu/packages/protobuf.scm
+++ b/gnu/packages/protobuf.scm
@@ -505,7 +505,7 @@ (define-public python-pure-protobuf
         (base32 "15dp5pvazd0jx4wzzh79080ah7hkpd3axh40al9vhzs2hf3v90hx"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-pytest python-pytest-cov python-isort))
+     (list python-pytest python-pytest-cov))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 54a31e1bae..de0f02c629 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1516,8 +1516,7 @@ (define-public python-ovh
     (build-system pyproject-build-system)
     (arguments (list #:tests? #f))      ; XXX: tests require networking
     (propagated-inputs (list python-requests))
-    (native-inputs (list python-isort
-                         python-pytest
+    (native-inputs (list python-pytest
                          python-pytest-cov
                          python-setuptools
                          python-sphinx
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 89aed7f961..99f5ded8b5 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2669,7 +2669,6 @@ (define-public python-statsmodels
     (native-inputs
      (list python-colorama
            python-cython
-           python-isort
            python-joblib
            python-matplotlib
            python-pytest
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index 9bde297c1f..5bdb0976d7 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -2105,7 +2105,6 @@ (define-public python-qemu-qmp
     (native-inputs
      (list python-avocado-framework
            python-flake8
-           python-isort
            python-pylint
            python-setuptools
            python-setuptools-scm
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 19/28] build-system/pyproject: Remove python-twine native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-20-ngraves@ngraves.fr

* gnu/packages/gettext.scm (mdpo)[native-inputs]: Remove python-twine.

* gnu/packages/machine-learning.scm (python-linear-operator,

python-gpytorch)[native-inputs]: Remove python-twine.

* gnu/packages/python-check.scm (python-testfixtures)[native-inputs]:

Remove python-twine.

* gnu/packages/python-web.scm (python-translation-finder, python-eventlet)

[native-inputs]: Remove python-twine.

* gnu/packages/python-xyz.scm (python-cftime)[native-inputs]: Remove

python-twine.

* gnu/packages/terminals.scm (python-halo)[native-inputs]: Remove

python-twine.

* gnu/packages/virtualization.scm (python-transient)[native-inputs]:

Remove python-twine.

---

gnu/packages/gettext.scm | 1 -

gnu/packages/machine-learning.scm | 6 ++----

gnu/packages/python-check.scm | 2 +-

gnu/packages/python-web.scm | 5 ++---

gnu/packages/python-xyz.scm | 2 --

gnu/packages/terminals.scm | 1 -

gnu/packages/virtualization.scm | 1 -

7 files changed, 5 insertions(+), 13 deletions(-)

Toggle diff (118 lines)diff --git a/gnu/packages/gettext.scm b/gnu/packages/gettext.scm
index 841d3e0c8b..25f4efe1fc 100644
--- a/gnu/packages/gettext.scm
+++ b/gnu/packages/gettext.scm
@@ -233,7 +233,6 @@ (define-public mdpo
            python-sphinx
            python-sphinx-argparse
            python-sphinx-rtd-theme
-           python-twine
            python-yamllint))
     (propagated-inputs
      (list python-polib python-pymd4c))
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 212a6f6288..d90d9a8c96 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -5889,8 +5889,7 @@ (define-public python-linear-operator
     (native-inputs (list python-flake8-print
                          python-pytest
                          python-setuptools
-                         python-setuptools-scm
-                         python-twine))
+                         python-setuptools-scm))
     (home-page "https://github.com/cornellius-gp/linear_operator/")
     (synopsis "Linear operator implementation")
     (description "LinearOperator is a PyTorch package for abstracting away the
@@ -5919,8 +5918,7 @@ (define-public python-gpytorch
     (native-inputs (list python-flake8-print
                          python-nbval
                          python-pytest
-                         python-setuptools
-                         python-twine))
+                         python-setuptools))
     (home-page "https://gpytorch.ai")
     (synopsis "Implementation of Gaussian Processes in PyTorch")
     (description
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 7b12c05926..9899b18efc 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -726,7 +726,7 @@ (define-public python-testfixtures
     (native-inputs
      (list python-pytest python-pytest-cov
            ;;("python-pytest-django" ,python-pytest-django)
-           python-twine python-wheel))
+           python-wheel))
     (synopsis "Tests components for Python")
     (description "Testfixtures is a collection of helpers and mock objects that
 are useful when writing automated tests in Python.")
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index de0f02c629..6e68f8d25a 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -356,8 +356,7 @@ (define-public python-eventlet
     (native-inputs
      (list python-hatch-vcs
            python-hatchling
-           python-pytest
-           python-twine))
+           python-pytest))
     (propagated-inputs
      (list python-dnspython
            python-greenlet
@@ -7356,7 +7355,7 @@ (define-public python-translation-finder
      (list python-chardet python-pathlib2 python-ruamel.yaml python-six))
     (native-inputs
      (list python-codecov python-codacy-coverage python-pytest-cov
-           python-pytest-runner python-twine))
+           python-pytest-runner))
     (home-page "https://weblate.org/")
     (synopsis "Translation file finder for Weblate")
     (description "This package provides a function to find translation file in
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 6c1d41c39a..61f6350bb5 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3607,7 +3607,6 @@ (define-public python-cftime
            python-cython
            python-pytest-cov
            python-sphinx
-           python-twine
            python-wheel))
     (home-page "https://unidata.github.io/cftime/")
     (synopsis "Library for time handling")
@@ -33234,7 +33233,6 @@ (define-public python-eliot
            python-sphinx
            python-sphinx-rtd-theme
            python-testtools
-           python-twine
            python-twisted
            python-wheel))
     (home-page "https://github.com/itamarst/eliot/")
diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index b32393c1ec..0d30ad7838 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -1178,7 +1178,6 @@ (define-public python-halo
     (native-inputs
      (list python-nose
            python-setuptools
-           python-twine
            python-wheel))
     (home-page "https://github.com/manrajgrover/halo")
     (synopsis "Python library to display graphical spinners in the terminal")
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index 5bdb0976d7..bd8b267be9 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -2973,7 +2973,6 @@ (define-public python-transient
     (native-inputs
      (list python-pyhamcrest
            python-setuptools
-           python-twine
            python-wheel))
     (propagated-inputs
      (list python-beautifultable
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 21/28] gnu: python-django-contact-form: Remove python-pytest-cov native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-22-ngraves@ngraves.fr

* gnu/packages/django.scm (python-django-contact-form):

[native-inputs]: Remove python-pytest-cov.

[build-system]: Upgrade to pyproject-build-system.

[arguments]<#:phases>: Remove coverage tests for check phase.

Change-Id: I4d0fc406401b7e923f7efa084dbe8ea3753e50fc

---

gnu/packages/django.scm | 7 ++-----

1 file changed, 2 insertions(+), 5 deletions(-)

Toggle diff (25 lines)diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index b4e6f02fe1..953df30338 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -887,16 +887,13 @@ (define-public python-django-contact-form
               (sha256
                (base32
                 "1my9hkrylckp5vfqg9b0kncrdlxjnwxll56sdciqn4v19i4wbq1y"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
          (replace 'check
            (lambda _
-             (invoke "coverage" "run" "--source" "contact_form"
-                     "runtests.py"))))))
-    (native-inputs
-     (list python-coverage))
+             (invoke "python" "runtests.py"))))))
     (propagated-inputs
      (list python-django))
     (home-page "https://github.com/ubernostrum/django-contact-form")
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 22/28] gnu: python-dateutil: Remove python-pytest-cov native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-23-ngraves@ngraves.fr

* gnu/packages/time.scm (python-dateutil):

[native-inputs]: Remove python-pytest-cov.

[arguments]<#:phases>: Add remove-pytest-cov-dep phase.

Change-Id: Id82a147d6e40383ecc2661ac896b65b858c181e0

---

gnu/packages/time.scm | 18 ++++++++++++------

1 file changed, 12 insertions(+), 6 deletions(-)

Toggle diff (33 lines)diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm
index 6c52f657ac..a1addf93bc 100644
--- a/gnu/packages/time.scm
+++ b/gnu/packages/time.scm
@@ -277,14 +277,20 @@ (define-public python-dateutil
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags '(list  ; avoid freezegun dependency
-                     "--ignore=dateutil/test/test_utils.py"
-                     "--ignore=dateutil/test/test_rrule.py"
-                     ;; XXX: Fails to get timezone from /etc/localtime.
-                     "--ignore=dateutil/test/test_tz.py")))
+      #:test-flags '(list "dateutil/test" "docs"
+                          ;; avoid freezegun dependency
+                          "--ignore=dateutil/test/test_utils.py"
+                          "--ignore=dateutil/test/test_rrule.py"
+                          ;; XXX: Fails to get timezone from /etc/localtime.
+                          "--ignore=dateutil/test/test_tz.py")
+      #:phases #~(modify-phases %standard-phases
+                   (add-after 'unpack 'remove-pytest-cov-dep
+                     (lambda _
+                       (substitute* "dateutil/test/conftest.py"
+                         (("item\\.add_marker\\(pytest\\.mark\\.no_cover\\)")
+                          "pass")))))))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-setuptools
            python-setuptools-scm
            python-wheel))
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 20/28] build-system/pyproject: Remove python-pytest-cov native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-21-ngraves@ngraves.fr

* gnu/packages/astronomy.scm (python-astroml, python-casa-formats-io,

python-cdflib, python-poliastro, python-tweakwcs)[native-inputs]:

Remove python-pytest-cov.

* gnu/packages/audio.scm (python-pysox)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/backup.scm (borgmatic)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/bioinformatics.scm (python-biom-format, python-pyfaidx,

python-cooler, python-screed)[native-inputs]: Remove python-pytest-cov.

* gnu/packages/build-tools.scm (meson-python)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/check.scm (python-pytest-nunit, python-pytest-enabler,

python-pytest-perf, python-pyhamcrest)[native-inputs]: Remove python-pytest-cov.

* gnu/packages/cpp.scm (cpplint)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/dav.scm (vdirsyncer, radicale)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/django.scm (python-django-extensions)[native-inputs]:

Remove python-pytest-cov.

* gnu/packages/embedded.scm (mbed-tools)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/engineering.scm (python-scikit-rf)[native-inputs]:

Remove python-pytest-cov.

* gnu/packages/fontutils.scm (psautohint)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/geo.scm (python-fiona, python-cartopy)[native-inputs]:

Remove python-pytest-cov.

* gnu/packages/gettext.scm (mdpo)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/graphviz.scm (python-graphviz, python-uqbar)

[native-inputs]: Remove python-pytest-cov.

* gnu/packages/jupyter.scm (python-jupyter-packaging,

python-jupyter-server, python-jupyterlite-core, python-ipydatawidgets)

[native-inputs]: Remove python-pytest-cov.

* gnu/packages/machine-learning.scm (python-persim,

python-scikit-learn-extra, python-imbalanced-learn,

python-keras-application, python-keras-preprocessing, python-keras,

python-tensorly, python-pytorch-geometric, python-captum,

python-torchmetrics)[native-inputs]: Remove python-pytest-cov.

* gnu/packages/mastodon.scm (python-mastodon-py)[native-inputs]:

Remove python-pytest-cov.

* gnu/packages/messaging.scm (zulip-term)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/package-management.scm (python-conda-package-handling):

[native-inputs]: Remove python-pytest-cov.

* gnu/packages/patchutils.scm (pwclient)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/protobuf.scm (python-pure-protobuf)[native-inputs]:

Remove python-pytest-cov.

* gnu/packages/python-check.scm (python-testfixtures, python-vcrpy,

python-pytest-filter-subpackage, python-atpublic, python-sybil,

python-vulture)[native-inputs]: Remove python-pytest-cov.

* gnu/packages/python-compression.scm (python-multivolumefile,

python-pybcj, python-bcj-cffi, python-pyppmd, python-ppmd-cffi,

python-py7zr)[native-inputs]: Remove python-pytest-cov.

* gnu/packages/python-crypto.scm (python-trustme)[native-inputs]:

Remove python-pytest-cov.

(python-certauth)[native-inputs]: Remove python-pytest-cov. Add

python-pytest.

* gnu/packages/python-science.scm (python-scipy, python-pandaparallel,

python-pyts, python-usetplot, python-pingouin, python-opt-einsum,

python-salib)[native-inputs]: Remove python-pytest-cov.

* gnu/packages/python-web.scm (python-apiron, python-huggingface-hub,

python-portend, python-aiosignal, python-aiostream, python-ovh,

python-cbor2, python-httplib2, python-cheroot, parfive, python-jose,

python-pyscss, python-mechanicalsoup, python-priority, hypercorn,

python-aioftp, python-oauthlib, python-tinycss, python-cssselect2,

python-httpcore, python-wsgiprox, python-venusian, python-siosocks,

python-zeep, gunicorn)[native-inputs]: Remove python-pytest-cov.

(python-warcio)[native-inputs]: Remove python-pytest-cov. Add

python-pytest.

* gnu/packages/python-xyz.scm (python-apprise, python-janus,

python-logbook, python-affine, python-mdit-py-plugins, python-pint,

python-rasterio, python-bidict, python-can, dosage, python-contourpy,

python-portalocker, python-extension-helpers, python-mizani,

python-cligj, python-ddlparse, python-robotframework-pythonlibcore,

python-lsp-server, python-sparse, python-pikepdf, python-imageio,

python-manimpango, python-importlib-resources, python-jaraco-classes,

python-jaraco-collections, python-jaraco-context,

python-jaraco-functools, python-jaraco-test, python-jaraco-text,

python-ipyparallel, python-three-merge, python-seaborn,

python-sentry-sdk, python-sniffio, python-get-version, python-path,

python-pip-run, python-debugpy, python-notebook, python-cookiecutter,

python-pyqtgraph, python-inflect, python-pymemcache, python-natsort,

python-mwclient, python-flasgger, python-tempora, python-outcome,

python-apscheduler, python-iocapture, python-argh, python-flit,

python-watchdog, python-watchgod, python-cmd2, python-inform,

python-qtsass, python-scikit-build, python-minikanren, python-tablib,

python-ansicolors, python-shtab, python-scooby, dynaconf,

python-pyan3, python-numpydoc, python-loguru, python-multidict)

[native-inputs]: Remove python-pytest-cov.

* gnu/packages/sphinx.scm (python-sphinx-gallery)[native-inputs]:

Remove python-pytest-cov.

* gnu/packages/statistics.scm (python-pymc, python-emcee,

python-rpy2)[native-inputs]: Remove python-pytest-cov.

* gnu/packages/task-management.scm (todoman)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/textutils.scm (python-panflute)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/time.scm (python-arrow, python-tzlocal)[native-inputs]:

Remove python-pytest-cov.

* gnu/packages/vpn.scm (sshuttle)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/web.scm (anonip, python-tibanna)[native-inputs]: Remove

python-pytest-cov.

* gnu/packages/wm.scm (qtile)[native-inputs]: Remove

python-pytest-cov. Add python-coverage.

---

gnu/packages/astronomy.scm | 6 +-

gnu/packages/audio.scm | 2 +-

gnu/packages/backup.scm | 1 -

gnu/packages/bioinformatics.scm | 9 +-

gnu/packages/build-tools.scm | 1 -

gnu/packages/check.scm | 351 +++++++++-------------------

gnu/packages/cpp.scm | 1 -

gnu/packages/dav.scm | 2 -

gnu/packages/django.scm | 1 -

gnu/packages/embedded.scm | 1 -

gnu/packages/engineering.scm | 1 -

gnu/packages/fediverse.scm | 1 -

gnu/packages/fontutils.scm | 1 -

gnu/packages/geo.scm | 3 +-

gnu/packages/gettext.scm | 1 -

gnu/packages/graphviz.scm | 2 -

gnu/packages/jupyter.scm | 7 +-

gnu/packages/machine-learning.scm | 18 +-

gnu/packages/messaging.scm | 4 +-

gnu/packages/package-management.scm | 1 -

gnu/packages/patchutils.scm | 2 +-

gnu/packages/protobuf.scm | 2 +-

gnu/packages/python-check.scm | 8 +-

gnu/packages/python-compression.scm | 9 +-

gnu/packages/python-crypto.scm | 3 +-

gnu/packages/python-science.scm | 16 +-

gnu/packages/python-web.scm | 55 ++---

gnu/packages/python-xyz.scm | 126 +++++-----

gnu/packages/sphinx.scm | 1 -

gnu/packages/statistics.scm | 4 +-

gnu/packages/task-management.scm | 1 -

gnu/packages/textutils.scm | 1 -

gnu/packages/time.scm | 2 -

gnu/packages/vpn.scm | 1 -

gnu/packages/web.scm | 3 +-

gnu/packages/wm.scm | 1 -

36 files changed, 216 insertions(+), 433 deletions(-)

Toggle diff (281 lines)diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index ad9dcffaed..6a1cd27dbd 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1906,7 +1906,7 @@ (define-public python-astroml
              (setenv "HOME" "/tmp"))))))
     (propagated-inputs (list python-astropy python-matplotlib python-numpy
                              python-scikit-learn python-scipy))
-    (native-inputs (list python-pytest-astropy-header python-pytest-cov
+    (native-inputs (list python-pytest-astropy-header python-pytest
                          python-pytest-doctestplus python-pytest-remotedata
                          python-wheel))
     (home-page "https://astroml.org")
@@ -1976,7 +1976,6 @@ (define-public python-casa-formats-io
               (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-pytest-openfiles
            python-setuptools
            python-wheel))
@@ -2050,7 +2049,6 @@ (define-public python-cdflib
      (list python-astropy
            python-hypothesis
            python-pytest
-           python-pytest-cov
            python-pytest-remotedata
            python-setuptools
            python-setuptools-scm
@@ -4344,7 +4342,6 @@ (define-public python-poliastro
      (list python-hypothesis
            python-flit-core
            python-pytest
-           python-pytest-cov
            python-pytest-doctestplus
            python-pytest-mpl
            python-pytest-mypy))
@@ -6399,7 +6396,6 @@ (define-public python-tweakwcs
            python-stsci-stimage))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-scipy
            python-setuptools
            python-setuptools-scm
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 5e9474707c..90aaa34e18 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -6476,7 +6476,7 @@ (define-public python-pysox
       (propagated-inputs
        (list python-numpy python-typing-extensions))
       (native-inputs
-       (list sox python-pytest python-pytest-cov python-soundfile))
+       (list sox python-pytest python-soundfile))
       (home-page "https://github.com/rabitt/pysox")
       (synopsis "Python wrapper around SoX")
       (description "@code{python-pysox} is a wrapper around the @command{sox}
diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index bc449a9591..16cbd0f8e3 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -1375,7 +1375,6 @@ (define-public borgmatic
     (native-inputs
      (list python-flexmock
            python-pytest
-           python-pytest-cov
            python-setuptools
            python-wheel))
     (inputs
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 11494c293a..408236635c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3818,7 +3818,8 @@ (define-public python-biom-format
            ;;python-scikit-bio ;mutually recursive dependency
            python-scipy))
     (native-inputs
-     (list python-cython python-pytest python-pytest-cov
+     (list python-cython
+           python-pytest
            python-wheel))
     (home-page "https://www.biom-format.org")
     (synopsis "Biological Observation Matrix (BIOM) format utilities")
@@ -11301,7 +11302,6 @@ (define-public python-screed
      (list python-importlib-resources
            python-pycodestyle
            python-pytest
-           python-pytest-cov
            python-setuptools
            python-setuptools-scm
            python-setuptools-scm-git-archive
@@ -19555,7 +19555,6 @@ (define-public python-pyfaidx
            python-mock
            python-numpy
            python-pytest
-           python-pytest-cov
            python-wheel))
     (propagated-inputs (list python-setuptools))
     (home-page "http://mattshirley.com")
@@ -19605,9 +19604,7 @@ (define-public python-cooler
            python-scipy
            python-simplejson))
     (native-inputs
-     (list python-hatchling
-           python-pytest
-           python-pytest-cov))
+     (list python-hatchling python-pytest))
     ;; Almost all the projects of the Mirnylab are moved under Open2C umbrella
     (home-page "https://github.com/open2c/cooler")
     (synopsis "Sparse binary format for genomic interaction matrices")
diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm
index 20fd7bafd8..6576fd82a8 100644
--- a/gnu/packages/build-tools.scm
+++ b/gnu/packages/build-tools.scm
@@ -365,7 +365,6 @@ (define-public meson-python
            python-cython-3
            python-gitpython
            python-pytest
-           python-pytest-cov
            python-pytest-mock))
     (home-page "https://github.com/mesonbuild/meson-python")
     (synopsis "Meson-based build backend for Python")
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index e9d9b5b9e1..9ba35bd360 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -1871,245 +1871,128 @@ (define-public python-pytest-nunit
     (arguments (list #:tests? #false)) ;no tests included
     (native-inputs
      (list python-pytest
-           python-pytest-cov
-           python-setuptools
-           python-wheel
-           python-xmlschema))
-    (propagated-inputs
-     (list python-attrs
-           python-pytest))
-    (home-page "https://github.com/pytest-dev/pytest-nunit")
-    (synopsis "Pytest plugin for generating NUnit3 test result XML output")
-    (description
-     "This package provides a pytest plugin for generating NUnit3 test result
-XML output")
-    (license license:expat)))
+           python-setuptools python-wheel python-xmlschema))
+(propagated-inputs (list python-attrs python-pytest)) (home-page
+"https://github.com/pytest-dev/pytest-nunit") (synopsis "Pytest plugin for
+generating NUnit3 test result XML output") (description "This package provides
+a pytest plugin for generating NUnit3 test result XML output") (license
+license:expat)))
 
-(define-public python-pytest-param-files
-  (package
-    (name "python-pytest-param-files")
-    (version "0.3.4")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "pytest_param_files" version))
-              (sha256
-               (base32
-                "0gc9nsqizrjapjnbcs1bdxfcl69dpmwbpd9sssjidgcikm7k433c"))))
-    (build-system pyproject-build-system)
-    (native-inputs (list python-flit-core))
-    (propagated-inputs (list python-pytest))
-    (home-page "https://github.com/chrisjsewell/pytest-param-files")
-    (synopsis "Pytest plugin to parameterize tests from external files")
-    (description "This Pytest plugin enables creating Pytest parametrize
-decorators from external files.")
-    (license license:expat)))
+(define-public python-pytest-param-files (package (name
+"python-pytest-param-files") (version "0.3.4") (source (origin (method
+url-fetch) (uri (pypi-uri "pytest_param_files" version)) (sha256 (base32
+"0gc9nsqizrjapjnbcs1bdxfcl69dpmwbpd9sssjidgcikm7k433c")))) (build-system
+pyproject-build-system) (native-inputs (list python-flit-core))
+(propagated-inputs (list python-pytest)) (home-page
+"https://github.com/chrisjsewell/pytest-param-files") (synopsis "Pytest plugin
+to parameterize tests from external files") (description "This Pytest plugin
+enables creating Pytest parametrize decorators from external files.")
+(license license:expat)))
 
-(define-public python-pytest-random-order
-  (package
-    (name "python-pytest-random-order")
-    (version "1.1.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "pytest-random-order" version))
-       (sha256
-        (base32 "104hww3b86jchk41kjhyycr541pd2dfgqkww6lx5y70z9z9xfwj4"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:test-flags
-      ;; AttributeError: module 'py' has no attribute 'code'.
-      #~(list "-k" (string-append "not test_it_works_with_actual_tests"
-                                  " and not test_failed_first"
-                                  " and not test_doctests"))))
-    (native-inputs
-     (list python-pytest-xdist
-           python-setuptools
-           python-py
-           python-wheel))
-    (propagated-inputs
-     (list python-pytest))
-    (home-page "https://github.com/jbasko/pytest-random-order")
-    (synopsis "Pytest plugin to randomize the order of tests")
-    (description "@code{pytest-random-order} is a Pytest plugin that
-randomizes the order of tests.  This can be useful to detect a test that
-passes just because it happens to run after an unrelated test that leaves the
-system in a favourable state.  The plugin allows user to control the level of
-randomness they want to introduce and to disable reordering on subsets of
-tests.  Tests can be rerun in a specific order by passing a seed value
-reported in a previous test run.")
-    (license license:expat)))
+(define-public python-pytest-random-order (package (name
+"python-pytest-random-order") (version "1.1.1") (source (origin (method
+url-fetch) (uri (pypi-uri "pytest-random-order" version)) (sha256 (base32
+"104hww3b86jchk41kjhyycr541pd2dfgqkww6lx5y70z9z9xfwj4")))) (build-system
+pyproject-build-system) (arguments (list #:test-flags ;; AttributeError:
+module 'py' has no attribute 'code'.  #~(list "-k" (string-append "not
+test_it_works_with_actual_tests" " and not test_failed_first" " and not
+test_doctests")))) (native-inputs (list python-pytest-xdist python-setuptools
+python-py python-wheel)) (propagated-inputs (list python-pytest)) (home-page
+"https://github.com/jbasko/pytest-random-order") (synopsis "Pytest plugin to
+randomize the order of tests") (description "@code{pytest-random-order} is a
+Pytest plugin that randomizes the order of tests.  This can be useful to
+detect a test that passes just because it happens to run after an unrelated
+test that leaves the system in a favourable state.  The plugin allows user to
+control the level of randomness they want to introduce and to disable
+reordering on subsets of tests.  Tests can be rerun in a specific order by
+passing a seed value reported in a previous test run.")  (license
+license:expat)))
 
-(define-public python-pytest-randomly
-  (package
-    (name "python-pytest-randomly")
-    (version "3.11.0")
-    (source (origin
-              (method git-fetch)        ;no tests in pypi archive
-              (uri (git-reference
-                    (url "https://github.com/pytest-dev/pytest-randomly")
-                    (commit version)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1sjgq49g8f8973vhmzrim79b6wz29a765n99azjk1maimqh7mmik"))))
-    (build-system python-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (replace 'check
-            (lambda* (#:key tests? #:allow-other-keys)
-              (when tests?
-                ;; The tests validating ordering fail, as well as as two
-                ;; others, for unknown reasons (see:
-                ;; https://github.com/pytest-dev/pytest-randomly/issues/454).
-                (invoke "pytest" "-vv" "-k"
-                        (string-append
-                         "not reordered "
-                         "and not test_it_runs_before_stepwise "
-                         "and not test_entrypoint_injection"))))))))
-    (native-inputs (list python-factory-boy
-                         python-faker
-                         python-numpy
-                         python-pytest-xdist))
-    (propagated-inputs (list python-importlib-metadata python-pytest))
-    (home-page "https://github.com/pytest-dev/pytest-randomly")
-    (synopsis "Pytest plugin to randomly order tests")
-    (description "This is a Pytest plugin to randomly order tests and control
-Python's @code{random.seed}.")
-    (license license:expat)))
+(define-public python-pytest-randomly (package (name "python-pytest-randomly")
+(version "3.11.0") (source (origin (method git-fetch) ;no tests in pypi
+archive (uri (git-reference (url
+"https://github.com/pytest-dev/pytest-randomly") (commit version))) (file-name
+(git-file-name name version)) (sha256 (base32
+"1sjgq49g8f8973vhmzrim79b6wz29a765n99azjk1maimqh7mmik")))) (build-system
+python-build-system) (arguments (list #:phases #~(modify-phases
+%standard-phases (replace '

This message was truncated. Download the full message here.

Nicolas Graves wrote 1 months ago

[PATCH v3 23/28] build-system/pyproject: Remove python-pytest-isort native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-24-ngraves@ngraves.fr

* gnu/packages/dav.scm (radicale):
  [native-inputs]: Remove python-pytest-isort.
---
 gnu/packages/dav.scm | 1 -
 1 file changed, 1 deletion(-)

Toggle diff (14 lines)diff --git a/gnu/packages/dav.scm b/gnu/packages/dav.scm
index 7688c9a994..ff5d8409b0 100644
--- a/gnu/packages/dav.scm
+++ b/gnu/packages/dav.scm
@@ -59,7 +59,6 @@ (define-public radicale
     (native-inputs
      (list python-pytest
            python-pytest-flake8
-           python-pytest-isort
            python-setuptools
            python-waitress
            python-wheel))
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 24/28] build-system/pyproject: Remove python-pytest-black native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-25-ngraves@ngraves.fr

* gnu/packages/check.scm (python-pytest-perf, python-pytest-enabler)
[native-inputs]: Remove python-pytest-black.

* gnu/packages/python-web.scm (python-portend)[native-inputs]:
Remove python-pytest-black.
---
 gnu/packages/check.scm      |  2 --
 gnu/packages/python-web.scm |  1 -
 gnu/packages/python-xyz.scm | 10 ----------
 3 files changed, 13 deletions(-)

Toggle diff (118 lines)diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 9ba35bd360..720405c100 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2830,7 +2830,6 @@ (define-public python-pytest-enabler
            python-jaraco-functools
            python-toml))
     (native-inputs (list python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-flake8
                          python-pytest-mypy
@@ -3036,7 +3035,6 @@ (define-public python-pytest-perf
                            "and not upstream_url"))))
     (native-inputs
      (list python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-enabler
            python-pytest-flake8
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index f97ccff187..cda6baec2a 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -628,7 +628,6 @@ (define-public python-portend
     (propagated-inputs (list python-tempora))
     ;; TODO: Add python-pytest-ruff to native-inputs once it has been packaged.
     (native-inputs (list python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-enabler
                          python-pytest-mypy
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 1b30eca4c7..136276c257 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -12555,7 +12555,6 @@ (define-public python-importlib-resources
                      (string-append (getcwd) "/_custom_build")))))))
     (native-inputs
      (list python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-enabler
            python-pytest-flake8
@@ -12705,7 +12704,6 @@ (define-public python-jaraco-classes
       #:test-flags '(list "-k" "not project")))
     (native-inputs
      (list python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-flake8
            python-pytest-mypy
@@ -12738,7 +12736,6 @@ (define-public python-jaraco-collections
     ;; TODO: Add python-pytest-ruff to native-inputs once it has been
     ;; packaged.
     (native-inputs (list python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-enabler
                          python-pytest-mypy
@@ -12798,7 +12795,6 @@ (define-public python-jaraco-context
            #:test-flags '(list "-k" "not project")))
     (native-inputs
      (list python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-flake8
            python-pytest-mypy
@@ -12832,7 +12828,6 @@ (define-public python-jaraco-functools
     (native-inputs
      (list python-jaraco-classes
            python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-flake8
            python-pytest-mypy
@@ -12926,7 +12921,6 @@ (define-public python-jaraco-text
     ;; TODO: Add python-pytest-ruff to native-inputs once it has been
     ;; packaged.
     (native-inputs (list python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-enabler
                          python-pytest-mypy
@@ -17732,7 +17726,6 @@ (define-public python-path
                python-packaging
                python-pygments
                python-pytest
-               python-pytest-black
                python-pytest-checkdocs
                python-pytest-enabler
                python-pytest-flake8
@@ -17837,7 +17830,6 @@ (define-public python-pip-run
        (append python-nbformat
                python-pygments
                python-pytest
-               python-pytest-black
                python-pytest-checkdocs
                python-pytest-enabler
                python-pytest-flake8
@@ -22446,7 +22438,6 @@ (define-public python-inflect
     (propagated-inputs (list python-pydantic))
     (native-inputs (list python-pygments
                          python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-enabler
                          python-pytest-flake8
@@ -27634,7 +27625,6 @@ (define-public python-tempora
     (native-inputs
      (list python-freezegun
            python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-enabler
            python-pytest-flake8
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 25/28] build-system/pyproject: Remove python-pytest-flake8 native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-26-ngraves@ngraves.fr

* gnu/packages/check.scm (python-pytest-enabler, python-pytest-perf):

[native-inputs]: Remove python-pytest-flake8.

* gnu/packages/dav.scm (radicale)[native-inputs]: Remove

python-pytest-flake8.

* gnu/packages/python-check.scm (python-pytest-csv):

[arguments]<#:test-flags>: Ignore flake8 test.

[native-inputs]: Remove python-pytest-flake8.

* gnu/packages/python-web.scm (python-mechanicalsoup)[native-inputs]:

Remove python-pytest-flake8.

* gnu/packages/python-xyz.scm (python-importlib-resources,

python-jaraco-classes, python-jaraco-context, python-jaraco-functools,

python-jaraco-packaging, python-jaraco-test, python-path,

python-pip-run, python-tempora, python-cairosvg) [native-inputs]:

Remove python-pytest-flake8.

---

gnu/packages/check.scm | 2 --

gnu/packages/dav.scm | 1 -

gnu/packages/python-check.scm | 5 +++--

gnu/packages/python-web.scm | 3 +--

gnu/packages/python-xyz.scm | 12 +-----------

5 files changed, 5 insertions(+), 18 deletions(-)

Toggle diff (151 lines)diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 720405c100..371736e6b3 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2831,7 +2831,6 @@ (define-public python-pytest-enabler
            python-toml))
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
-                         python-pytest-flake8
                          python-pytest-mypy
                          python-setuptools
                          python-setuptools-scm
@@ -3037,7 +3036,6 @@ (define-public python-pytest-perf
      (list python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools
            python-wheel))
diff --git a/gnu/packages/dav.scm b/gnu/packages/dav.scm
index ff5d8409b0..71d12a0ca1 100644
--- a/gnu/packages/dav.scm
+++ b/gnu/packages/dav.scm
@@ -58,7 +58,6 @@ (define-public radicale
     (build-system pyproject-build-system)
     (native-inputs
      (list python-pytest
-           python-pytest-flake8
            python-setuptools
            python-waitress
            python-wheel))
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index bf621d793f..6069d15b3d 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -651,9 +651,10 @@ (define-public python-pytest-csv
         (base32
          "17518f2fn5l98lyk9p8r7215c1whi61imzrh6ahrmcksr8w0zz04"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list #:test-flags '(list "--ignore=tests/test_flake8.py")))
     (native-inputs
-     (list python-pytest-flake8
-           python-pytest-xdist
+     (list python-pytest-xdist
            python-setuptools
            python-tabulate
            python-wheel))
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index cda6baec2a..9410d162de 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -2227,8 +2227,7 @@ (define-public python-mechanicalsoup
     (propagated-inputs
      (list python-beautifulsoup4 python-lxml python-requests python-six))
     (native-inputs
-     (list python-pytest-flake8
-           python-pytest-httpbin
+     (list python-pytest-httpbin
            python-pytest-mock
            python-pytest-runner
            python-requests-mock
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 136276c257..a6fb05c8b6 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -12557,7 +12557,6 @@ (define-public python-importlib-resources
      (list python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools-57
            python-setuptools-scm))
@@ -12705,7 +12704,6 @@ (define-public python-jaraco-classes
     (native-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools
            python-setuptools-scm
@@ -12796,7 +12794,6 @@ (define-public python-jaraco-context
     (native-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools
            python-setuptools-scm
@@ -12829,7 +12826,6 @@ (define-public python-jaraco-functools
      (list python-jaraco-classes
            python-pytest
            python-pytest-checkdocs
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools
            python-setuptools-scm
@@ -12859,7 +12855,6 @@ (define-public python-jaraco-packaging
     (propagated-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-flake8
            python-rst.linker
            python-setuptools
            python-setuptools-scm
@@ -17728,7 +17723,6 @@ (define-public python-path
                python-pytest
                python-pytest-checkdocs
                python-pytest-enabler
-               python-pytest-flake8
                python-pytest-mypy)))
     (properties (alist-delete 'hidden?
                               (package-properties
@@ -17832,7 +17826,6 @@ (define-public python-pip-run
                python-pytest
                python-pytest-checkdocs
                python-pytest-enabler
-               python-pytest-flake8
                python-pytest-mypy)))
     (properties (alist-delete 'hidden? (package-properties
                                         python-pip-run-bootstrap)))))
@@ -22440,7 +22433,6 @@ (define-public python-inflect
                          python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-flake8
                          python-pytest-mypy
                          ;; For the version number
                          python-setuptools-scm
@@ -27627,7 +27619,6 @@ (define-public python-tempora
            python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-flake8
            python-pytest-freezegun
            python-pytest-mypy
            python-setuptools-scm
@@ -31397,8 +31388,7 @@ (define-public python-cairosvg
      (list python-cairocffi python-cssselect2 python-defusedxml
            python-pillow python-tinycss2))
     (native-inputs
-     (list python-pytest-flake8
-           python-pytest-isort
+     (list python-pytest-isort
            python-pytest-runner
            python-setuptools
            python-wheel))
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 26/28] build-system/pyproject: Remove python-pytest-mypy inputs.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-27-ngraves@ngraves.fr

* gnu/packages/astronomy.scm (python-czml3, python-poliastro)

[native-inputs]: Remove python-pytest-mypy.

* gnu/packages/check.scm (python-pytest-perf)[native-inputs]: Remove

python-pytest-mypy.

* gnu/packages/python-web.scm (python-portend)[native-inputs]: Remove

python-pytest-mypy.

* gnu/packages/python-xyz.scm (python-importlib-resources,

python-jaraco-classes, python-jaraco-collections,

python-jaraco-context, python-jaraco-functools, python-jaraco-test,

python-path, python-pip-run, python-inflect, python-tempora,

python-portalocker)[native-inputs]: Remove python-pytest-mypy.

---

gnu/packages/astronomy.scm | 4 +---

gnu/packages/check.scm | 1 -

gnu/packages/python-web.scm | 1 -

gnu/packages/python-xyz.scm | 15 ++-------------

4 files changed, 3 insertions(+), 18 deletions(-)

Toggle diff (144 lines)diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 6a1cd27dbd..c4d9fef03a 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2204,7 +2204,6 @@ (define-public python-czml3
     (native-inputs
      (list python-astropy-minimal
            python-pytest
-           python-pytest-mypy
            python-setuptools
            python-wheel))
     (propagated-inputs
@@ -4343,8 +4342,7 @@ (define-public python-poliastro
            python-flit-core
            python-pytest
            python-pytest-doctestplus
-           python-pytest-mpl
-           python-pytest-mypy))
+           python-pytest-mpl))
     (propagated-inputs
      (list python-astropy
            python-astroquery
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 371736e6b3..af334f2bf6 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -3036,7 +3036,6 @@ (define-public python-pytest-perf
      (list python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-mypy
            python-setuptools
            python-wheel))
     (propagated-inputs
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 9410d162de..2f7a1af4d5 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -630,7 +630,6 @@ (define-public python-portend
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-mypy
                          python-setuptools
                          python-wheel))
     (home-page "https://github.com/jaraco/portend")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index a6fb05c8b6..7ed8cf2824 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -5523,7 +5523,6 @@ (define-public python-portalocker
                 "0lawjm736vs86wlnxc3qqh37l11z0yx81xq3dmrw33m86kaq2bh3"))))
     (build-system pyproject-build-system)
     (native-inputs (list python-pytest
-                         python-pytest-mypy
                          python-pytest-timeout
                          python-redis
                          python-setuptools
@@ -12557,7 +12556,6 @@ (define-public python-importlib-resources
      (list python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-mypy
            python-setuptools-57
            python-setuptools-scm))
     (propagated-inputs
@@ -12704,7 +12702,6 @@ (define-public python-jaraco-classes
     (native-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-mypy
            python-setuptools
            python-setuptools-scm
            python-wheel))
@@ -12736,7 +12733,6 @@ (define-public python-jaraco-collections
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-mypy
                          python-setuptools
                          python-wheel))
     (home-page "https://github.com/jaraco/jaraco.collections")
@@ -12794,7 +12790,6 @@ (define-public python-jaraco-context
     (native-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-mypy
            python-setuptools
            python-setuptools-scm
            python-wheel))
@@ -12826,7 +12821,6 @@ (define-public python-jaraco-functools
      (list python-jaraco-classes
            python-pytest
            python-pytest-checkdocs
-           python-pytest-mypy
            python-setuptools
            python-setuptools-scm
            python-wheel))
@@ -12918,7 +12912,6 @@ (define-public python-jaraco-text
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-mypy
                          python-setuptools
                          python-wheel))
     (home-page "https://github.com/jaraco/jaraco.text")
@@ -17722,8 +17715,7 @@ (define-public python-path
                python-pygments
                python-pytest
                python-pytest-checkdocs
-               python-pytest-enabler
-               python-pytest-mypy)))
+               python-pytest-enabler)))
     (properties (alist-delete 'hidden?
                               (package-properties
                                python-path-bootstrap)))))
@@ -17825,8 +17817,7 @@ (define-public python-pip-run
                python-pygments
                python-pytest
                python-pytest-checkdocs
-               python-pytest-enabler
-               python-pytest-mypy)))
+               python-pytest-enabler)))
     (properties (alist-delete 'hidden? (package-properties
                                         python-pip-run-bootstrap)))))
 
@@ -22433,7 +22424,6 @@ (define-public python-inflect
                          python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-mypy
                          ;; For the version number
                          python-setuptools-scm
                          python-setuptools
@@ -27620,7 +27610,6 @@ (define-public python-tempora
            python-pytest-checkdocs
            python-pytest-enabler
            python-pytest-freezegun
-           python-pytest-mypy
            python-setuptools-scm
            python-types-freezegun
            python-types-pytz
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 28/28] gnu: python-linear-operator: Remove python-flake8-print native-input

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-29-ngraves@ngraves.fr

* gnu/packages/machine-learning.scm (python-linear-operator):

[native-inputs]: Remove pytest-flake8-print.

Change-Id: Iba2670b47e479c20a3f4ae1c703ad9fe815e3764

---

gnu/packages/machine-learning.scm | 3 +--

1 file changed, 1 insertion(+), 2 deletions(-)

Toggle diff (16 lines)diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index ebea63515c..9faf444225 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -5878,8 +5878,7 @@ (define-public python-linear-operator
                              python-pytorch
                              python-scipy
                              python-typeguard))
-    (native-inputs (list python-flake8-print
-                         python-pytest
+    (native-inputs (list python-pytest
                          python-setuptools
                          python-setuptools-scm))
     (home-page "https://github.com/cornellius-gp/linear_operator/")
-- 
2.48.1

Nicolas Graves wrote 1 months ago

[PATCH v3 27/28] build-system/pyproject: Stop hiding options.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:20250131021009.7499-28-ngraves@ngraves.fr

* gnu/packages/pdf.scm (python-pydyf, weasyprint)[arguments]
<#:test-flags>: Remove arguments hiding coverage options.

* gnu/packages/python-crypto.scm (python-keyring)
[arguments]<#:test-flags>: Remove arguments hiding coverage options.

* gnu/packages/python-web.scm (python-asgi-lifespan,
python-openapi-schema-validator, python-openapi-spec-validator,
python-openapi-core)[arguments]<#:test-flags>: Remove arguments hiding
coverage options.
(python-openapi-schema-validator, python-openapi-spec-validator)
[arguments]<#:phases>: Remove 'remove-coverage-pytest-options phase.
(python-cssselect2)[arguments]: Remove uneeded field.
(python-jsonpickle)[arguments]<#:test-flags>: Remove uneeded
test-flags.

* gnu/packages/python-xyz.scm (python-cattrs)
[arguments]<#:phases>: Remove arguments hiding coverage options.
---
 gnu/packages/pdf.scm           |  6 +-----
 gnu/packages/python-crypto.scm |  1 -
 gnu/packages/python-web.scm    | 34 +++-------------------------------
 gnu/packages/python-xyz.scm    |  4 +---
 4 files changed, 5 insertions(+), 40 deletions(-)

Toggle diff (133 lines)diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm
index f1e72ecc57..a1671e12c1 100644
--- a/gnu/packages/pdf.scm
+++ b/gnu/packages/pdf.scm
@@ -805,9 +805,6 @@ (define-public python-pydyf
        (sha256
         (base32 "18q43g5d9455msipcgd5fvnh8m4a2rz189slzfg80yycjw66rshs"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:test-flags #~'("-c" "/dev/null")))
     (propagated-inputs (list python-pillow))
     (native-inputs
      (list ghostscript
@@ -1669,8 +1666,7 @@ (define-public weasyprint
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags #~(list "-c" "/dev/null"
-                           "-n" (number->string (parallel-job-count)))
+      #:test-flags #~(list "-n" (number->string (parallel-job-count)))
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-library-paths
diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm
index a29d7e4375..b62cc5c7d1 100644
--- a/gnu/packages/python-crypto.scm
+++ b/gnu/packages/python-crypto.scm
@@ -292,7 +292,6 @@ (define-public python-keyring
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags '(list "-c" "/dev/null") ;avoid extra test dependencies
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'check 'workaround-test-failure
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 2f7a1af4d5..695df26396 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1200,8 +1200,7 @@ (define-public python-asgi-lifespan
     (arguments
      (list
       #:test-flags
-      '(list "-c" "/dev/null"           ;ignore coverage-related options
-             "-k"
+      '(list "-k"
              (string-append
               ;; XXX: Some tests fail because of "Exceptions from Trio nursery"
               "not (test_lifespan_manager[trio-None-None-StartupFailed]"
@@ -2176,10 +2175,7 @@ (define-public python-jsonpickle
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags
-      ;; Prevent running the flake8 and black pytest plugins, which only tests
-      ;; style and frequently causes harmless failures.
-      '(list "-o" "addopts=''" "tests")
+      #:test-flags '(list "tests")
       #:phases
       '(modify-phases %standard-phases
          (add-before 'check 'pre-check
@@ -2934,10 +2930,6 @@ (define-public python-openapi-schema-validator
       '(list "-k" "not test_array_prefixitems_invalid")
       #:phases
       #~(modify-phases %standard-phases
-          (add-after 'unpack 'remove-coverage-pytest-options
-            (lambda _
-              (substitute* "pyproject.toml"
-                (("^--cov.*") ""))))
           ;; See https://github.com/python-openapi/openapi-schema-validator/issues/204
           (add-after 'unpack 'relax-requirements
             (lambda _
@@ -2981,13 +2973,7 @@ (define-public python-openapi-spec-validator
      (list
       ;; These tests attempt to fetch resources from the Internet
       #:test-flags '(list "--ignore-glob=tests/integration/validation/**"
-                          "-k" "not example")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'remove-coverage-pytest-options
-            (lambda _
-              (substitute* "pyproject.toml"
-                (("^--cov.*") "")))))))
+                          "-k" "not example")))
     (native-inputs
      (list python-poetry-core
            python-pytest))
@@ -3026,9 +3012,6 @@ (define-public python-openapi-core
      (list
       #:test-flags
       '(list "tests/unit"
-             ;; Ignore Pytest configuration in setup.cfg that adds
-             ;; unwanted flake8 and coverage options.
-             "-c" "/dev/null"
              "-k" "not test_chars_valid")))
     (native-inputs (list python-django
                          python-falcon
@@ -7009,17 +6992,6 @@ (define-public python-cssselect2
        (sha256
         (base32 "1j2fcr217rsvkipsg6zjq03rl64rxnvb5hqqpx0dv58fhspvkywk"))))
     (build-system pyproject-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'disable-linters
-           ;; Their check fails; none of our business.
-           (lambda _
-             (substitute* '("setup.py" "pyproject.toml")
-               (("'pytest-flake8',") "")
-               (("'pytest-isort',") "")
-               (("--flake8") "")
-               (("--isort") "")))))))
     (propagated-inputs
      (list python-tinycss2))
     (native-inputs
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 7ed8cf2824..59def98c44 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -22744,9 +22744,7 @@ (define-public python-cattrs
               (substitute* "pyproject.toml"
                 ;; Fix version string
                 (("dynamic = \\[\"version\"\\]")
-                 (string-append "version = \"" #$version "\""))
-                ;; Just run pytest with no frills
-                (("addopts = \"-l.*") ""))))
+                 (string-append "version = \"" #$version "\"")))))
           ;; XXX Our python-hypothesis package is too old.
           (add-after 'unpack 'compatibility
             (lambda _
-- 
2.48.1

Sharlatan Hellseher wrote 3 weeks ago

[PATCH 00/32] python-team: Remove native inputs

Recipients:(address . 70858@debbugs.gnu.org)(address . ngraves@ngraves.fr)

Message-ID:87ikp6c3ek.fsf@gmail.com

Hi Nocoal,

Me again, patch series fails to apply on python-team branch. May you

include the base commit and send v4 if it's still possible please?

You may clone https://codeberg.org/civodul/guixand open PR there is

it's easer (still in test mode,

https://lists.gnu.org/archive/html/guix-devel/2025-02/msg00313.html).

---

Thanks,

Oleg

Nicolas Graves wrote 2 weeks ago

[PATCH python-team v4 00/52]

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:87zfi9v29x.fsf@ngraves.fr

From 6d16c4ac864ff5a80211ec929561addcce2be564 Mon Sep 17 00:00:00 2001

Nicolas Graves (52):
  gnu: Remove python-pytest-pep8.
  gnu: Remove python-pep8.
  gnu: Add rust-notify-types-1.
  gnu: Add rust-notify-7.
  gnu: python-watchgod: Rename package to python-watchfiles.
  gnu: python-uvicorn: Rename python-watchgod native-input.
  guix: import: pypi: Ignore pypi-ignored-inputs.
  build-system/pyproject: Ignore unwanted pytest flags.
  build-system/pyproject: Remove python-black inputs.
  build-system/pyproject: Remove python-pylint native-input.
  build-system/pyproject: Remove python-flake8 inputs.
  build-system/pyproject: Remove python-coverage input.
  build-system/pyproject: Remove python-coverage native-input.
  build-system/pyproject: Remove python-pytest-black native-input.
  gnu: python-cram: Remove python-coverage native-input.
  gnu: u-boot-tools: Remove python-coverage native-input.
  gnu: python-aiosqlite: Remove python-coverage native-input.
  gnu: python-openid: Remove python-coverage native-input.
  build-system/pyproject: Remove python-coveralls native-input.
  build-system/pyproject: Remove python-pycodestyle native-input.
  gnu: python-re-assert: Remove python-covdefaults native-input.
  build-system/pyproject: Remove python-covdefaults native-input.
  build-system/pyproject: Remove python-codecov native-input.
  build-system/pyproject: Remove python-tox native-input.
  build-system/pyproject: Remove python-mypy native-input.
  gnu: python-immutables: Remove python-mypy native-input.
  build-system/pyproject: Remove python-isort native-input.
  build-system/pyproject: Remove python-twine native-input.
  build-system/pyproject: Remove python-pytest-cov native-input.
  gnu: python-django-contact-form: Remove python-pytest-cov
    native-input.
  gnu: python-dateutil: Remove python-pytest-cov native-input.
  build-system/pyproject: Remove python-pytest-isort native-input.
  build-system/pyproject: Remove python-pytest-flake8 native-input.
  build-system/pyproject: Remove python-pytest-mypy inputs.
  build-system/pyproject: Stop hiding options.
  gnu: python-linear-operator: Remove python-flake8-print native-input
  gnu: multidict: Remove python-pytest-cov native-input.
  gnu: python-isort: Remove python-black native-input.
  build-system/pyproject: Remove python-mypy native-input.
  build-system/pyproject: Add option #:use-pytest-plugin?
  gnu: python-pixell: Update to 0.28.1.
  build-system/pyproject: Remove python-check-manifest native-input.
  build-system/pyproject: Remove python-mypy-extensions native-input.
  gnu: python-matrix-nio: Remove python-mypy-extension native-input.
  build-system/pyproject: Remove python-pip native-input.
  build-system/pyproject: Remove python-pre-commit native-input.
  gnu: python-django-ldap: Remove uneeded native-inputs.
  gnu: python-docstring-to-markdown: Remove uneeded native-inputs.
  gnu: python-translation-finder: Remove python coverage native-inputs.
  gnu: python-pymanopt: Remove python-flake8-bugbear native-input.
  gnu: python-loguru: Remove python-pytest-mypy-plugins.
  gnu: gunicorn: Migrate 'check phase to pyproject-build-system.

 gnu/local.mk                                  |   1 +
 gnu/packages/android.scm                      |   6 +-
 gnu/packages/astronomy.scm                    |  41 +-
 gnu/packages/audio.scm                        |   5 +-
 gnu/packages/backup.scm                       |   1 -
 gnu/packages/bioinformatics.scm               |  59 +-
 gnu/packages/bootloaders.scm                  |  17 +-
 gnu/packages/build-tools.scm                  |   1 -
 gnu/packages/check.scm                        |  57 +-
 gnu/packages/cpp.scm                          |   4 +-
 gnu/packages/crates-io.scm                    |  68 +-
 gnu/packages/databases.scm                    |  13 +-
 gnu/packages/dav.scm                          |   4 -
 gnu/packages/debug.scm                        |   2 +-
 gnu/packages/django.scm                       |  23 +-
 gnu/packages/ebook.scm                        |   1 -
 gnu/packages/embedded.scm                     |   1 -
 gnu/packages/engineering.scm                  |   7 +-
 gnu/packages/fediverse.scm                    |   1 -
 gnu/packages/finance.scm                      |   9 +-
 gnu/packages/fontutils.scm                    |   1 -
 gnu/packages/games.scm                        |   1 -
 gnu/packages/geo.scm                          |   7 +-
 gnu/packages/gettext.scm                      |   4 -
 gnu/packages/gnome.scm                        |   1 -
 gnu/packages/gpodder.scm                      |   4 +-
 gnu/packages/graph.scm                        |   6 +-
 gnu/packages/graphviz.scm                     |   5 -
 gnu/packages/jupyter.scm                      |  24 +-
 gnu/packages/logging.scm                      |   2 +-
 gnu/packages/machine-learning.scm             |  70 +--
 gnu/packages/mail.scm                         |   2 -
 gnu/packages/maths.scm                        |   1 -
 gnu/packages/matrix.scm                       |   4 -
 gnu/packages/messaging.scm                    |   6 +-
 gnu/packages/mp3.scm                          |   3 +-
 gnu/packages/music.scm                        |   9 +-
 gnu/packages/networking.scm                   |   2 +-
 gnu/packages/openstack.scm                    |   7 +-
 gnu/packages/package-management.scm           |   8 +-
 ...-pixell-avoid-dependency-propagation.patch |  17 +
 gnu/packages/patchutils.scm                   |   2 +-
 gnu/packages/pdf.scm                          |   6 +-
 gnu/packages/potassco.scm                     |   3 +-
 gnu/packages/protobuf.scm                     |   4 +-
 gnu/packages/python-check.scm                 |  40 +-
 gnu/packages/python-compression.scm           |  25 +-
 gnu/packages/python-crypto.scm                |   6 +-
 gnu/packages/python-science.scm               |  39 +-
 gnu/packages/python-web.scm                   | 225 ++-----
 gnu/packages/python-xyz.scm                   | 587 ++++++------------
 gnu/packages/radio.scm                        |   4 +-
 gnu/packages/rdf.scm                          |   4 +-
 gnu/packages/serialization.scm                |   1 -
 gnu/packages/shells.scm                       |   1 -
 gnu/packages/simulation.scm                   |   3 -
 gnu/packages/sphinx.scm                       |   2 -
 gnu/packages/statistics.scm                   |  18 +-
 gnu/packages/syndication.scm                  |   8 +-
 gnu/packages/task-management.scm              |   1 -
 gnu/packages/telegram.scm                     |   4 +-
 gnu/packages/terminals.scm                    |  16 +-
 gnu/packages/textutils.scm                    |   4 -
 gnu/packages/time.scm                         |  23 +-
 gnu/packages/version-control.scm              |   2 -
 gnu/packages/virtualization.scm               |   7 +-
 gnu/packages/vpn.scm                          |   2 -
 gnu/packages/web.scm                          |   8 +-
 gnu/packages/wm.scm                           |   2 -
 gnu/packages/xml.scm                          |   2 +-
 guix/build-system/pyproject.scm               |   2 +
 guix/build/pyproject-build-system.scm         | 102 ++-
 guix/import/pypi.scm                          |  21 +-
 guix/lint.scm                                 |  10 +-
 tests/pypi.scm                                |   3 +-
 75 files changed, 630 insertions(+), 1062 deletions(-)
 create mode 100644 gnu/packages/patches/python-pixell-avoid-dependency-propagation.patch

-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH python-team v4 01/52] gnu: Remove python-pytest-pep8.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:87mse98kwv.fsf@ngraves.fr

This package is outdated.

* gnu/packages/check.scm (python-pytest-pep8): Delete variable.
(python-pytest-flakes)[native-inputs]: Remove python-pytest-pep8.
* gnu/packages/machine-learning.scm (python-keras,
python-keras-applications)[native-inputs]: Remove python-pytest-pep8.
* gnu/packages/python-science.scm (python-opt-einsum)[native-inputs]:
Remove python-pytest-pep8.
---
 gnu/packages/check.scm            | 35 +------------------------------
 gnu/packages/machine-learning.scm |  3 +--
 gnu/packages/python-science.scm   |  2 +-
 3 files changed, 3 insertions(+), 37 deletions(-)

Toggle diff (95 lines)diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 98f950142d..a0388da61d 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -3087,39 +3087,6 @@ (define-public python-pytest-mypy-testing
 expression this allows you to check mypys type interference.")
     (license (list license:expat license:asl2.0))))
 
-(define-public python-pytest-pep8
-  (package
-    (name "python-pytest-pep8")
-    (version "1.0.6")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "pytest-pep8" version))
-              (sha256
-               (base32
-                "06032agzhw1i9d9qlhfblnl3dw5hcyxhagn7b120zhrszbjzfbh3"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:tests? #f ; Fails with recent pytest and pep8. See upstream issues #8 and #12.
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-dependencies
-           (lambda _
-             (substitute* "setup.py"
-               (("'pytest-cache', ") ""))))  ; Included in recent pytest
-         (replace 'check
-            (lambda* (#:key tests? inputs outputs #:allow-other-keys)
-              (when tests?
-                (add-installed-pythonpath inputs outputs)
-                (invoke "pytest" "-v")))))))
-    (native-inputs
-     (list python-pytest))
-    (propagated-inputs
-     (list python-pep8))
-    (home-page "https://bitbucket.org/pytest-dev/pytest-pep8")
-    (synopsis "Py.test plugin to check PEP8 requirements")
-    (description "Pytest plugin for checking PEP8 compliance.")
-    (license license:expat)))
-
 (define-public python-pytest-perf
   (package
     (name "python-pytest-perf")
@@ -3198,7 +3165,7 @@ (define-public python-pytest-flakes
              (add-installed-pythonpath inputs outputs)
              (invoke "py.test" "-vv" "-k" "not test_syntax_error"))))))
     (native-inputs
-     (list python-coverage python-pytest python-pytest-pep8))
+     (list python-coverage python-pytest))
     (propagated-inputs
      (list python-pyflakes))
     (home-page "https://github.com/fschulze/pytest-flakes")
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 9cda6fe943..59a8445f23 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -3904,7 +3904,7 @@ (define-public python-keras-applications
     (propagated-inputs
      (list python-h5py python-numpy))
     (native-inputs
-     (list python-pytest python-pytest-cov python-pytest-pep8
+     (list python-pytest python-pytest-cov
            python-pytest-xdist))
     (home-page "https://github.com/keras-team/keras-applications")
     (synopsis "Reference implementations of popular deep learning models")
@@ -4074,7 +4074,6 @@ (define-public python-keras
            python-pandas
            python-pytest
            python-pytest-cov
-           python-pytest-pep8
            python-pytest-timeout
            python-pytest-xdist
            python-pyux
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 30e2c9ba61..844bddf3ce 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -3815,7 +3815,7 @@ (define-public python-opt-einsum
              (when tests?
                (invoke "pytest" "-vv")))))))
     (propagated-inputs (list python-numpy))
-    (native-inputs (list python-pytest python-pytest-cov python-pytest-pep8))
+    (native-inputs (list python-pytest python-pytest-cov))
     (home-page "https://github.com/dgasmith/opt_einsum")
     (synopsis "Optimizing numpys einsum function")
     (description
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Nicolas Graves wrote 2 weeks ago

[PATCH python-team v4 02/52] gnu: Remove python-pep8.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:87ldtt8kwc.fsf@ngraves.fr

* gnu/packages/python-xyz.scm (python-pep8): Delete variable.
(python-shortuuid, python-cliapp, python-ttystatus)[native-inputs]:
Remove python-pep8.
* gnu/packages/gnome.scm (d-feet)[native-inputs]: Remove python-pep8.
* gnu/packages/radio.scm (chirp)[native-inputs]: Remove python-pep8.
---
 gnu/packages/gnome.scm      |  1 -
 gnu/packages/python-xyz.scm | 29 ++---------------------------
 gnu/packages/radio.scm      |  1 -
 3 files changed, 2 insertions(+), 29 deletions(-)

Toggle diff (93 lines)diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 1e8d813682..e2d2013f47 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -7398,7 +7398,6 @@ (define-public d-feet
            itstool
            libxml2
            pkg-config
-           python-pep8
            xorg-server-for-tests))
     (inputs
      (list bash-minimal
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 2063dceeea..38612df7c5 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3235,8 +3235,6 @@ (define-public python-shortuuid
         (base32
          "1f8i4zwj5vmpzbz6b17bljy4399gx5aq7vsyw63sz2qgyjcd73yh"))))
     (build-system python-build-system)
-    (native-inputs
-     (list python-pep8))
     (home-page "https://github.com/skorokithakis/shortuuid")
     (synopsis "Generator library for concise, unambiguous and URL-safe UUIDs")
     (description
@@ -15746,29 +15744,6 @@ (define-public python-sentry-sdk
 application monitoring and error tracking software.")
     (license license:bsd-2)))
 
-(define-public python-pep8
-  ;; This package has been renamed to ‘pycodestyle’ and is no longer updated.
-  ;; Its last release (1.7.1) adds only a scary warning to this effect, breaking
-  ;; some dependents' test suites, and nothing more.
-  (package
-    (name "python-pep8")
-    (version "1.7.0")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "pep8" version))
-        (sha256
-          (base32
-           "002rkl4lsn6x2mxmf8ar00l0m8i3mzrc6pnzz77blyksmpsxa4x1"))
-        (patches (search-patches "python-pep8-stdlib-tokenize-compat.patch"))))
-    (build-system python-build-system)
-    (home-page "https://pep8.readthedocs.org/")
-    (synopsis "Python style guide checker")
-    (description
-     "This tools checks Python code against some of the style conventions in
-PEP 8.")
-    (license license:expat)))
-
 (define-public python-pep8-naming
   (package
     (name "python-pep8-naming")
@@ -25902,7 +25877,7 @@ (define-public python-cliapp
        ;; fails due to deprecation warnings, etc.
        #:tests? #f))
     (native-inputs
-     (list python-coverage-test-runner python-pep8))
+     (list python-coverage-test-runner))
     (propagated-inputs
      (list python-pyaml))
     (home-page "https://liw.fi/cliapp/")
@@ -25928,7 +25903,7 @@ (define-public python-ttystatus
        (file-name (git-file-name name version))))
     (build-system python-build-system)
     (native-inputs
-     (list python-coverage-test-runner python-pep8))
+     (list python-coverage-test-runner))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index cda2f1907c..d2c8bee76b 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -3272,7 +3272,6 @@ (define-public chirp
       (native-inputs
        (list python-mock
              python-mox3
-             python-pep8
              python-pytest
              python-pytest-mock
              python-pyyaml
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Nicolas Graves wrote 3 weeks ago

[PATCH python-team v4 03/52] gnu: Add rust-notify-types-1.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:87jz9d8kw1.fsf@ngraves.fr

* gnu/packages/crates-io.scm (rust-notify-types-1): New variable.

---

gnu/packages/crates-io.scm | 23 +++++++++++++++++++++++

1 file changed, 23 insertions(+)

Toggle diff (42 lines)diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm
index 3429e5488a..8e8f803943 100644
--- a/gnu/packages/crates-io.scm
+++ b/gnu/packages/crates-io.scm
@@ -47517,6 +47517,29 @@ (define-public rust-notify-rust-4
 Rust dbus client and server.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-notify-types-1
+  (package
+    (name "rust-notify-types")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "notify-types" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "0x5idrpxzf70ng88rz28dqmgx1jyddf0vxx1x3csw09fw6skqpaq"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-instant" ,rust-instant-0.1)
+                       ("rust-serde" ,rust-serde-1))
+       #:cargo-development-inputs (("rust-insta" ,rust-insta-1)
+                                   ("rust-rstest" ,rust-rstest-0.21)
+                                   ("rust-serde-json" ,rust-serde-json-1))))
+    (home-page "https://github.com/notify-rs/notify")
+    (synopsis "Types used by the notify crate")
+    (description "This package provides rust types used by the notify crate.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-notmuch-0.8
   (package
     (name "rust-notmuch")
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Nicolas Graves wrote 3 weeks ago

[PATCH python-team v4 04/52] gnu: Add rust-notify-7.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:87ikox8kvr.fsf@ngraves.fr

* gnu/packages/crates-io.scm (rust-notify-7): New variable.
(rust-notify-6): Inherit from rust-notify-7.
---
 gnu/packages/crates-io.scm | 45 ++++++++++++++++++++++++++++++++------
 1 file changed, 38 insertions(+), 7 deletions(-)

Toggle diff (80 lines)diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm
index 8e8f803943..bc89fd5afb 100644
--- a/gnu/packages/crates-io.scm
+++ b/gnu/packages/crates-io.scm
@@ -47322,8 +47322,45 @@ (define-public rust-normpath-0.2
         ("rust-rustversion" ,rust-rustversion-1)
         ("rust-tempfile" ,rust-tempfile-3))))))
 
+(define-public rust-notify-7
+  (package
+    (name "rust-notify")
+    (version "7.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "notify" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "02a0a1n0raxqslwhfprwmz7w34v54r42006q0m8bmy89jz1v8cy5"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list
+      #:cargo-inputs (list rust-bitflags-2
+                           rust-crossbeam-channel-0.5
+                           rust-filetime-0.2
+                           rust-fsevent-sys-4
+                           rust-inotify-0.10
+                           rust-kqueue-1
+                           rust-libc-0.2
+                           rust-log-0.4
+                           rust-mio-1
+                           rust-notify-types-1
+                           rust-walkdir-2
+                           rust-windows-sys-0.52)
+      #:cargo-development-inputs (list rust-insta-1
+                                       rust-nix-0.27
+                                       rust-serde-json-1
+                                       rust-tempfile-3)))
+    (home-page "https://github.com/notify-rs/notify")
+    (synopsis "Cross-platform filesystem notification library")
+    (description "This package contains a cross-platform filesystem
+notification library.")
+    (license license:cc0)))
+
 (define-public rust-notify-6
   (package
+    (inherit rust-notify-7)
     (name "rust-notify")
     (version "6.1.1")
     (source
@@ -47333,7 +47370,6 @@ (define-public rust-notify-6
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32 "0bad98r0ilkhhq2jg3zs11zcqasgbvxia8224wpasm74n65vs1b2"))))
-    (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs (("rust-bitflags" ,rust-bitflags-2)
                        ("rust-crossbeam-channel" ,rust-crossbeam-channel-0.5)
@@ -47349,12 +47385,7 @@ (define-public rust-notify-6
                        ("rust-windows-sys" ,rust-windows-sys-0.48))
        #:cargo-development-inputs (("rust-nix" ,rust-nix-0.23)
                                    ("rust-serde-json" ,rust-serde-json-1)
-                                   ("rust-tempfile" ,rust-tempfile-3))))
-    (home-page "https://github.com/notify-rs/notify")
-    (synopsis "Cross-platform filesystem notification library")
-    (description "This package contains a cross-platform filesystem
-notification library.")
-    (license license:cc0)))
+                                   ("rust-tempfile" ,rust-tempfile-3))))))
 
 (define-public rust-notify-5
   (package
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Nicolas Graves wrote 3 weeks ago

[PATCH python-team v4 05/52] gnu: python-watchgod: Rename package to python-watchfiles.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:87h64h8kvf.fsf@ngraves.fr

* gnu/packages/python-xyz.scm (python-watchgod): Define in terms of
'deprecated-package'.
[version]: Update to 1.0.4.
[build-system]: Switch to cargo-build-system.
[arguments]: Likewise.
[native-inputs]: Add maturin, python-dirty-equals,
python-pytest-timeout, python-wrapper. Remove python-pygments,
python-pytest-sygar, python-setuptools and python-wheel.
(python-watchfiles): New variable, formerly known as
"python-watchgod".
---
 gnu/packages/python-xyz.scm | 61 +++++++++++++++++++++++++------------
 1 file changed, 41 insertions(+), 20 deletions(-)

Toggle diff (107 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 38612df7c5..252c13ee13 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -300,6 +300,7 @@ (define-module (gnu packages python-xyz)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xdisorg)
   #:use-module (gnu packages xorg)
+  #:use-module (guix deprecation)
   #:use-module (guix packages)
   #:use-module (guix build-system cargo)
   #:use-module (guix build-system cmake)
@@ -32628,39 +32629,56 @@ (define-public python-watchdog
 but portable.")
     (license license:asl2.0)))
 
-(define-public python-watchgod
+(define-public python-watchfiles
   (package
-    (name "python-watchgod")
-    (version "0.8.1")
+    (name "python-watchfiles")
+    (version "1.0.4")
     (source
      (origin
        ;; There are no tests in the PyPI tarball.
        (method git-fetch)
        (uri (git-reference
-             (url "https://github.com/samuelcolvin/watchgod")
+             (url "https://github.com/samuelcolvin/watchfiles")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0zm9xd2qf3d74l67yv8j3zhhhvi0vp25vhkg46l9d7flh9m04qrp"))))
-    (build-system pyproject-build-system)
+        (base32 "1kaxq0drjwlvcsg4in25w1bhjjgm1zlz06rr2macyi6s5x96g46h"))))
+    (build-system cargo-build-system)
     (arguments
-     (list #:test-flags '(list "-o" "asyncio_mode=auto"
-                               ;; PytestUnraisableExceptionWarning
-                               "-k" "not test_watch_log and not test_awatch")
-       #:phases #~(modify-phases %standard-phases
-                  (delete 'sanity-check))))
+     (list
+      #:install-source? #f
+      #:imported-modules `(,@%cargo-build-system-modules
+                           ,@%pyproject-build-system-modules)
+      #:modules '((guix build cargo-build-system)
+                  ((guix build pyproject-build-system) #:prefix py:)
+                  (guix build utils))
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'build
+            (assoc-ref py:%standard-phases 'build))
+          (add-after 'build 'install-rust-library
+            (lambda _
+              (copy-file "target/release/lib_rust_notify.so"
+                         "watchfiles/_rust_notify.so")))
+          (replace 'check
+            (lambda* (#:key tests? test-flags #:allow-other-keys)
+              (if tests?
+                  ;; Missing file in source.
+                  (invoke "pytest" "-vv" "-k" "not test_docs_examples")
+                  (format #t "test suite not run~%"))))
+          (replace 'install
+            (assoc-ref py:%standard-phases 'install)))
+      #:cargo-inputs
+      (list rust-crossbeam-channel-0.5 rust-notify-7 rust-pyo3-0.23)))
     (native-inputs
-     (list python-anyio
-           python-coverage
-           python-pygments
+     (list maturin
+           python-anyio
+           python-dirty-equals
            python-pytest
-           python-pytest-asyncio
-           python-pytest-cov
            python-pytest-mock
-           python-pytest-sugar
-           python-setuptools
-           python-wheel))
-    (home-page "https://github.com/samuelcolvin/watchgod")
+           python-pytest-timeout
+           python-wrapper))
+    (home-page "https://github.com/samuelcolvin/watchfiles")
     (synopsis "Simple, modern file watching and code reload in Python")
     (description
      "Simple, modern file watching and code reload in Python inspired by
@@ -32668,6 +32686,9 @@ (define-public python-watchgod
 operating systems and an elegant approach to concurrency using threading.")
     (license license:expat)))
 
+(define-deprecated/alias python-watchgod python-watchfiles)
+(export python-watchgod)
+
 (define-public python-wget
   (package
     (name "python-wget")
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Nicolas Graves wrote 3 weeks ago

[PATCH python-team v4 06/52] gnu: python-uvicorn: Rename python-watchgod native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:87frk18kue.fsf@ngraves.fr

* gnu/packages/python-web.scm (python-uvicorn)[native-inputs]: Rename
python-watchgod to python-watchfiles. Add python-a2wsgi.
---
 gnu/packages/python-web.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

Toggle diff (29 lines)diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index e6918a530e..5ea9e5a709 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -7439,13 +7439,14 @@ (define-public python-uvicorn
            python-trustme
            python-wsproto))
     (propagated-inputs
-     (list python-click
+     (list python-a2wsgi
+           python-click
            python-dotenv
            python-h11
            python-httptools
            python-pyyaml
            python-uvloop
-           python-watchgod
+           python-watchfiles
            python-websockets))
     (home-page "https://github.com/encode/uvicorn")
     (synopsis "Fast ASGI server implementation")
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Nicolas Graves wrote 9 months ago

[PATCH python-team v4 07/52] guix: import: pypi: Ignore pypi-ignored-inputs.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:87eczl8kst.fsf@ngraves.fr

* guix/import/pypi.scm (pypi-ignored-inputs): New variable.

(compute-inputs): Use it.

* tests/pypi.scm (parse-requires.txt): Add ignored input to test the

feature.

* guix/lint.scm (check-inputs-should-be-native): Adapt list.

(check-inputs-should-not-be-an-input-at-all): Use pypi-ignored-list.

Change-Id: I774e526c5a090026e778ee44049637174a1dca95

---

guix/import/pypi.scm | 21 ++++++++++++++++++---

guix/lint.scm | 10 ++++++----

tests/pypi.scm | 3 ++-

3 files changed, 26 insertions(+), 8 deletions(-)

Toggle diff (123 lines)diff --git a/guix/import/pypi.scm b/guix/import/pypi.scm
index 4af02dd250..a49ab1e429 100644
--- a/guix/import/pypi.scm
+++ b/guix/import/pypi.scm
@@ -14,6 +14,7 @@
 ;;; Copyright © 2022 Vivien Kraus <vivien@planete-kraus.eu>
 ;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2022 Hartmut Goebel <h.goebel@crazy-compilers.com>
+;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -62,6 +63,7 @@ (define-module (guix import pypi)
   #:use-module (guix upstream)
   #:use-module ((guix licenses) #:prefix license:)
   #:export (%pypi-base-url
+            pypi-ignored-inputs
             parse-requires.txt
             parse-wheel-metadata
             specification->requirement-name
@@ -78,6 +80,18 @@ (define %pypi-base-url
   ;; Base URL of the PyPI API.
   (make-parameter "https://pypi.org/pypi/"))
 
+(define pypi-ignored-inputs
+  ;; This list contains packages that are useful for development or quality
+  ;; testing, but that most of the time are not necessary to have as an input.
+  (list "argparse"  ; native
+        "tox" ; test wrapper for other environments
+        "codecov" "coverage"  ; coverage
+        "black" "isort" "pycodestyle" "pep8"  ; style
+        "pyflakes" "flake8" "pylint" "mypy"  ; style+lint
+        "coveralls" "twine"  ; upload integration tools
+        "pytest-isort" "pytest-flake8" "pytest-cov" "pytest-black"
+        "pytest-pep8" "pytest-mypy" "pytest-pep8" "pre-commit"))  ; variants
+
 (define non-empty-string-or-false
   (match-lambda
     ("" #f)
@@ -464,9 +478,10 @@ (define (compute-inputs source-url wheel-url archive)
   "Given the SOURCE-URL and WHEEL-URL of an already downloaded ARCHIVE, return
 the corresponding list of <upstream-input> records."
   (define (requirements->upstream-inputs deps type)
-    (filter-map (match-lambda
-                  ("argparse" #f)
-                  (name (upstream-input
+    (filter-map (lambda (name)
+                  (if (member name pypi-ignored-inputs)
+                      #f
+                      (upstream-input
                          (name name)
                          (downstream-name (python->package-name name))
                          (type type))))
diff --git a/guix/lint.scm b/guix/lint.scm
index d54db725b5..caa4f63f88 100644
--- a/guix/lint.scm
+++ b/guix/lint.scm
@@ -73,6 +73,7 @@ (define-module (guix lint)
                                     hg-reference-url)
   #:autoload   (guix bzr-download) (bzr-reference?
                                     bzr-reference-url)
+  #:use-module ((guix import pypi) #:select (pypi-ignored-inputs))
   #:use-module (guix import stackage)
   #:use-module (ice-9 match)
   #:use-module (ice-9 regex)
@@ -588,14 +589,12 @@ (define (check-inputs-should-be-native package)
             "m4"
             "qttools-5"
             "yasm" "nasm" "fasm"
-            "python-coverage"
             "python-cython"
             "python-docutils"
             "python-mock"
             "python-nose"
             "python-pbr"
             "python-pytest"
-            "python-pytest-cov"
             "python-setuptools-scm"
             "python-sphinx"
             "scdoc"
@@ -617,8 +616,11 @@ (define (check-inputs-should-be-native package)
 (define (check-inputs-should-not-be-an-input-at-all package)
   ;; Emit a warning if some inputs of PACKAGE are likely to should not be
   ;; an input at all.
-  (let ((input-names '("python-pip"
-                       "python-pre-commit")))
+  (let ((input-names (append
+                      '("python-pip"
+                       "python-pre-commit")
+                      (map (cut string-append "python-" <>)
+                           pypi-ignored-inputs))))
     (map (lambda (input)
            (make-warning
             package
diff --git a/tests/pypi.scm b/tests/pypi.scm
index 3fbce1786f..f848325ad7 100644
--- a/tests/pypi.scm
+++ b/tests/pypi.scm
@@ -97,6 +97,7 @@ (define test-requires.txt "\
 
 [test]
 pytest (>=2.5.0)
+pytest-cov  # read but ignored
 ")
 
 ;; Beaker contains only optional dependencies.
@@ -258,7 +259,7 @@ (define-syntax-rule (with-pypi responses body ...)
   (map specification->requirement-name test-specifications))
 
 (test-equal "parse-requires.txt"
-  (list '("foo" "bar") '("pytest"))
+  (list '("foo" "bar") '("pytest" "pytest-cov"))
   (mock ((ice-9 ports) call-with-input-file
          call-with-input-string)
         (parse-requires.txt test-requires.txt)))
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Nicolas Graves wrote 9 months ago

[PATCH python-team v4 08/52] build-system/pyproject: Ignore unwanted pytest flags.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:87cyf58ksl.fsf@ngraves.fr

* guix/build/pyproject-build-system.scm : Ignore unwanted pytest flags.

Change-Id: Ib9f1602e5af11227e5b7ce124f0f9be4fa2b78e4

---

guix/build/pyproject-build-system.scm | 99 ++++++++++++++++++++++++++-

1 file changed, 96 insertions(+), 3 deletions(-)

Toggle diff (143 lines)diff --git a/guix/build/pyproject-build-system.scm b/guix/build/pyproject-build-system.scm
index 947d240114..2df9f2f479 100644
--- a/guix/build/pyproject-build-system.scm
+++ b/guix/build/pyproject-build-system.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2021 Lars-Dominik Braun <lars@6xq.net>
 ;;; Copyright © 2022 Marius Bakke <marius@gnu.org>
+;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -35,7 +36,8 @@ (define-module (guix build pyproject-build-system)
             add-installed-pythonpath
             site-packages
             python-version
-            pyproject-build))
+            pyproject-build
+            with-guix-pytest-plugin))
 
 ;;; Commentary:
 ;;;
@@ -142,7 +144,94 @@ (define* (build #:key outputs build-backend backend-path configure-flags #:allow
      wheel-dir
      config-settings)))
 
-(define* (check #:key tests? test-backend test-flags #:allow-other-keys)
+(define pytest-default-ignore-alist
+  '(("cov" . ("--cov" "--cov-reset" "--cov-report" "--cov-config"
+              "--no-cov-on-fail" "--no-cov" "--cov-fail-under"
+              "--cov-append" "--cov-branch" "--cov-context"))
+    ("mypy" . ("--mypy" "--mypy-config-file" "--mypy-ignore-missing-imports"))
+    ("isort" . ("--isort"))
+    ("flake8" . ("--flake8"))
+    ("black" . ("--black"))
+    ("flakes" . ("--flakes"))
+    ("pep8" . ("--pep8"))))
+
+(define (pytest-ignore-flags-plugin flags)
+  "This function converts an list of flags into a string that can
+  be instantiated as a python pytest plugin."
+  (format #f "\
+import pytest
+
+def pytest_addoption(parser):
+    group = parser.getgroup('guix','Guix ignored options')
+    options = [~{~s, ~}]
+    for option in options:
+        group.addoption(option, action='append', nargs='?')"
+          flags))
+
+(define (call-with-guix-pytest-plugin inputs thunk)
+  "This function emulates command line options provided by pytest plugins in
+the absence of the plugins defining these options.
+
+This is done by selecting absent plugins, gettings their flags defined in
+PYTEST-DEFAULT-IGNORE-ALIST, and generating the plugin from there with
+PYTEST-IGNORE-FLAGS-PLUGIN."
+  (let* ((former-path (getenv "PYTHONPATH"))
+         (input-names
+          (map car
+               (filter (match-lambda
+                         ((name . _)
+                          (if (string-prefix? "python-pytest-" name)
+                              name
+                              #f))
+                         ( _ #f))
+                       inputs)))
+         (filtered-flags
+          (filter identity
+                  (append-map
+                   (match-lambda
+                     ((group . flags)
+                      (if (member (string-append "python-pytest-" group)
+                                  input-names)
+                          (list #f)
+                          flags))
+                     (_ (list #f)))
+                   pytest-default-ignore-alist)))
+         (dir (string-append
+               (if (access? (dirname (getcwd)) W_OK)
+                   (dirname (getcwd))
+                   ;; fallback if we're already out-of-source
+                   (getcwd))
+               "/.guix-pytest")))
+    (dynamic-wind
+      (lambda ()
+        (setenv "PYTHONPATH"
+                (string-append
+                 (if former-path
+                     (string-append former-path ":")
+                     "")
+                 dir))
+        (setenv "PYTEST_PLUGINS"
+                (string-append
+                 (if (getenv "PYTEST_PLUGINS")
+                     (string-append former-path ",")
+                     "")
+                 "pytest_guix_plugin"))
+        (mkdir-p dir)
+        (with-output-to-file (string-append dir "/__init__.py")
+          (lambda _ (display "")))
+        (with-output-to-file (string-append dir "/pytest_guix_plugin.py")
+          (lambda _
+            (display (pytest-ignore-flags-plugin filtered-flags)))))
+      thunk
+      (lambda ()
+        (setenv "PYTHONPATH" former-path)
+        (unsetenv "PYTEST_PLUGINS")))))
+
+(define-syntax-rule (with-guix-pytest-plugin inputs exp ...)
+  "Evaluate EXP in a context where the Guix pytest plugin is added."
+  (call-with-guix-pytest-plugin inputs (lambda () exp ...)))
+
+(define* (check #:key inputs tests? test-backend test-flags #:allow-other-keys)
   "Run the test suite of a given Python package."
   (if tests?
       ;; Unfortunately with PEP 517 there is no common method to specify test
@@ -165,7 +254,8 @@ (define* (check #:key tests? test-backend test-flags #:allow-other-keys)
         (format #t "Using ~a~%" use-test-backend)
         (match use-test-backend
           ('pytest
-           (apply invoke pytest "-vv" test-flags))
+           (with-guix-pytest-plugin inputs
+             (apply invoke pytest "-vv" test-flags)))
           ('nose
            (apply invoke nosetests "-v" test-flags))
           ('nose2
@@ -386,3 +476,6 @@ (define* (pyproject-build #:key inputs (phases %standard-phases)
   (apply python:python-build #:inputs inputs #:phases phases args))
 
 ;;; pyproject-build-system.scm ends here
+;;; Local Variables:
+;;; eval: (put 'with-guix-pytest-plugin 'scheme-indent-function 1)
+;;; End:
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Nicolas Graves wrote 1 months ago

[PATCH python-team v4 09/52] build-system/pyproject: Remove python-black inputs.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:87bjup8kse.fsf@ngraves.fr

* gnu/packages/bioinformatics.scm (python-doubletdetection,
python-liana-py, python-metacells, python-ngesh, scvelo)
* gnu/packages/databases.scm (datasette)
* gnu/packages/finance.scm (python-trezor)
* gnu/packages/graph.scm (python-graphtools)
* gnu/packages/jupyter.scm (python-papermill)
* gnu/packages/machine-learning.scm (python-funsor,
python-imbalanced-learn, python-hyperopt, python-captum)
* gnu/packages/python-check.scm (python-vcrpy)
* gnu/packages/python-web.scm (python-ovh, python-openai,
* gnu/packages/python-science.scm (python-scikit-survival)
python-starsessions-for-pytorch-lightning)
* gnu/packages/python-xyz.scm (python-archspec, python-pydantic-cli,
python-imageio, python-update-checker, python-eliot,
python-minikanren)
* gnu/packages/virtualization.scm (python-transient)
[native-inputs]: Remove python-black.

* gnu/packages/python-xyz.scm (ptpython,
python-get-version)[propagated-inputs]: Remove python-black.
---
 gnu/packages/bioinformatics.scm   | 16 +++++-----------
 gnu/packages/databases.scm        |  1 -
 gnu/packages/finance.scm          |  1 -
 gnu/packages/graph.scm            |  1 -
 gnu/packages/jupyter.scm          |  1 -
 gnu/packages/machine-learning.scm | 10 +++-------
 gnu/packages/python-science.scm   |  3 +--
 gnu/packages/python-web.scm       |  8 +++-----
 gnu/packages/python-xyz.scm       | 19 ++++++-------------
 gnu/packages/virtualization.scm   |  3 +--
 10 files changed, 19 insertions(+), 44 deletions(-)

Toggle diff (293 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3e8a9def35..ed05470c0f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2824,8 +2824,7 @@ (define-public python-doubletdetection
            python-scipy
            python-tqdm))
     (native-inputs
-     (list python-black
-           python-flake8
+     (list python-flake8
            python-poetry-core
            python-pytest))
     (home-page "https://github.com/JonathanShor/DoubletDetection")
@@ -3053,10 +3052,7 @@ (define-public python-liana-py
                              python-tqdm
                              tzdata))
     (native-inputs
-     (list python-black
-           python-poetry-core
-           python-pytest
-           python-pytest-cov))
+     (list python-poetry-core python-pytest python-pytest-cov))
     (home-page "https://github.com/saezlab/liana-py")
     (synopsis "LIANA is a ligand-receptor analysis framework")
     (description "This is a Ligand-Receptor inference framework.  The
@@ -3172,8 +3168,7 @@ (define-public python-metacells
                              python-scipy
                              python-threadpoolctl
                              python-umap-learn))
-    (native-inputs (list python-black
-                         python-bumpversion
+    (native-inputs (list python-bumpversion
                          python-flake8
                          python-isort
                          python-mypy
@@ -3213,7 +3208,7 @@ (define-public python-ngesh
         (base32 "07sj4x95b5hvx57pw24f80sk4ag4hkg1z6wzym3pzi8n5gn85n1z"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-ete3 python-numpy python-six))
-    (native-inputs (list python-black python-flake8 python-pytest python-twine
+    (native-inputs (list python-flake8 python-pytest python-twine
                          python-wheel))
     (home-page "https://github.com/tresoldi/ngesh")
     (synopsis "Library for phylogenetic tree simulation")
@@ -24006,8 +24001,7 @@ (define-public scvelo
            python-umap-learn
            pybind11))
     (native-inputs
-     (list python-black
-           python-flake8
+     (list python-flake8
            python-hypothesis
            python-pytest
            python-setuptools-scm
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 9b8c95047b..40ffe3e084 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -5801,7 +5801,6 @@ (define-public datasette
     (native-inputs
      (list nss-certs-for-test
            python-beautifulsoup4
-           python-black
            python-cogapp
            python-pip
            python-pytest
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index bb1234ebd9..9805679597 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -1160,7 +1160,6 @@ (define-public python-trezor
            python-typing-extensions))
     (native-inputs ; Only needed for running the tests
      (list protobuf
-           python-black
            python-isort
            python-pillow
            python-protobuf
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index f29a71c0d7..75ebbff2db 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -482,7 +482,6 @@ (define-public python-graphtools
     (native-inputs
      (list util-linux ;for lscpu
            python-anndata
-           python-black
            python-coverage
            python-coveralls
            python-nose
diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm
index 6c2f549583..f47d8de295 100644
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -1157,7 +1157,6 @@ (define-public python-papermill
                              python-tenacity
                              python-tqdm))
     (native-inputs (list python-attrs
-                         python-black
                          python-boto3
                          python-botocore
                          python-bumpversion
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 59a8445f23..37ccaf2b52 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -229,8 +229,7 @@ (define-public python-funsor
     (propagated-inputs (list python-makefun python-multipledispatch
                              python-numpy python-opt-einsum
                              python-typing-extensions))
-    (native-inputs (list python-black
-                         python-flake8
+    (native-inputs (list python-flake8
                          python-isort
                          python-nbsphinx
                          python-pandas
@@ -2155,8 +2154,7 @@ (define-public python-imbalanced-learn
                               (getcwd)))))))
     (propagated-inputs (list python-joblib python-numpy python-scikit-learn
                              python-scipy python-threadpoolctl))
-    (native-inputs (list python-black
-                         python-flake8
+    (native-inputs (list python-flake8
                          python-keras
                          python-mypy
                          python-pandas
@@ -2595,8 +2593,7 @@ (define-public python-hyperopt
            python-six
            python-tqdm))
     (native-inputs
-     (list python-black
-           python-nose
+     (list python-nose
            python-pymongo
            python-pytest
            python-wheel))
@@ -5326,7 +5323,6 @@ (define-public python-captum
      (list python-matplotlib python-numpy python-pytorch python-tqdm))
     (native-inputs (list jupyter
                          python-annoy
-                         python-black
                          python-flake8
                          python-flask
                          python-flask-compress
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 844bddf3ce..f18da4a326 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -888,8 +888,7 @@ (define-public python-scikit-survival
              python-scikit-learn
              python-scipy))
       (native-inputs
-       (list python-black
-             python-pypa-build
+       (list python-pypa-build
              python-coverage
              python-cython-3
              python-packaging
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 5ea9e5a709..c17485feff 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1614,8 +1614,7 @@ (define-public python-ovh
     (build-system pyproject-build-system)
     (arguments (list #:tests? #f))      ; XXX: tests require networking
     (propagated-inputs (list python-requests))
-    (native-inputs (list python-black
-                         python-coverage
+    (native-inputs (list python-coverage
                          python-flake8
                          python-isort
                          python-pytest
@@ -3024,7 +3023,7 @@ (define-public python-openai
  and not test_file_cli")))
     (propagated-inputs (list python-aiohttp python-requests python-tqdm
                              python-typing-extensions))
-    (native-inputs (list python-black python-pytest python-pytest-asyncio
+    (native-inputs (list python-pytest python-pytest-asyncio
                          python-pytest-mock python-setuptools python-wheel))
     (home-page "https://github.com/openai/openai-python")
     (synopsis "Python client library for the OpenAI API")
@@ -10327,8 +10326,7 @@ (define-public python-starsessions
            python-itsdangerous
            python-starlette))
     (native-inputs
-     (list python-black
-           python-flake8
+     (list python-flake8
            python-httpx
            python-mypy
            python-poetry-core
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 252c13ee13..0f92e69c6c 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -395,8 +395,7 @@ (define-public python-archspec
                              python-scikit-learn
                              python-tables
                              python-typing-extensions))
-    (native-inputs (list python-black
-                         python-flake8
+    (native-inputs (list python-flake8
                          python-isort
                          python-poetry-core
                          python-pylint
@@ -8858,8 +8857,7 @@ (define-public python-pydantic-cli
     (propagated-inputs
      (list python-pydantic))
     (native-inputs
-     (list python-black
-           python-mypy
+     (list python-mypy
            python-pytest))
     (home-page "https://github.com/mpkocher/pydantic-cli")
     (synopsis "Turn Pydantic defined data models into CLI tools")
@@ -11983,8 +11981,7 @@ (define-public python-imageio
     (propagated-inputs
      (list python-imageio-ffmpeg python-numpy python-pillow python-tifffile))
     (native-inputs
-     (list python-black
-           python-flake8
+     (list python-flake8
            python-fsspec
            python-pytest
            python-pytest-cov
@@ -17551,7 +17548,6 @@ (define-public python-get-version
     (propagated-inputs
      (list python-pygments
            python-pytest
-           python-pytest-black
            python-pytest-cov
            python-setuptools
            python-testpath))
@@ -23842,8 +23838,7 @@ (define-public ptpython
     (arguments
      `(#:tests? #f)) ;there are no tests
     (propagated-inputs
-     (list python-appdirs python-black python-jedi python-prompt-toolkit
-           python-pygments))
+     (list python-appdirs python-jedi python-prompt-toolkit python-pygments))
     (home-page "https://github.com/jonathanslenders/ptpython")
     (synopsis "Python Read-Eval-Print-Loop with nice IDE-like features")
     (description
@@ -29209,7 +29204,7 @@ (define-public python-update-checker
         (base32 "04yb5a9mi45ax50m2m0ih6gdvkk1j7gfmy83dd58i1f59axlabba"))))
     (build-system python-build-system)
     (propagated-inputs (list python-requests))
-    (native-inputs (list python-black python-flake8 python-pytest))
+    (native-inputs (list python-flake8 python-pytest))
     (home-page "https://github.com/bboe/update_checker")
     (synopsis "Python module that will check for package updates")
     (description "This package provides a Python module that will check for
@@ -33534,8 +33529,7 @@ (define-public python-eliot
     (propagated-inputs
      (list python-boltons python-orjson python-pyrsistent python-zope-interface))
     (native-inputs
-     (list python-black
-           python-coverage
+     (list python-coverage
            python-flake8
            python-hypothesis
            python-pytest
@@ -36846,7 +36840,6 @@ (define-public python-minikanren
            python-pytest
            python-pytest-cov
            python-pylint
-           python-black
            python-sympy
            python-versioneer
            python-coverage))
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index 9ab65e6c6c..cc0346297e 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -2987,8 +2987,7 @@ (define-public python-transient
                         (("==")
                          ">=")))))))
     (native-inputs
-     (list python-black
-           python-mypy
+     (list python-mypy
            python-pyhamcrest
            python-setuptools
            python-twine
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Nicolas Graves wrote 1 months ago

[PATCH python-team v4 10/52] build-system/pyproject: Remove python-pylint native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:87a5a98ks8.fsf@ngraves.fr

* gnu/packages/bioinformatics.scm (python-metacells)
* gnu/packages/games.scm (open-adventure)
* gnu/packages/machine-learning.scm (python-ml-collections)
* gnu/packages/potassco.scm (python-clingraph)
* gnu/packages/python-xyz.scm (python-archspec, python-lsp-jsonrpc,
python-lsp-server, python-mediapy, python-minikanren)
* gnu/packages/syndication.scm (rtv, tuir)
* gnu/packages/terminals.scm (python-halo, python-log-symbols,
python-spinners)
* gnu/packages/virtualization.scm (python-qemu-qmp)
[native-inputs]: Remove python-pylint.

build-system/pyproject: Remove python-pylint native-input.

[native-inputs]: Remove python-pylint.
---
 gnu/packages/bioinformatics.scm   | 1 -
 gnu/packages/games.scm            | 1 -
 gnu/packages/machine-learning.scm | 3 +--
 gnu/packages/potassco.scm         | 3 +--
 gnu/packages/python-xyz.scm       | 5 -----
 gnu/packages/syndication.scm      | 2 --
 gnu/packages/terminals.scm        | 3 ---
 gnu/packages/virtualization.scm   | 1 -
 8 files changed, 2 insertions(+), 17 deletions(-)

Toggle diff (164 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ed05470c0f..705a1e6a04 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3174,7 +3174,6 @@ (define-public python-metacells
                          python-mypy
                          python-mypy-extensions
                          python-pandas-stubs
-                         python-pylint
                          python-pytest
                          python-pytest-cov
                          python-setuptools
diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 30aaf0767a..81933aaae8 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -7794,7 +7794,6 @@ (define-public open-adventure
              cppcheck
              libedit
              pkg-config
-             python-pylint
              python-pyyaml
              python-wrapper)
        (if (supported-package? ruby-asciidoctor)
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 37ccaf2b52..0bcb6be210 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -379,8 +379,7 @@ (define-public python-ml-collections
       #:test-flags '(list "--pyargs" "ml_collections/config_dict/tests")))
     (propagated-inputs
      (list python-absl-py python-pyyaml))
-    (native-inputs (list python-pylint
-                         python-pytest
+    (native-inputs (list python-pytest
                          python-pytest-xdist
                          python-flit-core))
     (home-page "https://github.com/google/ml_collections")
diff --git a/gnu/packages/potassco.scm b/gnu/packages/potassco.scm
index 43e56ec8bf..7c3fe2e309 100644
--- a/gnu/packages/potassco.scm
+++ b/gnu/packages/potassco.scm
@@ -697,8 +697,7 @@ (define-public python-clingraph
                              python-jsonschema
                              python-networkx
                              python-setuptools))
-    (native-inputs (list dot2tex graphviz python-pylint python-pytest
-                         python-wheel))
+    (native-inputs (list dot2tex graphviz python-pytest python-wheel))
     (home-page "https://github.com/potassco/clingraph")
     (synopsis "Visualizer for graphs defined as logic programs")
     (description
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 0f92e69c6c..1bdb479774 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -398,7 +398,6 @@ (define-public python-archspec
     (native-inputs (list python-flake8
                          python-isort
                          python-poetry-core
-                         python-pylint
                          python-pytest
                          python-pytest-cov))
     (home-page "https://github.com/archspec/archspec")
@@ -5104,7 +5103,6 @@ (define-public python-mediapy
                              python-pillow))
     (native-inputs
      (list python-flit-core
-           python-pylint
            python-pytest
            python-pytest-xdist))
     (home-page "https://github.com/google/mediapy")
@@ -8685,7 +8683,6 @@ (define-public python-lsp-jsonrpc
      (list python-coverage
            python-pycodestyle
            python-pyflakes
-           python-pylint
            python-pytest
            python-pytest-cov
            python-setuptools
@@ -9061,7 +9058,6 @@ (define-public python-lsp-server
            python-matplotlib
            python-numpy
            python-pandas
-           python-pylint
            python-pytest
            python-rope
            python-setuptools
@@ -36839,7 +36835,6 @@ (define-public python-minikanren
            python-pydocstyle
            python-pytest
            python-pytest-cov
-           python-pylint
            python-sympy
            python-versioneer
            python-coverage))
diff --git a/gnu/packages/syndication.scm b/gnu/packages/syndication.scm
index f717cbb3af..fc563a657f 100644
--- a/gnu/packages/syndication.scm
+++ b/gnu/packages/syndication.scm
@@ -501,7 +501,6 @@ (define-public rtv
            python-coveralls
            python-coverage
            python-mock
-           python-pylint
            python-pytest
            python-vcrpy))
     (home-page "https://github.com/michael-lazar/rtv")
@@ -545,7 +544,6 @@ (define-public tuir
      (list python-coverage
            python-coveralls
            python-mock
-           python-pylint
            python-pytest
            python-setuptools
            python-vcrpy
diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index 9fdd378cf2..b9dd12803d 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -1178,7 +1178,6 @@ (define-public python-halo
     (native-inputs
      (list python-coverage
            python-nose
-           python-pylint
            python-setuptools
            python-tox
            python-twine
@@ -1211,7 +1210,6 @@ (define-public python-log-symbols
     (native-inputs
      (list python-coverage
            python-nose
-           python-pylint
            python-setuptools
            python-tox
            python-wheel))
@@ -1245,7 +1243,6 @@ (define-public python-spinners
     (native-inputs
      (list python-coverage
            python-nose
-           python-pylint
            python-setuptools
            python-tox
            python-wheel))
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index cc0346297e..bde357763f 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -2121,7 +2121,6 @@ (define-public python-qemu-qmp
      (list python-avocado-framework
            python-flake8
            python-isort
-           python-pylint
            python-setuptools
            python-setuptools-scm
            python-wheel))
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Nicolas Graves wrote 1 months ago

[PATCH python-team v4 11/52] build-system/pyproject: Remove python-flake8 inputs.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:878qpt8ks2.fsf@ngraves.fr

* gnu/packages/bioinformatics.scm (python-doubletdetection,
python-biom-format, python-metacells, python-ngesh)
* gnu/packages/ebook.scm (calibre)
* gnu/packages/engineering.scm (python-scikit-rf)
* gnu/packages/finance.scm (python-mt-940)
* gnu/packages/geo.scm (python-geopy)
* gnu/packages/gettext.scm (python-mdpo)
* gnu/packages/graph.scm (python-pygsp)
* gnu/packages/graphviz.scm (python-uqbar)
* gnu/packages/machine-learning.scm (python-funsor,
python-imbalanced-learn, python-captum, python-pymanopt,
python-pyro-api, python-pyro-ppl, python-linear-operator,
python-gpytorch)
* gnu/packages/python-web.scm (python-ovh, python-furl,
python-httplib2, python-http-ece, python-woob,
python-starsessions-for-pytorch-lightning)
* gnu/packages/python-xyz.scm (python-archspec, python-colorful,
python-pymd4c, python-flasgger, python-imageio,
python-importlib-ressources, python-seaborn, python-inflect,
python-yq, python-update-checker, python-eliot, python-dateparser,
python-jinja2-cli, python-verspec, python-mike,
python-simple-websocket)
* gnu/packages/simulation.scm (python-dolfin-adjoint)
* gnu/packages/statistics.scm (python-statsmodels)
* gnu/packages/vpn.scm (sshuttle)
* gnu/packages/wm.scm (qtile)
* gnu/packages/textutils.scm (python-panflute)
[native-inputs]: Remove python-flake8.

* gnu/packages/music.scm (python-mutagen):
  [arguments]<#:test-flags>: Ignore flake8 quality tests.
  [native-inputs]: Remove python-flake8.

* gnu/packages/protobuf.scm (python-pure-protobuf):
  [arguments]<#:phases>: Remove flake8 invocation from check phase.
  [native-inputs]: Remove python-flake8.
---
 gnu/packages/bioinformatics.scm   | 10 +++------
 gnu/packages/ebook.scm            |  1 -
 gnu/packages/engineering.scm      |  1 -
 gnu/packages/finance.scm          |  4 +---
 gnu/packages/gettext.scm          |  1 -
 gnu/packages/graph.scm            |  3 +--
 gnu/packages/graphviz.scm         |  1 -
 gnu/packages/machine-learning.scm | 15 ++++----------
 gnu/packages/music.scm            |  4 ++--
 gnu/packages/protobuf.scm         |  4 +---
 gnu/packages/python-web.scm       | 15 ++++----------
 gnu/packages/python-xyz.scm       | 34 ++++++++++++-------------------
 gnu/packages/simulation.scm       |  1 -
 gnu/packages/statistics.scm       |  1 -
 gnu/packages/textutils.scm        |  1 -
 gnu/packages/vpn.scm              |  1 -
 gnu/packages/wm.scm               |  1 -
 17 files changed, 29 insertions(+), 69 deletions(-)

Toggle diff (423 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 705a1e6a04..b989c87842 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2824,8 +2824,7 @@ (define-public python-doubletdetection
            python-scipy
            python-tqdm))
     (native-inputs
-     (list python-flake8
-           python-poetry-core
+     (list python-poetry-core
            python-pytest))
     (home-page "https://github.com/JonathanShor/DoubletDetection")
     (synopsis
@@ -3169,7 +3168,6 @@ (define-public python-metacells
                              python-threadpoolctl
                              python-umap-learn))
     (native-inputs (list python-bumpversion
-                         python-flake8
                          python-isort
                          python-mypy
                          python-mypy-extensions
@@ -3207,7 +3205,7 @@ (define-public python-ngesh
         (base32 "07sj4x95b5hvx57pw24f80sk4ag4hkg1z6wzym3pzi8n5gn85n1z"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-ete3 python-numpy python-six))
-    (native-inputs (list python-flake8 python-pytest python-twine
+    (native-inputs (list python-pytest python-twine
                          python-wheel))
     (home-page "https://github.com/tresoldi/ngesh")
     (synopsis "Library for phylogenetic tree simulation")
@@ -3879,7 +3877,6 @@ (define-public python-biom-format
     (propagated-inputs
      (list python-anndata
            python-click
-           python-flake8
            python-future
            python-h5py
            python-numpy
@@ -24000,8 +23997,7 @@ (define-public scvelo
            python-umap-learn
            pybind11))
     (native-inputs
-     (list python-flake8
-           python-hypothesis
+     (list python-hypothesis
            python-pytest
            python-setuptools-scm
            python-wheel))
diff --git a/gnu/packages/ebook.scm b/gnu/packages/ebook.scm
index 46ec951916..75e14801dd 100644
--- a/gnu/packages/ebook.scm
+++ b/gnu/packages/ebook.scm
@@ -156,7 +156,6 @@ (define-public calibre
     (native-inputs
      (list bash-minimal
            pkg-config
-           python-flake8
            python-pyqt-builder
            qtbase-5                     ; for qmake
            xdg-utils))
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index 8ca3b87ff2..3882a35d6b 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -2965,7 +2965,6 @@ (define-public python-scikit-rf
                              python-qtpy
                              python-scipy))
     (native-inputs (list python-coverage
-                         python-flake8
                          python-nbval
                          python-networkx
                          python-pytest
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index 9805679597..f3be674c01 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -2310,9 +2310,7 @@ (define-public python-mt-940
                         ;; Remove custom --cov flags.
                         (delete-file "pytest.ini")
                         (invoke "pytest" "-vv")))))))
-    (native-inputs (list python-flake8
-                         python-pytest
-                         python-pyyaml))
+    (native-inputs (list python-pytest python-pyyaml))
     (home-page "https://mt940.readthedocs.io/")
     (synopsis "Python parser for MT940-encoded SWIFT data")
     (description
diff --git a/gnu/packages/gettext.scm b/gnu/packages/gettext.scm
index 7862c296bd..29cdbab915 100644
--- a/gnu/packages/gettext.scm
+++ b/gnu/packages/gettext.scm
@@ -226,7 +226,6 @@ (define-public mdpo
     (build-system python-build-system)
     (native-inputs
      (list python-bump2version
-           python-flake8
            python-flake8-implicit-str-concat
            python-flake8-print
            python-isort
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 75ebbff2db..57c4bd05ed 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -570,8 +570,7 @@ (define-public python-pygsp
                 "")))))))
     (propagated-inputs (list python-numpy python-scikit-image python-scipy))
     (native-inputs
-     (list python-coverage python-coveralls python-flake8
-           python-pytest))
+     (list python-coverage python-coveralls python-pytest))
     (home-page "https://github.com/epfl-lts2/pygsp")
     (synopsis "Graph Signal Processing in Python")
     (description "The PyGSP is a Python package to ease signal processing on
diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm
index defd53df73..0d3db31212 100644
--- a/gnu/packages/graphviz.scm
+++ b/gnu/packages/graphviz.scm
@@ -224,7 +224,6 @@ (define-public python-uqbar
 and not test_sphinx_book_text_broken_strict")))
     (native-inputs
      (list graphviz
-           python-flake8
            python-isort
            python-mypy
            python-pytest
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 0bcb6be210..bb134a6618 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -229,8 +229,7 @@ (define-public python-funsor
     (propagated-inputs (list python-makefun python-multipledispatch
                              python-numpy python-opt-einsum
                              python-typing-extensions))
-    (native-inputs (list python-flake8
-                         python-isort
+    (native-inputs (list python-isort
                          python-nbsphinx
                          python-pandas
                          python-pillow
@@ -1143,7 +1142,6 @@ (define-public python-pymanopt
                ((",!=1.12\\.\\*") "")))))))
     (propagated-inputs (list python-numpy python-scipy))
     (native-inputs (list python-autograd
-                         python-flake8
                          python-flake8-bugbear
                          python-isort
                          python-matplotlib
@@ -2153,8 +2151,7 @@ (define-public python-imbalanced-learn
                               (getcwd)))))))
     (propagated-inputs (list python-joblib python-numpy python-scikit-learn
                              python-scipy python-threadpoolctl))
-    (native-inputs (list python-flake8
-                         python-keras
+    (native-inputs (list python-keras
                          python-mypy
                          python-pandas
                          python-pytest
@@ -5322,7 +5319,6 @@ (define-public python-captum
      (list python-matplotlib python-numpy python-pytorch python-tqdm))
     (native-inputs (list jupyter
                          python-annoy
-                         python-flake8
                          python-flask
                          python-flask-compress
                          python-ipython
@@ -5843,8 +5839,7 @@ (define-public python-pyro-api
     (build-system python-build-system)
     (arguments '(#:tests? #false)) ;requires pyro
     (native-inputs
-     (list python-flake8
-           python-ipython
+     (list python-ipython
            python-pytest
            python-sphinx
            python-sphinx-rtd-theme))
@@ -5901,8 +5896,7 @@ (define-public python-linear-operator
                              python-pytorch
                              python-scipy
                              python-typeguard))
-    (native-inputs (list python-flake8
-                         python-flake8-print
+    (native-inputs (list python-flake8-print
                          python-pytest
                          python-setuptools
                          python-setuptools-scm
@@ -5933,7 +5927,6 @@ (define-public python-gpytorch
                              python-scikit-learn
                              python-scipy))
     (native-inputs (list python-coverage
-                         python-flake8
                          python-flake8-print
                          python-nbval
                          python-pytest
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index bf47489d34..7d28ef4b58 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -4116,6 +4116,7 @@ (define-public python-mutagen
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags '(list "--ignore=tests/quality/test_flake8.py")
        #:phases
        #~(modify-phases %standard-phases
            (add-before 'check 'remove-hypothesis-deadlines
@@ -4126,8 +4127,7 @@ (define-public python-mutagen
                  (("( +)@given" all spaces)
                   (string-append spaces "@settings(deadline=None)\n" all))))))))
     (native-inputs
-     (list python-flake8
-           python-hypothesis
+     (list python-hypothesis
            python-pytest
            python-setuptools
            python-wheel))
diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm
index 9d81b1c508..203e4909d6 100644
--- a/gnu/packages/protobuf.scm
+++ b/gnu/packages/protobuf.scm
@@ -502,7 +502,7 @@ (define-public python-pure-protobuf
         (base32 "15dp5pvazd0jx4wzzh79080ah7hkpd3axh40al9vhzs2hf3v90hx"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-flake8 python-pytest python-pytest-cov python-isort))
+     (list python-pytest python-pytest-cov python-isort))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
@@ -510,8 +510,6 @@ (define-public python-pure-protobuf
            (lambda _
              (invoke "pytest" "--cov-report" "term-missing" "--cov"
                      "pure_protobuf")
-             (invoke "flake8" "pure_protobuf" "tests"
-                     "--ignore=F541")
              (invoke "isort" "-rc" "-c" "pure_protobuf" "tests"))))))
     (home-page "https://pypi.org/project/pure-protobuf/")
     (synopsis "Protobuf implementation using dataclasses")
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index c17485feff..dc5ad03f92 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1615,7 +1615,6 @@ (define-public python-ovh
     (arguments (list #:tests? #f))      ; XXX: tests require networking
     (propagated-inputs (list python-requests))
     (native-inputs (list python-coverage
-                         python-flake8
                          python-isort
                          python-pytest
                          python-pytest-cov
@@ -1931,8 +1930,6 @@ (define-public python-furl
     (build-system python-build-system)
     (propagated-inputs
      (list python-six python-orderedmultidict))
-    (native-inputs
-     (list python-flake8))
     (home-page "https://github.com/gruns/furl")
     (synopsis "URL manipulation in Python")
     (description "Furl provides an easy-to-use alternative to the
@@ -1965,7 +1962,6 @@ (define-public python-httplib2
                  (("==") ">=")))))))
     (native-inputs
      (list python-cryptography
-           python-flake8
            python-future
            python-mock
            python-pytest
@@ -8588,7 +8584,7 @@ (define-public python-http-ece
     (propagated-inputs
      (list python-cryptography))
     (native-inputs
-     (list python-coverage python-flake8 python-mock python-nose))
+     (list python-coverage python-mock python-nose))
     (home-page "https://github.com/web-push-libs/encrypted-content-encoding")
     (synopsis "Encrypted Content Encoding for HTTP")
     (description
@@ -9053,8 +9049,7 @@ (define-public python-simple-websocket
      ;; Requires Internet access to resolve example.com
      (list #:test-flags '(list "--ignore=tests/test_client.py")))
     (propagated-inputs (list python-wsproto))
-    (native-inputs (list python-flake8
-                         python-pytest
+    (native-inputs (list python-pytest
                          python-pytest-cov
                          python-setuptools
                          python-tox
@@ -9665,8 +9660,7 @@ (define-public python-woob
            python-six
            python-unidecode))
     (native-inputs
-     (list python-coverage python-flake8 python-nose python-selenium
-           python-xunitparser))
+     (list python-coverage python-nose python-selenium python-xunitparser))
     (home-page "https://woob.tech/")
     (synopsis "Woob, Web Outside Of Browsers")
     (description "Woob is a collection of applications able to interact with
@@ -10326,8 +10320,7 @@ (define-public python-starsessions
            python-itsdangerous
            python-starlette))
     (native-inputs
-     (list python-flake8
-           python-httpx
+     (list python-httpx
            python-mypy
            python-poetry-core
            python-pytest
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 1bdb479774..6b8aa6257c 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -395,8 +395,7 @@ (define-public python-archspec
                              python-scikit-learn
                              python-tables
                              python-typing-extensions))
-    (native-inputs (list python-flake8
-                         python-isort
+    (native-inputs (list python-isort
                          python-poetry-core
                          python-pytest
                          python-pytest-cov))
@@ -1554,8 +1553,7 @@ (define-public python-colorful
         (base32 "0kyy9qhvrb5m9h8xmri7c88i0k1g5qc7017anw39gx44an7mn33y"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage python-flake8 python-pytest python-setuptools
-           python-wheel))
+     (list python-coverage python-pytest python-setuptools python-wheel))
     (propagated-inputs
      (list python-colorama))
     (home-page "http://github.com/timofurrer/colorful")
@@ -2925,7 +2923,7 @@ (define-public python-pymd4c
     (inputs
      (list md4c))
     (native-inputs
-     (list python-flake8 python-pkgconfig pkg-config))
+     (list python-pkgconfig pkg-config))
     (home-page "https://github.com/dominickpastore/pymd4c")
     (synopsis "Python bindings for MD4C")
     (description
@@ -11977,8 +11975,7 @@ (define-public python-imageio
     (propagated-inputs
      (list python-imageio-ffmpeg python-numpy python-pillow python-tifffile))
     (native-inputs
-     (list python-flake8
-           python-fsspec
+     (list python-fsspec
            python-pytest
            python-pytest-cov
            python-setuptools
@@ -12792,8 +12789,7 @@ (define-public python-importlib-resources
              (setenv "PYTHONPATH"
                      (string-append (getcwd) "/_custom_build")))))))
     (native-inputs
-     (list python-flake8
-           python-pytest
+     (list python-pytest
            python-pytest-black
            python-pytest-checkdocs
            python-pytest-cov
@@ -15065,8 +15061,7 @@ (define-public python-seaborn
            python-scipy
            python-statsmodels))
     (native-inputs
-     (list python-flake8
-           python-flit-core
+     (list python-flit-core
            python-ipykernel
            python-nbconvert
            python-numpydoc
@@ -22642,8 +22637,7 @@ (define-public python-inflect
              (setenv "PYTHONPATH"
                      (string-append (getcwd) "/_custom_build")))))))
     (propagated-inputs (list python-pydantic))
-    (native-inputs (list python-flake8
-                         python-pygments
+    (native-inputs (list python-pygments
                          python-pytest
                          python-pytest-black
                          python-pytest-checkdocs
@@ -28192,7 +28186,7 @@ (define-public python-yq
     (inputs
      (list python-argcomplete python-pyyaml python-xmltodict python-toml jq))
     (native-inputs
-     (list python-coverage python-flake8 python-setuptools-scm python-wheel))
+     (list python-coverage python-setuptools-scm python-wheel))
     (home-page "https://github.com/kislyuk/yq")
     (synopsis "Command-line YAML/XML processor")
     (description
@@ -29200,7 +29194,7 @@ (define-public python-update-checker
         (base32 "04yb5a9mi45ax50m2m0ih6gdvkk1j7gfmy83dd58i1f59axlabba"))))
     (build-system python-build-system)
     (propagated-inputs (list python-requests))
-    (native-inputs (list python-flake8 python-pytest))
+    (native-inputs (list python-pytest))
     (home-page "https://github.com/bboe/update_checker")
     (synopsis "Python module that will check for package updates")
     (description "This package provides a Python module that will check for
@@ -33526,7 +33520,6 @@ (define-public python-eliot
      (list python-boltons python-orjson python-pyrsistent python-zope-interface))
     (native-inputs
      (list python-coverage
-           python-flake8
            python-hypothesis
            python-pytest
            python-pytest-xdist
@@ -34314,7 +34307,7 @@ (define-public python-dateparser
      (list python-dateutil python-pytz python-regex python-ruamel.yaml
            python-tzlocal))
     (native-inputs
-     (list python-flake8 python-pytest python-parameterized tzdata-for-tests
+     (list python-pytest python-parameterized tzdata-for-tests
            python-setuptools python-wheel))
     (arguments
      `(#:phases
@@ -35740,8 +35733,7 @@ (define-public python-jinja2-cli
     (propagated-inputs
      (list python-jinja2))
     (native-inputs
-     (list python-flake8
-           python-jinja2
+     (list python-jinja2
            python-pytest
            python-setup

This message was truncated. Download the full message here.

Nicolas Graves wrote 2 weeks ago

[PATCH python-team v4 12/52] build-system/pyproject: Remove python-coverage input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:877c5d8krq.fsf@ngraves.fr

* gnu/packages/astronomy.scm (python-asdf-astropy,
python-poliastro)
* gnu/packages/bioinformatics.scm (python-ega-download-client,
python-scikit-bio, python-cooler)
* gnu/packages/check.scm (python-pytest-randomly,
python-pytest-flakes, python-aiounittest)
* gnu/packages/cpp.scm (cpplint)
* gnu/packages/django.scm (python-django-haystack)
* gnu/packages/engineering.scm (python-scikit-rf)
* gnu/packages/geo.scm (python-geopy)
* gnu/packages/gpodder.scm (gpodder)
* gnu/packages/graph.scm (python-graphtools, python-pygsp)
* gnu/packages/jupyter.scm (python-jupyter-packaging)
* gnu/packages/machine-learning.scm (onnx, onnx-optimizer,
python-lightning-utilities, python-pytorch-lightning,
python-torchmetrics, python-gpytorch)
* gnu/packages/music.scm (python-pylast)
* gnu/packages/package-management.scm (python-anaconda-client, conda)
* gnu/packages/python-check.scm (python-vcrpy,
python-re-assert)
* gnu/packages/python-compression.scm (python-multivolumefile,
python-pybcj, python-bcj-cffi, python-pyppmd, python-ppmd-cffi,
python-py7zr)
* gnu/packages/python-web.scm (python-ovh, python-zope-interface,
python-zope-hookable, python-url, python-transaction, python-sanic,
python-woob, python-flask-combo-jsonapi)
* gnu/packages/python-xyz.scm (python-affine, python-colorful,
python-lunr, python-mdit-py-plugins, python-bidict, python-sh,
python-can, python-jsonargparse, python-pyjwt,
python-virtualenv-clone, python-pikepdf, python-tasklogger,
python-notebook, python-structlog, binwalk, python-argcomplete,
python-attrs, python-yq, python-stone, python-identify,
python-nodeenv, python-forbiddenfruit, python-eliot,
python-pem, python-scikit-build, python-minikanren, python-verspec,
python-mike)
* gnu/packages/simulation.scm (python-dolfin-adjoint)
* gnu/packages/statistics.scm (python-emcee, python-rpy2)
* gnu/packages/syndication.scm (rtv, tuir)
* gnu/packages/terminals.scm (python-halo, python-log-symbols,
python-spinners)
* gnu/packages/textutils.scm (python-panflute)
* gnu/packages/version-control.scm (pre-commit)
* gnu/packages/web.scm (python-httpretty)
* gnu/packages/xml.scm (python-xmltodict)
[native-inputs]: Remove python-coverage.

* gnu/packages/android.scm (python-androguard):
  [native-inputs]: Remove python-coverage.
  [arguments]<#:phases>: Adapt 'check phase replacement.
---
 gnu/packages/android.scm            |  6 ++--
 gnu/packages/astronomy.scm          |  6 ++--
 gnu/packages/bioinformatics.scm     |  8 ++---
 gnu/packages/check.scm              |  7 ++--
 gnu/packages/cpp.scm                |  3 +-
 gnu/packages/django.scm             |  3 +-
 gnu/packages/engineering.scm        |  3 +-
 gnu/packages/gpodder.scm            |  3 +-
 gnu/packages/graph.scm              |  3 +-
 gnu/packages/jupyter.scm            |  2 +-
 gnu/packages/machine-learning.scm   | 12 ++-----
 gnu/packages/music.scm              |  3 +-
 gnu/packages/package-management.scm |  6 ++--
 gnu/packages/python-check.scm       |  2 +-
 gnu/packages/python-compression.scm | 14 +++-----
 gnu/packages/python-web.scm         | 18 ++++------
 gnu/packages/python-xyz.scm         | 55 ++++++++++-------------------
 gnu/packages/simulation.scm         |  1 -
 gnu/packages/statistics.scm         |  6 ++--
 gnu/packages/syndication.scm        |  4 +--
 gnu/packages/terminals.scm          |  9 ++---
 gnu/packages/textutils.scm          |  1 -
 gnu/packages/version-control.scm    |  1 -
 gnu/packages/web.scm                |  1 -
 gnu/packages/xml.scm                |  2 +-
 25 files changed, 59 insertions(+), 120 deletions(-)

Toggle diff (415 lines)diff --git a/gnu/packages/android.scm b/gnu/packages/android.scm
index bafca18abe..58d3815d2a 100644
--- a/gnu/packages/android.scm
+++ b/gnu/packages/android.scm
@@ -1076,11 +1076,9 @@ (define-public python-androguard
          (replace 'check
            ;; Adapted from .travis.yml
            (lambda _
-             (invoke "nosetests" "--with-coverage" "--with-timer"
-                     "--timer-top-n" "50"))))))
+             (invoke "nosetests" "--with-timer" "--timer-top-n" "50"))))))
     (native-inputs
-     (list python-codecov python-coverage python-mock python-nose
-           python-nose-timer))
+     (list python-codecov python-mock python-nose python-nose-timer))
     (propagated-inputs
      (list python-asn1crypto
            python-colorama
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index a3aedac986..8c47e7c61c 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1729,8 +1729,7 @@ (define-public python-asdf-astropy
           (add-before 'check 'set-home-env
             (lambda _ (setenv "HOME" "/tmp"))))))
     (native-inputs
-     (list python-coverage
-           python-h5py
+     (list python-h5py
            python-pandas
            python-pytest
            python-pytest-astropy
@@ -4630,8 +4629,7 @@ (define-public python-poliastro
             (lambda _
               (setenv "HOME" "/tmp"))))))
     (native-inputs
-     (list python-coverage
-           python-hypothesis
+     (list python-hypothesis
            python-mypy
            python-flit-core
            python-pytest
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b989c87842..9183a4e382 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3657,8 +3657,7 @@ (define-public python-ega-download-client
     (propagated-inputs (list python-htsget python-psutil python-requests
                              python-tqdm python-urllib3))
     (native-inputs
-     (list python-coverage
-           python-mock
+     (list python-mock
            python-pyfakefs
            python-pytest
            python-responses
@@ -6418,7 +6417,7 @@ (define-public python-scikit-bio
            python-requests
            python-scipy))
     (native-inputs
-     (list python-coverage python-pytest))
+     (list python-pytest))
     (home-page "https://scikit-bio.org")
     (synopsis "Data structures, algorithms and educational resources for bioinformatics")
     (description
@@ -19887,8 +19886,7 @@ (define-public python-cooler
            python-scipy
            python-simplejson))
     (native-inputs
-     (list python-coverage
-           python-hatchling
+     (list python-hatchling
            python-isort
            python-pytest
            python-pytest-cov))
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index a0388da61d..5b088c0e8e 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -1969,8 +1969,7 @@ (define-public python-pytest-randomly
                          "not reordered "
                          "and not test_it_runs_before_stepwise "
                          "and not test_entrypoint_injection"))))))))
-    (native-inputs (list python-coverage
-                         python-factory-boy
+    (native-inputs (list python-factory-boy
                          python-faker
                          python-numpy
                          python-pytest-xdist))
@@ -3165,7 +3164,7 @@ (define-public python-pytest-flakes
              (add-installed-pythonpath inputs outputs)
              (invoke "py.test" "-vv" "-k" "not test_syntax_error"))))))
     (native-inputs
-     (list python-coverage python-pytest))
+     (list python-pytest))
     (propagated-inputs
      (list python-pyflakes))
     (home-page "https://github.com/fschulze/pytest-flakes")
@@ -4129,7 +4128,7 @@ (define-public python-aiounittest
                       #t)))))
     (propagated-inputs (list python-wrapt))
     (native-inputs
-     (list python-coverage python-nose))
+     (list python-nose))
     (home-page
      "https://github.com/kwarunek/aiounittest")
     (synopsis "Test asyncio code more easily")
diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index b9650e22fc..6c9c70baf4 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -1348,8 +1348,7 @@ (define-public cpplint
                    (setenv "GUIX_PYTHONPATH"
                            (getenv "TMP_PYTHONPATH")))))))
     (native-inputs
-     (list python-coverage
-           python-pytest
+     (list python-pytest
            python-pytest-cov
            python-pytest-runner
            python-setuptools
diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index 9aadc8257c..878e1fed2b 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -510,8 +510,7 @@ (define-public python-django-haystack
      (list python-django python-packaging))
     ;; (inputs (list gdal)) ; it's optional, tests fail when provided
     (native-inputs
-     (list python-coverage
-           python-dateutil
+     (list python-dateutil
            python-geopy
            python-pysolr
            python-requests
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index 3882a35d6b..cc84a760e9 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -2964,8 +2964,7 @@ (define-public python-scikit-rf
                              python-pyqtgraph
                              python-qtpy
                              python-scipy))
-    (native-inputs (list python-coverage
-                         python-nbval
+    (native-inputs (list python-nbval
                          python-networkx
                          python-pytest
                          python-pytest-cov
diff --git a/gnu/packages/gpodder.scm b/gnu/packages/gpodder.scm
index c3e1c9b496..57e14ee93f 100644
--- a/gnu/packages/gpodder.scm
+++ b/gnu/packages/gpodder.scm
@@ -65,7 +65,6 @@ (define-public gpodder
     (build-system python-build-system)
     (native-inputs
      (list intltool
-           python-coverage
            python-minimock
            python-pytest
            python-pytest-cov
@@ -169,7 +168,7 @@ (define-public python-mygpoclient
          "05hmjdb73m7vl6lzvh58bnliy4227pv8hprwfka0bg19cnvgpyf5"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-coverage python-minimock python-nose python-pytest))
+     (list python-minimock python-nose python-pytest))
     (arguments
      '(#:phases
        (modify-phases %standard-phases
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 57c4bd05ed..a11667b678 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -482,7 +482,6 @@ (define-public python-graphtools
     (native-inputs
      (list util-linux ;for lscpu
            python-anndata
-           python-coverage
            python-coveralls
            python-nose
            python-nose2
@@ -570,7 +569,7 @@ (define-public python-pygsp
                 "")))))))
     (propagated-inputs (list python-numpy python-scikit-image python-scipy))
     (native-inputs
-     (list python-coverage python-coveralls python-pytest))
+     (list python-coveralls python-pytest))
     (home-page "https://github.com/epfl-lts2/pygsp")
     (synopsis "Graph Signal Processing in Python")
     (description "The PyGSP is a Python package to ease signal processing on
diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm
index f47d8de295..70d894939c 100644
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -519,7 +519,7 @@ (define-public python-jupyter-packaging
      (list python-deprecation python-packaging python-setuptools
            python-tomlkit python-wheel))
     (native-inputs
-     (list python-pypa-build python-coverage python-pytest
+     (list python-pypa-build python-pytest
            python-pytest-cov python-pytest-mock))
     (home-page "https://jupyter.org")
     (synopsis "Jupyter packaging utilities")
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index bb134a6618..350c2d2b39 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1589,7 +1589,6 @@ (define args
       (list cmake-minimal
             googletest
             pybind11
-            python-coverage
             python-fb-re2
             python-parameterized
             python-pytest
@@ -1667,8 +1666,7 @@ (define-public onnx-optimizer
                              " and not test_fuse_transpose")))))))))
     (native-inputs
      (append
-      (list cmake-minimal python-pytest python-pytest-runner
-            python-coverage)
+      (list cmake-minimal python-pytest python-pytest-runner)
       (filter
        (lambda (pkg)
          (member (or (%current-target-system)
@@ -5280,8 +5278,7 @@ (define-public python-lightning-utilities
                 "016zikn39apig3y6xyipw34w0w02c73z483radddbf68ivpjgz3r"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage
-           python-setuptools
+     (list python-setuptools
            python-wheel))
     (propagated-inputs
      (list python-importlib-metadata
@@ -5472,7 +5469,6 @@ (define-public python-pytorch-lightning
       (native-inputs
        (list python-aiohttp
              python-cloudpickle
-             python-coverage
              python-flaky
              python-pympler
              python-pytest
@@ -5510,7 +5506,6 @@ (define-public python-torchmetrics
            python-lightning-utilities))
     (native-inputs
      (list python-cloudpickle
-           python-coverage
            python-fire
            python-mir-eval
            python-mypy
@@ -5926,8 +5921,7 @@ (define-public python-gpytorch
                              python-mpmath
                              python-scikit-learn
                              python-scipy))
-    (native-inputs (list python-coverage
-                         python-flake8-print
+    (native-inputs (list python-flake8-print
                          python-nbval
                          python-pytest
                          python-setuptools
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 7d28ef4b58..ae2afb8441 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -4229,8 +4229,7 @@ (define-public python-pylast
     ;; https://github.com/pylast/pylast/issues/105
     (arguments '(#:tests? #f))
     (native-inputs
-     (list python-coverage python-pytest python-flaky python-pyyaml
-           python-setuptools-scm))
+     (list python-pytest python-flaky python-pyyaml python-setuptools-scm))
     (home-page "https://github.com/pylast/pylast")
     (synopsis "Python interface to Last.fm and Libre.fm")
     (description "A Python interface to Last.fm and other API-compatible
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 8c629ba722..01b05fb9e1 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -1107,8 +1107,7 @@ (define-public python-anaconda-client
            python-requests
            python-setuptools))
     (native-inputs
-     (list python-coverage
-           python-dateutil
+     (list python-dateutil
            python-freezegun
            python-mock
            python-pillow
@@ -1296,8 +1295,7 @@ (define-public conda
            ;; XXX: This is dragged in by libarchive and is needed at runtime.
            zstd))
     (native-inputs
-     (list python-coverage
-           python-flaky
+     (list python-flaky
            python-pytest-cov
            python-pytest-timeout
            python-pytest-xprocess
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index d0319fcbc0..1348c9651f 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -1625,7 +1625,7 @@ (define-public python-re-assert
            (lambda _
              (invoke "pytest" "-vv"))))))
     (native-inputs
-     (list python-covdefaults python-coverage python-pytest))
+     (list python-covdefaults python-pytest))
     (propagated-inputs
      (list python-regex))
     (home-page "https://github.com/asottile/re-assert")
diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm
index 5b994d408f..dfe819733e 100644
--- a/gnu/packages/python-compression.scm
+++ b/gnu/packages/python-compression.scm
@@ -163,7 +163,6 @@ (define-public python-multivolumefile
     (build-system pyproject-build-system)
     (native-inputs
      (list python-setuptools-scm
-           python-coverage
            python-coveralls
            python-hypothesis
            python-pyannotate
@@ -306,8 +305,7 @@ (define-public python-pybcj
     (build-system pyproject-build-system)
     (propagated-inputs (list python-importlib-metadata))
     (native-inputs
-     (list python-coverage
-           python-hypothesis
+     (list python-hypothesis
            python-pytest
            python-pytest-cov
            python-setuptools-scm
@@ -340,8 +338,7 @@ (define-public python-bcj-cffi
     (propagated-inputs
      (list python-cffi python-toml python-setuptools-scm))
     (native-inputs
-     (list python-setuptools python-coverage python-pytest
-           python-pytest-cov))
+     (list python-setuptools python-pytest python-pytest-cov))
     (home-page "https://github.com/miurahr/bcj-cffi")
     (synopsis "Branch / Call /Jump CFFI library in Python")
     (description "This package provides an implementation of the Branch / Call /
@@ -466,8 +463,7 @@ (define-public python-pyppmd
                 "03w4x26mar0ha73c3v39psn1i0k6xrzwmaxfsxysic73jz99np07"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage
-           python-hypothesis
+     (list python-hypothesis
            python-pytest
            python-pytest-benchmark
            python-pytest-cov
@@ -500,7 +496,6 @@ (define-public python-ppmd-cffi
     (native-inputs
      (list python-hypothesis
            python-setuptools-scm
-           python-coverage
            python-pytest
            python-pytest-cov))
     (home-page "https://github.com/miurahr/ppmd")
@@ -535,8 +530,7 @@ (define-public python-py7zr
            python-pyzstd
            python-texttable))
     (native-inputs
-     (list python-coverage
-           python-setuptools
+     (list python-setuptools
            python-coveralls
            python-libarchive-c
            python-py-cpuinfo
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index dc5ad03f92..91c542ee73 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1614,8 +1614,7 @@ (define-public python-ovh
     (build-system pyproject-build-system)
     (arguments (list #:tests? #f))      ; XXX: tests require networking
     (propagated-inputs (list python-requests))
-    (native-inputs (list python-coverage
-                         python-isort
+    (native-inputs (list python-isort
                          python-pytest
                          python-pytest-cov
                          python-setuptools
@@ -3865,8 +3864,7 @@ (define-public python-zope-interface
     (build-system python-build-system)
     (arguments '(#:tests? #f))  ; test suite can't find python-zope-testing
     (native-inputs
-     (list python-coverage python-nose python-zope-event
-           python-zope-testing))
+     (list python-nose python-zope-event python-zope-testing))
     (home-page "https://github.com/zopefoundation/zope.interface")
     (synopsis "Python implementation of the \"design by contract\"
 methodology")
@@ -4162,7 +4160,7 @@ (define-public python-zope-hookable
           "0hc82lfr7bk53nvbxvjkibkarngyrzgfk2i6bg8wshl0ly0pdl19"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-coverage python-zope-testing))
+     (list python-zope-testing))
     (home-page "https://github.com/zopefoundation/zope.hookable")
     (synopsis "Zope hookable")
     (description "This package supports the efficient creation of hookable
@@ -5621,7 +5619,7 @@ (define-public python-url
     (propagated-inputs
      (list python-publicsuffix))
     (native-inputs
-     (list python-coverage python-nose))
+     (list python-nose))
     (arguments
      `(#:tests? #f)) ; FIXME: tests fail with "ImportError: No module named 'tests'"
     (home-page "https://

This message was truncated. Download the full message here.

Nicolas Graves wrote 2 weeks ago

[PATCH python-team v4 13/52] build-system/pyproject: Remove python-coverage native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:875xkx8kri.fsf@ngraves.fr

* gnu/packages/jupyter.scm (python-nbclassic, python-papermill)
* gnu/packages/openstack.scm (python-hacking, python-oslo.context)
* gnu/packages/python-check.scm (python-pytest-testmon)
* gnu/packages/python-science.scm (python-scikit-survival, python-modin,
  python-pynetdicom)
* gnu/packages/python-web.scm (python-aioitertools, python-python3-saml,
  python-zope-i18n-messageid, python-rangehttpserver, python-http-ece,
  python-zeep)
* gnu/packages/python-xyz.scm (python-argopt, python-case, python-pypugjs,
  python-repoze-lru, python-lsp-jsonrpc, python-pillow-heif,
  python-legacy-api-wrap, python-waitress, python-gevent, python-twisted,
  python-mamba, python-bagit, python-typer, python-numcodecs, python-diceware,
  python-param)
* gnu/packages/statistics.scm (python-radian)
[native-inputs]: Remove python-coverage.
---
 gnu/packages/jupyter.scm        |  4 +---
 gnu/packages/openstack.scm      |  6 ++----
 gnu/packages/python-check.scm   |  3 +--
 gnu/packages/python-science.scm |  3 ---
 gnu/packages/python-web.scm     | 13 +++++--------
 gnu/packages/python-xyz.scm     | 32 +++++++++++---------------------
 gnu/packages/statistics.scm     |  3 +--
 7 files changed, 21 insertions(+), 43 deletions(-)

Toggle diff (317 lines)diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm
index 70d894939c..a9f57b2ccc 100644
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -81,8 +81,7 @@ (define-public python-nbclassic
                              python-terminado
                              python-tornado-6
                              python-traitlets))
-    (native-inputs (list python-coverage
-                         python-nbval
+    (native-inputs (list python-nbval
                          python-jupyter-packaging
                          python-pytest
                          python-pytest-cov
@@ -1162,7 +1161,6 @@ (define-public python-papermill
                          python-bumpversion
                          python-check-manifest
                          python-codecov
-                         python-coverage
                          python-ipython
                          python-ipywidgets
                          python-moto
diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index ac283bd019..84696a586f 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -153,8 +153,7 @@ (define-public python-hacking
     (propagated-inputs
      (list python-flake8))
     (native-inputs
-     (list python-coverage
-           python-ddt
+     (list python-ddt
            python-eventlet
            python-fixtures
            python-setuptools
@@ -551,8 +550,7 @@ (define-public python-oslo.context
     (propagated-inputs
      (list python-debtcollector))
     (native-inputs
-     (list python-coverage
-           python-fixtures
+     (list python-fixtures
            python-hacking
            python-mypy
            python-oslotest
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 1348c9651f..af6c0deb65 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -1651,8 +1651,7 @@ (define-public python-pytest-testmon
     (build-system pyproject-build-system)
     (arguments (list #:tests? #false)) ;there are none
     (native-inputs
-     (list python-coverage
-           python-pytest
+     (list python-pytest
            python-setuptools
            python-wheel))
     (home-page "https://github.com/tarpas/pytest-testmon")
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index f18da4a326..3baee53a29 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -889,7 +889,6 @@ (define-public python-scikit-survival
              python-scipy))
       (native-inputs
        (list python-pypa-build
-             python-coverage
              python-cython-3
              python-packaging
              python-pytest
@@ -3052,7 +3051,6 @@ (define-public python-modin
            python-s3fs))
     (native-inputs
      (list python-boto3
-           python-coverage
            python-jinja2
            python-lxml
            python-matplotlib
@@ -3960,7 +3958,6 @@ (define-public python-pynetdicom
                     " and not test_pr_level_series"
                     " and not test_scp_cancelled"))))
     (native-inputs (list python-codespell
-                         python-coverage
                          python-poetry-core
                          python-pytest
                          python-pytest-cov
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 91c542ee73..11dfeeb54c 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -903,8 +903,7 @@ (define-public python-aioitertools
     (arguments (list #:tests? #false))
     (propagated-inputs (list python-typing-extensions))
     (native-inputs
-     (list python-coverage
-           python-flake8
+     (list python-flake8
            python-flit-core
            python-mypy
            python-pytest
@@ -1587,8 +1586,7 @@ (define-public python-python3-saml
               (setenv "LD_LIBRARY_PATH"
                       (dirname (search-input-file inputs "lib/libxmlsec1-openssl.so.1.2.37"))))))))
     (propagated-inputs (list python-isodate python-lxml python-xmlsec))
-    (native-inputs (list python-coverage
-                         python-flake8
+    (native-inputs (list python-flake8
                          python-freezegun
                          python-poetry-core
                          python-pytest
@@ -3997,7 +3995,7 @@ (define-public python-zope-i18nmessageid
         (base32 "14mx62khys82p2gmmf3m40x4jmvcz3rndvl6qik2n2qfp13n7ds7"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage python-setuptools
+     (list python-setuptools
            python-wheel python-zope-testrunner))
     (propagated-inputs
      (list python-six))
@@ -8222,7 +8220,7 @@ (define-public python-rangehttpserver
        (sha256
         (base32 "1dx533fsbq1mbz3by7qkm5bh2c253nwvm8214pqbwbfq07kqkwf2"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-coverage python-coveralls python-pytest
+    (native-inputs (list python-coveralls python-pytest
                          python-setuptools python-wheel))
     (home-page "https://github.com/danvk/RangeHTTPServer")
     (synopsis "SimpleHTTPServer with support for range requests")
@@ -8582,7 +8580,7 @@ (define-public python-http-ece
     (propagated-inputs
      (list python-cryptography))
     (native-inputs
-     (list python-coverage python-mock python-nose))
+     (list python-mock python-nose))
     (home-page "https://github.com/web-push-libs/encrypted-content-encoding")
     (synopsis "Encrypted Content Encoding for HTTP")
     (description
@@ -10139,7 +10137,6 @@ (define-public python-zeep
            python-requests-toolbelt))
     (native-inputs
      (list nss-certs-for-test
-           python-coverage
            python-flake8
            python-flake8-blind-except
            python-flake8-debugger
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e4b3dab43a..e639c6ae4d 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1407,7 +1407,7 @@ (define-public python-argopt
               "0ybs7kkp0cpl8zn1lvf7481xhssg1bbhh5la2cjzdm5yibashyxa"))))
    (build-system python-build-system)
    (native-inputs
-    (list python-coverage python-nose python-setuptools ; Won't build without this.
+    (list python-nose python-setuptools ; Won't build without this.
           python-setuptools-scm))
    (propagated-inputs
     (list python-toml python-flake8))
@@ -4687,8 +4687,6 @@ (define-public python-case
     (build-system python-build-system)
     (propagated-inputs
      (list python-mock python-nose python-six))
-    (native-inputs
-     (list python-coverage))
     (home-page "https://github.com/celery/case")
     (synopsis "Unittest utilities and convenience methods")
     (description
@@ -7193,8 +7191,7 @@ (define-public python-pypugjs
                        ;; pyramid is outdated and pyramid-mako is unpackaged.
                        (substitute* "setup.cfg"
                          (("'(pyramid|pyramid-mako)[^']*',") "")))))))
-    (native-inputs (list python-coverage
-                         python-django
+    (native-inputs (list python-django
                          python-jinja2
                          python-flake8
                          python-flask
@@ -7804,7 +7801,7 @@ (define-public python-repoze-lru
         (base32 "0xzz1aw2smy8hdszrq8yhnklx6w1r1mf55061kalw3iq35gafa84"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage python-nose python-setuptools python-wheel))
+     (list python-nose python-setuptools python-wheel))
     (home-page "https://www.repoze.org")
     (synopsis "Tiny LRU cache implementation and decorator")
     (description
@@ -8669,8 +8666,7 @@ (define-public python-lsp-jsonrpc
          "04n95h0cqnsrdyh1gv0abh2i5ynyrq2wfqpppx9djp7mxr9y9226"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage
-           python-pycodestyle
+     (list python-pycodestyle
            python-pyflakes
            python-pytest
            python-pytest-cov
@@ -11418,7 +11414,6 @@ (define-public python-pillow-heif
     (inputs (list libheif))
     (propagated-inputs (list python-pillow))
     (native-inputs (list opencv         ; for opencv-python
-                         python-coverage
                          python-defusedxml
                          python-numpy
                          python-packaging
@@ -17643,8 +17638,7 @@ (define-public python-legacy-api-wrap
          "1d5jyd8d2wxm6y0s39wwqw87gdm4zqlbyz78cf3yqbrim1xdch4w"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage
-           python-hatch-vcs
+     (list python-hatch-vcs
            python-hatchling
            python-pytest))
     (home-page "https://github.com/flying-sheep/legacy-api-wrap")
@@ -20771,7 +20765,7 @@ (define-public python-waitress
      ;; https://github.com/Pylons/waitress/issues/443
      (list #:test-flags #~(list "-k" "not test_service_port")))
     (native-inputs
-     (list python-coverage python-pytest python-pytest-cov
+     (list python-pytest python-pytest-cov
            python-setuptools python-wheel))
     (home-page "https://github.com/Pylons/waitress")
     (synopsis "Waitress WSGI server")
@@ -22265,7 +22259,6 @@ (define-public python-gevent
      (list python-greenlet python-zope-event python-zope-interface))
     (native-inputs
      (list python-cffi
-           python-coverage
            python-cython
            python-dnspython
            python-idna
@@ -22368,7 +22361,6 @@ (define-public python-twisted
            python-zope-interface))
     (native-inputs
      (list glibc-utf8-locales ;for OpenTestLogTests.test_utf8
-           python-coverage
            python-hatch-fancy-pypi-readme
            python-hatchling
            python-httpx
@@ -26099,7 +26091,7 @@ (define-public python-mamba
     (build-system python-build-system)
     (arguments `(#:tests? #f))  ; No test
     (propagated-inputs
-     (list python-clint python-coverage))
+     (list python-clint))
     (home-page "https://nestorsalceda.com/mamba/")
     (synopsis "Test runner for Python")
     (description
@@ -26863,7 +26855,7 @@ (define-public python-bagit
           "1m6y04qmig0b5hzb35lnaw3d2yfydb7alyr1579yblvgs3da6j7j"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-setuptools-scm python-coverage python-mock))
+     (list python-setuptools-scm python-mock))
     (home-page "https://libraryofcongress.github.io/bagit-python/")
     (synopsis "Create and validate BagIt packages")
     (description "Bagit is a Python library and command line utility for working
@@ -28503,7 +28495,7 @@ (define-public python-typer
     (propagated-inputs
      (list python-click))
     (native-inputs
-     (list python-coverage python-flit python-pytest python-rich
+     (list python-flit python-pytest python-rich
            python-shellingham))
     (home-page "https://github.com/tiangolo/typer")
     (synopsis "Typer builds CLI based on Python type hints")
@@ -29890,8 +29882,7 @@ (define-public python-numcodecs
      (list c-blosc lz4 zlib
            `(,zstd "lib")))
     (propagated-inputs
-     (list python-coverage
-           python-google-crc32c
+     (list python-google-crc32c
            python-importlib-metadata
            python-msgpack
            python-numpy
@@ -33682,7 +33673,7 @@ (define-public python-diceware
          "0klb0ysybzlh2wihvir82hgq62v0jjmlcqklwajyms7c0p529yby"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-coverage python-pytest python-pytest-runner))
+     (list python-pytest python-pytest-runner))
     (home-page "https://github.com/ulif/diceware/")
     (synopsis "Generates memorable passphrases")
     (description "This package generates passphrases by concatenating words
@@ -34777,7 +34768,6 @@ (define-public python-param
     (build-system pyproject-build-system)
     (native-inputs
      (list python-cloudpickle
-           python-coverage
            python-hatchling
            python-hatch-vcs
            python-ipython
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 736b90b384..7a02786ab6 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -7208,8 +7208,7 @@ (define-public python-radian
                        (setenv "HOME" "/tmp"))))))
     (propagated-inputs (list python-prompt-toolkit python-pygments
                              python-rchitect))
-    (native-inputs (list python-coverage
-                         python-pexpect
+    (native-inputs (list python-pexpect
                          python-ptyprocess
                          python-pyte
                          python-pytest
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Nicolas Graves wrote 1 months ago

[PATCH python-team v4 14/52] build-system/pyproject: Remove python-pytest-black native-input.

Recipients:(address . 70858@debbugs.gnu.org)

Message-ID:874j0h8kr9.fsf@ngraves.fr

* gnu/packages/check.scm (python-pytest-perf, python-pytest-enabler)
[native-inputs]: Remove python-pytest-black.

* gnu/packages/python-web.scm (python-portend)[native-inputs]:
Remove python-pytest-black.
---
 gnu/packages/check.scm      |  2 --
 gnu/packages/python-web.scm |  1 -
 gnu/packages/python-xyz.scm | 10 ----------
 3 files changed, 13 deletions(-)

Toggle diff (124 lines)diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 5b088c0e8e..da8f42c315 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2941,7 +2941,6 @@ (define-public python-pytest-enabler
            python-jaraco-functools
            python-toml))
     (native-inputs (list python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-cov
                          python-pytest-flake8
@@ -3115,7 +3114,6 @@ (define-public python-pytest-perf
                            "and not upstream_url"))))
     (native-inputs
      (list python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-cov
            python-pytest-enabler
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 11dfeeb54c..4375608457 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -702,7 +702,6 @@ (define-public python-portend
     (propagated-inputs (list python-tempora))
     ;; TODO: Add python-pytest-ruff to native-inputs once it has been packaged.
     (native-inputs (list python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-cov
                          python-pytest-enabler
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e639c6ae4d..13e6bb948f 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -12775,7 +12775,6 @@ (define-public python-importlib-resources
                      (string-append (getcwd) "/_custom_build")))))))
     (native-inputs
      (list python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-cov
            python-pytest-enabler
@@ -12926,7 +12925,6 @@ (define-public python-jaraco-classes
       #:test-flags '(list "-k" "not project")))
     (native-inputs
      (list python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-cov
            python-pytest-flake8
@@ -12960,7 +12958,6 @@ (define-public python-jaraco-collections
     ;; TODO: Add python-pytest-ruff to native-inputs once it has been
     ;; packaged.
     (native-inputs (list python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-cov
                          python-pytest-enabler
@@ -13021,7 +13018,6 @@ (define-public python-jaraco-context
            #:test-flags '(list "-k" "not project")))
     (native-inputs
      (list python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-cov
            python-pytest-flake8
@@ -13056,7 +13052,6 @@ (define-public python-jaraco-functools
     (native-inputs
      (list python-jaraco-classes
            python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-cov
            python-pytest-flake8
@@ -13151,7 +13146,6 @@ (define-public python-jaraco-text
     ;; TODO: Add python-pytest-ruff to native-inputs once it has been
     ;; packaged.
     (native-inputs (list python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-cov
                          python-pytest-enabler
@@ -17900,7 +17894,6 @@ (define-public python-path
                python-packaging
                python-pygments
                python-pytest
-               python-pytest-black
                python-pytest-checkdocs
                python-pytest-cov
                python-pytest-enabler
@@ -18006,7 +17999,6 @@ (define-public python-pip-run
        (append python-nbformat
                python-pygments
                python-pytest
-               python-pytest-black
                python-pytest-checkdocs
                python-pytest-cov
                python-pytest-enabler
@@ -22619,7 +22611,6 @@ (define-public python-inflect
     (propagated-inputs (list python-pydantic))
     (native-inputs (list python-pygments
                          python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-cov
                          python-pytest-enabler
@@ -27897,7 +27888,6 @@ (define-public python-tempora
     (native-inputs
      (list python-freezegun
            python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-cov
            python-pytest-enabler
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Nicolas Graves wrote 2 weeks ago

[PATCH v4 16/52] gnu: u-boot-tools: Remove python-coverage native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-16-ngraves@ngraves.fr

* gnu/packages/bootloaders.scm (u-boot-tools):

[native-inputs]: Remove python-coverage.

[arguments]<#:phases>: Adapt patch phase.

Change-Id: I94394544079197b4a3f8c53cc0b3d78d1f5dc8be

---

gnu/packages/bootloaders.scm | 17 ++++-------------

1 file changed, 4 insertions(+), 13 deletions(-)

Toggle diff (44 lines)diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm
index 4dab7bd0b7..753064cc43 100644
--- a/gnu/packages/bootloaders.scm
+++ b/gnu/packages/bootloaders.scm
@@ -825,8 +825,7 @@ (define-public u-boot-tools
     (name "u-boot-tools")
     (native-inputs
      (modify-inputs (package-native-inputs u-boot)
-       (prepend python-coverage
-                python-filelock
+       (prepend python-filelock
                 python-pycryptodomex
                 python-pytest
                 python-pytest-xdist)))
@@ -842,14 +841,6 @@ (define-public u-boot-tools
                (("/bin/false") (which "false")))
              (substitute* "tools/dtoc/fdt_util.py"
                (("'cc'") "'gcc'"))
-             (substitute* "tools/u_boot_pylib/test_util.py"
-               ;; python3-coverage is simply called coverage in guix.
-               (("python3-coverage") "coverage")
-
-               ;; Don't require 100% coverage since it's brittle and can
-               ;; fail with newer versions of coverage or dependencies.
-               (("raise ValueError\\('Test coverage failure'\\)")
-                "print('Continuing anyway since Guix does not care :O')"))
              (substitute* "test/run"
                ;; Make it easier to find test failures.
                (("#!/bin/bash") "#!/bin/bash -x")
@@ -862,9 +853,9 @@ (define-public u-boot-tools
                 "# run_test \"sandbox_noinst\"")
                (("run_test \"sandbox_vpl\"")
                 "# run_test \"sandbox_vpl\"")
-               ;; FIXME: code coverage not working
-               (("run_test \"binman code coverage\"")
-                "# run_test \"binman code coverage\"")
+               ;; Disable code coverage tests.
+               (("run_test \"(\\w+) code coverage\"" all)
+                (string-append "# " all))
                ;; This test would require internet access.
                (("\\./tools/buildman/buildman") (which "true")))
              (substitute* "test/py/tests/test_sandbox_exit.py"
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 17/52] gnu: python-aiosqlite: Remove python-coverage native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-17-ngraves@ngraves.fr

* gnu/packages/databases.scm (python-aiosqlite):

[arguments]<#:phases>: Adapt check phase.

[native-inputs]: Remove python-coverage.

Change-Id: I165d174426022f0603223e3def91ffe280f15899

---

gnu/packages/databases.scm | 5 +----

1 file changed, 1 insertion(+), 4 deletions(-)

Toggle diff (19 lines)diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 40ffe3e084..984598e2b4 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -4141,11 +4141,8 @@ (define-public python-aiosqlite
                         (replace 'check
                           (lambda* (#:key tests? #:allow-other-keys)
                             (when tests?
-                              (invoke "python" "-m" "coverage" "run" "-m"
-                                      "aiosqlite.tests")
-                              (invoke "python" "-m" "coverage" "report")))))))
+                              (invoke "python" "-m" "aiosqlite.tests")))))))
     (native-inputs (list python-flit-core
-                         python-coverage
                          python-mypy))
     (home-page "https://github.com/jreese/aiosqlite")
     (synopsis
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 18/52] gnu: python-openid: Remove python-coverage native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-18-ngraves@ngraves.fr

* gnu/packages/python-web.scm (python-openid):

[native-inputs]: Remove python-coverage.

[arguments]<#:phases>: Rewrite check phase.

Change-Id: Id4ea5abc531f5fd84b60ff22407eb608f1e6ac29

---

gnu/packages/python-web.scm | 17 +++++++++--------

1 file changed, 9 insertions(+), 8 deletions(-)

Toggle diff (33 lines)diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 4375608457..09cc355998 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -3189,17 +3189,18 @@ (define-public python-openid
          "1bxf9a3ny1js422j962zfzl4a9dhj192pvai05whn7j0iy9gdyrk"))))
     (build-system python-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-        (replace 'check
-          (lambda* (#:key tests? #:allow-other-keys)
-            (when tests?
-              (invoke "coverage" "run" "-m"
-                      "unittest" "openid.test.test_suite")))))))
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (if tests?
+                  (invoke "python" "-m" "unittest" "openid.test.test_suite")
+                  (format #t "test suite not run~%")))))))
     (propagated-inputs
      (list python-defusedxml))
     (native-inputs
-     (list python-coverage python-psycopg2 python-django))
+     (list python-psycopg2 python-django))
     (home-page "https://github.com/necaris/python3-openid")
     (synopsis "OpenID support for servers and consumers")
     (description "This library provides OpenID authentication for Python, both
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 19/52] build-system/pyproject: Remove python-coveralls native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-19-ngraves@ngraves.fr

* gnu/packages/django.scm (python-django-pipeline)[native-inputs]:

Remove python-coveralls.

* gnu/packages/geo.scm (python-cartopy)[native-inputs]: Remove

python-coveralls.

* gnu/packages/graph.scm (python-graphtools,

python-pygsp)[native-inputs]: Remove python-coveralls.

* gnu/packages/python-compression.scm (python-multivolumefile,

python-py7zr)[native-inputs]: Remove python-coveralls.

* gnu/packages/python-science.scm (python-trimesh)[native-inputs]:

Remove python-coveralls.

* gnu/packages/python-web.scm (python-flask-combo-jsonapi,

python-rangehttpserver) [native-inputs]: Remove python-coveralls.

* gnu/packages/python-xyz.scm (python-affine, python-ddlparse,

python-tasklogger, python-minikanren)

[native-inputs]: Remove python-coveralls.

* gnu/packages/syndication.scm (rtv, tuir)[native-inputs]: Remove

python-coveralls.

* gnu/packages/telegram.scm (tgcli)[native-inputs]: Remove

python-coveralls.

---

gnu/packages/django.scm | 3 +--

gnu/packages/graph.scm | 3 +--

gnu/packages/python-compression.scm | 2 --

gnu/packages/python-science.scm | 3 +--

gnu/packages/python-web.scm | 6 ++----

gnu/packages/python-xyz.scm | 8 +++-----

gnu/packages/syndication.scm | 4 +---

gnu/packages/telegram.scm | 3 +--

8 files changed, 10 insertions(+), 22 deletions(-)

Toggle diff (171 lines)diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index 878e1fed2b..3e56a20110 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -992,8 +992,7 @@ (define-public python-django-pipeline
      (list python-jsmin
            python-css-html-js-minify))
     (native-inputs
-     (list python-coveralls
-           python-django
+     (list python-django
            python-setuptools
            python-setuptools-scm
            python-tox
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index a11667b678..f45ab42f0b 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -482,7 +482,6 @@ (define-public python-graphtools
     (native-inputs
      (list util-linux ;for lscpu
            python-anndata
-           python-coveralls
            python-nose
            python-nose2
            python-pandas
@@ -569,7 +568,7 @@ (define-public python-pygsp
                 "")))))))
     (propagated-inputs (list python-numpy python-scikit-image python-scipy))
     (native-inputs
-     (list python-coveralls python-pytest))
+     (list python-pytest))
     (home-page "https://github.com/epfl-lts2/pygsp")
     (synopsis "Graph Signal Processing in Python")
     (description "The PyGSP is a Python package to ease signal processing on
diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm
index dfe819733e..b2e62e1d49 100644
--- a/gnu/packages/python-compression.scm
+++ b/gnu/packages/python-compression.scm
@@ -163,7 +163,6 @@ (define-public python-multivolumefile
     (build-system pyproject-build-system)
     (native-inputs
      (list python-setuptools-scm
-           python-coveralls
            python-hypothesis
            python-pyannotate
            python-pytest
@@ -531,7 +530,6 @@ (define-public python-py7zr
            python-texttable))
     (native-inputs
      (list python-setuptools
-           python-coveralls
            python-libarchive-c
            python-py-cpuinfo
            python-pyannotate
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 3baee53a29..0dc0edcb0e 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -978,8 +978,7 @@ (define-public python-trimesh
           ;; module 'trimesh' has no attribute '__main__'.
           (delete 'sanity-check))))
     (native-inputs
-     (list python-coveralls
-           python-pyinstrument
+     (list python-pyinstrument
            python-pytest))
     (propagated-inputs
      (list ;; python-cascadio       ; not packed yet, optional
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 09cc355998..e50eb17c66 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -8220,8 +8220,7 @@ (define-public python-rangehttpserver
        (sha256
         (base32 "1dx533fsbq1mbz3by7qkm5bh2c253nwvm8214pqbwbfq07kqkwf2"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-coveralls python-pytest
-                         python-setuptools python-wheel))
+    (native-inputs (list python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/danvk/RangeHTTPServer")
     (synopsis "SimpleHTTPServer with support for range requests")
     (description
@@ -9704,8 +9703,7 @@ (define-public python-flask-combo-jsonapi
            python-simplejson
            python-six))
     (native-inputs
-     (list python-coveralls
-           python-pytest
+     (list python-pytest
            python-pytest-runner))
     (home-page "https://github.com/AdCombo/flask-combo-jsonapi")
     (synopsis "Flask extension to quickly create JSON:API 1.0 REST Web APIs")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 8df126b45c..d88eb9a11d 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1386,7 +1386,7 @@ (define-public python-affine
                (base32
                 "1shyvajayyzbkp9dihb4mz835jnkp0kqqbyjfqci6v43da6q2kd2"))))
     (build-system pyproject-build-system)
-    (propagated-inputs (list python-coveralls python-pydocstyle
+    (propagated-inputs (list python-pydocstyle
                              python-pytest python-pytest-cov))
     (native-inputs (list python-flit-core))
     (home-page "https://github.com/rasterio/affine")
@@ -6412,7 +6412,6 @@ (define-public python-ddlparse
     (build-system pyproject-build-system)
     (native-inputs
      (list python-codecov
-           python-coveralls
            python-pytest
            python-pytest-cov
            python-setuptools
@@ -17341,7 +17340,7 @@ (define-public python-tasklogger
         (base32 "1901mibcp6aiyjy8afnybrxnb0dkbdxlbvjqbr3gginlw7dr18xh"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-deprecated))
-    (native-inputs (list python-coveralls python-nose2
+    (native-inputs (list python-nose2
                          python-numpy python-setuptools python-wheel))
     (home-page "https://github.com/scottgigante/tasklogger")
     (synopsis "Extension to the core Python logging library")
@@ -36778,8 +36777,7 @@ (define-public python-minikanren
                         (invoke "python" "-m" "pytest" "-v" "tests/" "kanren/"))
                       #t)))))
     (native-inputs
-     (list python-coveralls
-           python-pydocstyle
+     (list python-pydocstyle
            python-pytest
            python-pytest-cov
            python-sympy
diff --git a/gnu/packages/syndication.scm b/gnu/packages/syndication.scm
index ff9e18f064..56677ef91f 100644
--- a/gnu/packages/syndication.scm
+++ b/gnu/packages/syndication.scm
@@ -498,7 +498,6 @@ (define-public rtv
            python-requests python-six))
     (native-inputs
      (list ncurses
-           python-coveralls
            python-mock
            python-pytest
            python-vcrpy))
@@ -540,8 +539,7 @@ (define-public tuir
      (list python-beautifulsoup4 python-decorator python-kitchen
            python-requests python-six))
     (native-inputs
-     (list python-coveralls
-           python-mock
+     (list python-mock
            python-pytest
            python-setuptools
            python-vcrpy
diff --git a/gnu/packages/telegram.scm b/gnu/packages/telegram.scm
index cfcd92fcbc..a4cfc6a9ef 100644
--- a/gnu/packages/telegram.scm
+++ b/gnu/packages/telegram.scm
@@ -839,8 +839,7 @@ (define-public tgcli
                (add-installed-pythonpath inputs outputs)
                (invoke "pytest" "tests")))))))
     (native-inputs
-     `(("coveralls" ,python-coveralls)
-       ("pytest" ,python-pytest)
+     `(("pytest" ,python-pytest)
        ("pytest-click" ,python-pytest-click)
        ("pytest-cov" ,python-pytest-cov)
        ("mkdocs" ,python-mkdocs)
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 20/52] build-system/pyproject: Remove python-pycodestyle native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-20-ngraves@ngraves.fr

* gnu/packages/bioinformatics.scm (python-screed)
* gnu/packages/python-science.scm (python-scipy)
* gnu/packages/python-xyz.scm (python-lsp-jsonrpc, python-diff-cover,
python-fuzzywuzzy, python-jsonargparse, python-lsp-server,
python-orderedmultidict, python-stem)
[native-inputs]: Remove python-pycodestyle.
---
 gnu/packages/bioinformatics.scm |  1 -
 gnu/packages/python-science.scm |  1 -
 gnu/packages/python-xyz.scm     | 14 +++++---------
 3 files changed, 5 insertions(+), 11 deletions(-)

Toggle diff (93 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9183a4e382..38e623f3a6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11513,7 +11513,6 @@ (define-public python-screed
     (build-system pyproject-build-system)
     (native-inputs
      (list python-importlib-resources
-           python-pycodestyle
            python-pytest
            python-pytest-cov
            python-setuptools
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 0dc0edcb0e..a647053d8f 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -462,7 +462,6 @@ (define-public python-scipy
            python-doit
            python-hypothesis
            python-pooch
-           python-pycodestyle
            python-pydevtool
            python-pytest
            python-pytest-cov
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index d88eb9a11d..aa3397f262 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -5203,7 +5203,6 @@ (define-public python-jsonargparse
            python-typeshed-client))
     (native-inputs
      (list python-attrs
-           python-pycodestyle
            python-pydantic
            python-pytest
            python-pytest-subtests
@@ -8665,8 +8664,7 @@ (define-public python-lsp-jsonrpc
          "04n95h0cqnsrdyh1gv0abh2i5ynyrq2wfqpppx9djp7mxr9y9226"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-pycodestyle
-           python-pyflakes
+     (list python-pyflakes
            python-pytest
            python-pytest-cov
            python-setuptools
@@ -9030,7 +9028,6 @@ (define-public python-lsp-server
            python-jedi
            python-lsp-jsonrpc
            python-pluggy
-           python-pycodestyle
            python-pydocstyle
            python-ujson
            python-whatthepatch
@@ -10989,7 +10986,7 @@ (define-public python-orderedmultidict
     (propagated-inputs
      (list python-six))
     (native-inputs
-     (list python-flake8 python-pycodestyle python-setuptools python-wheel))
+     (list python-flake8 python-setuptools python-wheel))
     (home-page "https://github.com/gruns/orderedmultidict")
     (synopsis "Python Ordered Multivalue Dictionary - omdict")
     (description "This package contains a library for ordered multivalue
@@ -23895,7 +23892,7 @@ (define-public python-stem
              (invoke "./run_tests.py" "--unit")
              #t)))))
     (native-inputs
-     (list python-mock python-pycodestyle python-pyflakes))
+     (list python-mock python-pyflakes))
     (home-page "https://stem.torproject.org/")
     (synopsis
      "Python controller library that allows applications to interact with Tor")
@@ -26207,8 +26204,7 @@ (define-public python-diff-cover
       ;; Dropp check of flake8 in tests.
       #~(list "-k" "not test_file_does_not_exist")))
     (native-inputs
-     (list python-pycodestyle
-           python-poetry-core
+     (list python-poetry-core
            python-pyflakes
            python-pylint
            python-pytest
@@ -32778,7 +32774,7 @@ (define-public python-fuzzywuzzy
          "1s00zn75y2dkxgnbw8kl8dw4p1mc77cv78fwfa4yb0274s96w0a5"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-hypothesis python-pycodestyle python-pytest))
+     (list python-hypothesis python-pytest))
     (propagated-inputs
      (list python-levenshtein))
     (home-page "https://github.com/seatgeek/fuzzywuzzy")
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 21/52] gnu: python-re-assert: Remove python-covdefaults native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-21-ngraves@ngraves.fr

* gnu/packages/python-check.scm (python-re-assert):

[native-inputs]: Remove python-covdefaults.

Change-Id: Ib30c58b69aef7f255e5893ae6f9a33bdf41ac85d

---

gnu/packages/python-check.scm | 2 +-

1 file changed, 1 insertion(+), 1 deletion(-)

Toggle diff (15 lines)diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index af6c0deb65..b336631edc 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -1625,7 +1625,7 @@ (define-public python-re-assert
            (lambda _
              (invoke "pytest" "-vv"))))))
     (native-inputs
-     (list python-covdefaults python-pytest))
+     (list python-pytest))
     (propagated-inputs
      (list python-regex))
     (home-page "https://github.com/asottile/re-assert")
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 22/52] build-system/pyproject: Remove python-covdefaults native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-22-ngraves@ngraves.fr

* gnu/packages/python-web.scm (python-devpi-process)
* gnu/packages/python-xyz.scm (python-pyproject-api, python-platformdirs)
* gnu/packages/version-control.scm (pre-commit)
[native-inputs]: Remove python-covdefaults.
---
 gnu/packages/python-web.scm      | 1 -
 gnu/packages/python-xyz.scm      | 4 +---
 gnu/packages/version-control.scm | 1 -
 3 files changed, 1 insertion(+), 5 deletions(-)

Toggle diff (48 lines)diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index e50eb17c66..2d6de6badc 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -260,7 +260,6 @@ (define-public python-devpi-process
                              python-typing-extensions))
     (native-inputs
      (list nss-certs-for-test
-           python-covdefaults
            python-hatchling
            python-hatch-vcs
            python-httpx
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index aa3397f262..0b566a4b89 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -23098,8 +23098,7 @@ (define-public python-pyproject-api
                    ;; This fails because wheel shows up in requirements
                    " and not test_setuptools_get_requires_for_build_wheel"))))
     (native-inputs
-     (list python-covdefaults
-           python-hatch-vcs
+     (list python-hatch-vcs
            python-hatchling
            python-pytest
            python-pytest-cov
@@ -37148,7 +37147,6 @@ (define-public python-platformdirs
     (build-system pyproject-build-system)
     (native-inputs
      (list python-appdirs
-           python-covdefaults
            python-hatchling
            python-hatch-vcs
            python-pytest
diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 019ce62d74..c1eb761d94 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -2463,7 +2463,6 @@ (define-public pre-commit
               (invoke "git" "config" "--global" "user.email" "you@example.com"))))))
     (native-inputs
      (list git-minimal/pinned
-           python-covdefaults
            python-distlib
            python-pytest
            python-pytest-env
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 23/52] build-system/pyproject: Remove python-codecov native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-23-ngraves@ngraves.fr

* gnu/packages/android.scm (python-androguard)
* gnu/packages/astronomy.scm (python-wiimatch, python-tweakwcs)
* gnu/packages/geo.scm (python-geopandas)
* gnu/packages/jupyter.scm (python-papermill)
* gnu/packages/python-xyz.scm (python-can, python-ddlparse)
[native-inputs]: Remove python-codecov.
---
 gnu/packages/android.scm    | 2 +-
 gnu/packages/astronomy.scm  | 9 +++++----
 gnu/packages/geo.scm        | 3 +--
 gnu/packages/jupyter.scm    | 1 -
 gnu/packages/python-xyz.scm | 4 +---
 5 files changed, 8 insertions(+), 11 deletions(-)

Toggle diff (90 lines)diff --git a/gnu/packages/android.scm b/gnu/packages/android.scm
index 58d3815d2a..aa806c475e 100644
--- a/gnu/packages/android.scm
+++ b/gnu/packages/android.scm
@@ -1078,7 +1078,7 @@ (define-public python-androguard
            (lambda _
              (invoke "nosetests" "--with-timer" "--timer-top-n" "50"))))))
     (native-inputs
-     (list python-codecov python-mock python-nose python-nose-timer))
+     (list python-mock python-nose python-nose-timer))
     (propagated-inputs
      (list python-asn1crypto
            python-colorama
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 8c47e7c61c..6b31414940 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -6703,8 +6703,7 @@ (define-public python-tweakwcs
            python-stsci-imagestats
            python-stsci-stimage))
     (native-inputs
-     (list python-codecov
-           python-pytest
+     (list python-pytest
            python-pytest-cov
            python-scipy
            python-setuptools
@@ -6828,8 +6827,10 @@ (define-public python-wiimatch
                 "15kq7z30m9i286ncs9xvpaq3dq1p5fa47jz21prq146qwr7j6dm8"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-numpy python-scipy))
-    (native-inputs (list python-codecov python-pytest python-pytest-cov
-                         python-pytest-doctestplus python-setuptools-scm
+    (native-inputs (list python-pytest
+                         python-pytest-cov
+                         python-pytest-doctestplus
+                         python-setuptools-scm
                          python-wheel))
     (home-page "https://github.com/spacetelescope/wiimatch")
     (synopsis
diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 54f96fef2b..cf8c140040 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -1075,8 +1075,7 @@ (define-public python-geopandas
             python-pyproj
             python-shapely))
     (native-inputs
-      (list python-codecov
-            python-pytest
+      (list python-pytest
             python-pytest-cov
             python-pytest-xdist
             python-setuptools
diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm
index a9f57b2ccc..1ee99c8602 100644
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -1160,7 +1160,6 @@ (define-public python-papermill
                          python-botocore
                          python-bumpversion
                          python-check-manifest
-                         python-codecov
                          python-ipython
                          python-ipywidgets
                          python-moto
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 0b566a4b89..b840493eb4 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4291,7 +4291,6 @@ (define-public python-can
            python-setuptools))
     (native-inputs
      (list ;; python-canalystii ; Not packed yet
-           python-codecov
            python-future
            python-hypothesis
            python-mock
@@ -6410,8 +6409,7 @@ (define-public python-ddlparse
         (base32 "1nh8m6rxslwk05daxshxmgk41qfp18yynydba49b13l4m8dnh634"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-codecov
-           python-pytest
+     (list python-pytest
            python-pytest-cov
            python-setuptools
            python-tox
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 24/52] build-system/pyproject: Remove python-tox native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-24-ngraves@ngraves.fr

* gnu/packages/bioinformatics.scm (python-metacells)
* gnu/packages/django.scm (python-django-pipeline, python-django-extensions)
* gnu/packages/jupyter.scm (python-papermill)
* gnu/packages/logging.scm (tailon)
* gnu/packages/messaging.scm (python-harmony)
* gnu/packages/mp3.scm (python-audioread)
* gnu/packages/networking.scm (gandi.cli)
* gnu/packages/python-check.scm (python-pytest-qt, python-nox)
* gnu/packages/python-science.scm (python-scikit-survival)
* gnu/packages/python-web.scm (python-flask-htpasswd,
  python-simple-websocket, python-omnipath, python-sanic)
* gnu/packages/python-xyz.scm (python-lunr, python-bidict,
  python-jsonargparse, python-ddlparse, python-virtualenv-clone,
  python-honcho, python-shshsh, python-ansicolors)
* gnu/packages/radio.scm (chirp)
* gnu/packages/terminals.scm (python-halo, python-log-symbols,
  python-spinners)
* gnu/packages/textutils.scm (txt2tags)
[native-inputs]: Remove python-tox.
---
 gnu/packages/bioinformatics.scm |  1 -
 gnu/packages/django.scm         |  2 --
 gnu/packages/jupyter.scm        |  1 -
 gnu/packages/logging.scm        |  2 +-
 gnu/packages/messaging.scm      |  2 --
 gnu/packages/mp3.scm            |  3 +--
 gnu/packages/networking.scm     |  2 +-
 gnu/packages/python-check.scm   |  4 +---
 gnu/packages/python-science.scm |  3 +--
 gnu/packages/python-web.scm     |  5 +----
 gnu/packages/python-xyz.scm     | 18 +++++-------------
 gnu/packages/radio.scm          |  3 +--
 gnu/packages/terminals.scm      |  3 ---
 gnu/packages/textutils.scm      |  1 -
 14 files changed, 12 insertions(+), 38 deletions(-)

Toggle diff (304 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 38e623f3a6..e139a60bd7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3177,7 +3177,6 @@ (define-public python-metacells
                          python-setuptools
                          python-sphinx
                          python-sphinx-rtd-theme
-                         python-tox
                          python-twine
                          python-wheel))
     (home-page "https://github.com/tanaylab/metacells.git")
diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index 3e56a20110..b8c72c55d9 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -268,7 +268,6 @@ (define-public python-django-extensions
     (native-inputs
      (list python-mock
            python-factory-boy
-           python-tox
            python-pytest
            python-pytest-cov
            python-pytest-django
@@ -995,7 +994,6 @@ (define-public python-django-pipeline
      (list python-django
            python-setuptools
            python-setuptools-scm
-           python-tox
            python-wheel))
     (home-page
      "https://github.com/jazzband/django-pipeline")
diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm
index 1ee99c8602..8f900d3f88 100644
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -1171,7 +1171,6 @@ (define-public python-papermill
                          python-recommonmark
                          python-requests
                          python-setuptools
-                         python-tox
                          python-twine
                          python-wheel))
     (home-page "https://github.com/nteract/papermill")
diff --git a/gnu/packages/logging.scm b/gnu/packages/logging.scm
index 9cc28279d7..55a1db4123 100644
--- a/gnu/packages/logging.scm
+++ b/gnu/packages/logging.scm
@@ -159,7 +159,7 @@ (define-public tailon
          "0xkmrivzilsc9wqr8ms67v7399gxnh7pv5687k4rdpdgz4309fwc"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-tox python-wheel))
+     (list python-wheel))
     (inputs
      (list python-pyyaml-5 python-sockjs-tornado python-tornado-http-auth
            python-tornado python-deepmerge))
diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index 1ee8255593..fcb05dbda6 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -3626,8 +3626,6 @@ (define-public python-harmony
                (base32
                 "1bm9xcnzpnpj6rlhbrnl2abwclzl7ivgh1vb5644y9mnhcs489js"))))
     (build-system python-build-system)
-    (native-inputs
-     (list python-tox))
     (inputs
      (list python-librecaptcha python-keyring python-requests))
     (synopsis "Discord account management")
diff --git a/gnu/packages/mp3.scm b/gnu/packages/mp3.scm
index 9dfce6313f..ccf105d7be 100644
--- a/gnu/packages/mp3.scm
+++ b/gnu/packages/mp3.scm
@@ -688,8 +688,7 @@ (define-public python-audioread
      (list gstreamer
            gst-plugins-base
            python-flit-core
-           python-pytest
-           python-tox))
+           python-pytest))
     (home-page "https://github.com/sampsyo/audioread")
     (synopsis "Decode audio files using whichever backend is available")
     (description
diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index 1b97853a59..96561fff3a 100644
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@ -1941,7 +1941,7 @@ (define-public gandi.cli
                #t))))))
     (native-inputs
      (list python-docutils ; for rst2man.py
-           python-pytest python-pytest-cov python-tox))
+           python-pytest python-pytest-cov))
     (propagated-inputs
      (list openssh))           ; used by gandi/cli/modules/iass.py
     (inputs
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index b336631edc..5bb38e091a 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -2295,7 +2295,6 @@ (define-public python-pytest-qt
      (list python-pre-commit
            python-setuptools
            python-setuptools-scm
-           python-tox
            python-wheel))
     (home-page "https://github.com/pytest-dev/pytest-qt")
     (synopsis "Pytest support for PyQt and PySide applications")
@@ -3012,8 +3011,7 @@ (define-public python-nox
     (native-inputs
      (list python-hatchling
            python-jinja2
-           python-pytest
-           python-tox))
+           python-pytest))
     (home-page "https://nox.thea.codes/")
     (synopsis "Flexible test automation")
     (description
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index a647053d8f..c747b43361 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -893,8 +893,7 @@ (define-public python-scikit-survival
              python-pytest
              python-setuptools
              python-setuptools-scm
-             python-tomli
-             python-tox))
+             python-tomli))
       (home-page "https://github.com/sebp/scikit-survival")
       (synopsis "Survival analysis built on top of scikit-learn")
       (description "Scikit-survival is a Python module for survival analysis
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 2d6de6badc..8177c63fa2 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -2984,7 +2984,6 @@ (define-public python-omnipath
              python-requests-mock
              python-setuptools
              python-setuptools-scm
-             python-tox
              python-wheel))
       (home-page "https://omnipathdb.org/")
       (synopsis "Python client for the OmniPath web service")
@@ -5836,7 +5835,7 @@ (define-public python-flask-htpasswd
     (build-system pyproject-build-system)
     (arguments (list #:tests? #false)) ;none included
     (propagated-inputs
-     (list python-flask python-passlib python-pyjwt python-tox))
+     (list python-flask python-passlib python-pyjwt))
     (native-inputs (list python-pytest
                          python-setuptools
                          python-wheel))
@@ -8921,7 +8920,6 @@ (define-public python-sanic
            python-setuptools
            python-slotscheck
            python-towncrier
-           python-tox
            python-types-ujson
            python-uvicorn
            python-wheel))
@@ -9045,7 +9043,6 @@ (define-public python-simple-websocket
     (native-inputs (list python-pytest
                          python-pytest-cov
                          python-setuptools
-                         python-tox
                          python-wheel))
     (home-page "https://github.com/miguelgrinberg/simple-websocket")
     (synopsis "Simple WebSocket server and client for Python")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index b840493eb4..1fe3e020a8 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1681,8 +1681,7 @@ (define-public python-lunr
      (list python-hatch-fancy-pypi-readme
            python-hatchling
            python-pytest
-           python-pytest-timeout
-           python-tox))
+           python-pytest-timeout))
     (propagated-inputs
      (list python-importlib-metadata python-typing-extensions))
     (home-page
@@ -3341,8 +3340,7 @@ (define-public python-bidict
            python-sortedcollections
            python-sortedcontainers
            python-sphinx
-           python-sphinx-autodoc-typehints
-           python-tox))
+           python-sphinx-autodoc-typehints))
     (arguments
      `(#:phases (modify-phases %standard-phases
                   (add-after 'unpack 'relax-reqs
@@ -5206,7 +5204,6 @@ (define-public python-jsonargparse
            python-pytest
            python-pytest-subtests
            python-responses
-           python-tox
            python-types-requests
            python-setuptools
            python-wheel))
@@ -6412,7 +6409,6 @@ (define-public python-ddlparse
      (list python-pytest
            python-pytest-cov
            python-setuptools
-           python-tox
            python-wheel))
     (propagated-inputs (list python-pyparsing))
     (home-page "https://github.com/shinichi-takii/ddlparse")
@@ -6982,7 +6978,6 @@ (define-public python-virtualenv-clone
                               (delete-file "tox.ini")
                               (invoke "pytest" "-vvv" "tests")))))))
     (native-inputs (list python-pytest
-                         python-tox
                          python-virtualenv
                          python-wheel
                          python-tomli
@@ -12510,7 +12505,7 @@ (define-public python-honcho
         (base32 "1y0r8dw4pqcq7r4n58ixjdg1iy60lp0gxsd7d2jmhals16ij71rj"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-pytest python-mock python-tox which)) ;for tests
+     (list python-pytest python-mock which)) ;for tests
     (propagated-inputs
      (list python-jinja2))
     (arguments
@@ -22765,9 +22760,7 @@ (define-public python-shshsh
          "1wzqyj1a6jj6cyv5ymzy834qm2lyq80yy1kfz0q0zayq9gm1cj7f"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-poetry-core
-           python-pytest
-           python-tox))
+     (list python-poetry-core python-pytest))
     (home-page "https://github.com/zqqqqz2000/shshsh")
     (synopsis "Write Shell commands simply and safely within Python")
     (description "This package provides a way to write Shell commands from
@@ -38009,8 +38002,7 @@ (define-public python-ansicolors
         (base32 "1q3jqglkq4z0f6nkkn8bswcwqg012i2grrc27kabr8286dg4zycr"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-tox
-           python-pytest-cov
+     (list python-pytest-cov
            unzip))
     (home-page "https://github.com/jonathaneunice/colors/")
     (synopsis "ANSI colors for Python")
diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index d2c8bee76b..51d00e68f4 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -3274,8 +3274,7 @@ (define-public chirp
              python-mox3
              python-pytest
              python-pytest-mock
-             python-pyyaml
-             python-tox))
+             python-pyyaml))
       (inputs
        (list python-future
              python-importlib-resources
diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index da9f0e3483..36ad457ca2 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -1178,7 +1178,6 @@ (define-public python-halo
     (native-inputs
      (list python-nose
            python-setuptools
-           python-tox
            python-twine
            python-wheel))
     (home-page "https://github.com/manrajgrover/halo")
@@ -1209,7 +1208,6 @@ (define-public python-log-symbols
     (native-inputs
      (list python-nose
            python-setuptools
-           python-tox
            python-wheel))
     (propagated-inputs (list python-colorama))
     (home-page "https://github.com/manrajgrover/py-log-symbols")
@@ -1241,7 +1239,6 @@ (define-public python-spinners
     (native-inputs
      (list python-nose
            python-setuptools
-           python-tox
            python-wheel))
     (home-page "https://github.com/manrajgrover/py-spinners")
     (synopsis "Python library with graphical spinners for the terminal")
diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index ce9847a168..a471ec63fc 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -1086,7 +1086,6 @@ (define-public txt2tags
                (base32
                 "0ik7gpr3gymgxnj0p86k8768kyxncbncv93zq67sbak3dbdl8hky"))))
     (build-system python-build-system)
-    (native-inputs (list python-tox))
     (home-page "https://txt2tags.org")
     (synopsis "Convert between markup languages")
     (description
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 26/52] gnu: python-immutables: Remove python-mypy native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-26-ngraves@ngraves.fr

* gnu/packages/python-xyz.scm (python-immutables):
  [origin]: Use git-fetch to use upstream test-data directory.
  [native-inputs]: Remove python-mypy.
  [arguments]<#:phases>: Add phase to remove python-mypy native-input.
---
 gnu/packages/python-xyz.scm | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

Toggle diff (33 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 9817da029a..3259be0f2f 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -17157,13 +17157,22 @@ (define-public python-immutables
     (version "0.21")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "immutables" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/MagicStack/immutables")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "0jpw9nr2mbzqykigjhqa3a095bx7krwsnmjcxcpj944p8kqglpxm"))))
+        (base32 "1p5g20y7di5xglk6yyhb010vdmz73q9fsxpq0cm2gksp8mj856y1"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list #:phases #~(modify-phases %standard-phases
+                        (add-after 'unpack 'remove-mypy-dependency
+                          (lambda _
+                            (delete-file "tests/test_mypy.py")
+                            (delete-file "tests/conftest.py"))))))
     (native-inputs
-     (list python-mypy python-pytest python-setuptools python-wheel))
+     (list python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/MagicStack/immutables")
     (synopsis "High-performance immutable mapping type for Python")
     (description
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 25/52] build-system/pyproject: Remove python-mypy native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-25-ngraves@ngraves.fr

* gnu/packages/astronomy.scm (python-poliastro)[native-inputs]: Remove

python-mypy.

* gnu/packages/databases.scm (python-psycopg2)[native-inputs]: Remove

python-mypy.

* gnu/packages/engineering.scm (uranium, cura)[native-inputs]: Remove

python-mypy.

* gnu/packages/graphviz.scm (python-uqbar)[native-inputs]: Remove

python-mypy.

* gnu/packages/machine-learning.scm (python-imbalanced-learn,

python-captum, python-torchmetrics)[native-inputs]: Remove python-mypy.

* gnu/packages/python-science.scm (python-scipy)[native-inputs]:

Remove python-mypy.

* gnu/packages/python-web.scm (python-huggingface-hub, python-asgiref,

python-starsessions-for-pytorch-lightning)[native-inputs]:

Remove python-mypy.

* gnu/packages/python-xyz.scm (kalamine, python-pydantic-cli,

python-apispec, python-typeguard, python-verspec,

python-catalogue)[native-inputs]: Remove python-mypy.

* gnu/packages/serialization.scm (python-msgspec)[native-inputs]: Remove

python-mypy.

* gnu/packages/virtualization.scm (python-transient)[native-inputs]:

Remove python-mypy.

---

gnu/packages/astronomy.scm | 1 -

gnu/packages/databases.scm | 1 -

gnu/packages/engineering.scm | 2 --

gnu/packages/graphviz.scm | 1 -

gnu/packages/machine-learning.scm | 3 ---

gnu/packages/python-science.scm | 1 -

gnu/packages/python-web.scm | 6 +++---

gnu/packages/python-xyz.scm | 13 +++++--------

gnu/packages/serialization.scm | 1 -

gnu/packages/virtualization.scm | 3 +--

10 files changed, 9 insertions(+), 23 deletions(-)

Toggle diff (214 lines)diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 6b31414940..b4c29480ac 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4630,7 +4630,6 @@ (define-public python-poliastro
               (setenv "HOME" "/tmp"))))))
     (native-inputs
      (list python-hypothesis
-           python-mypy
            python-flit-core
            python-pytest
            python-pytest-cov
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 984598e2b4..055bc94e3d 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -4305,7 +4305,6 @@ (define-public python-psycopg
                           "-c" "CREATE DATABASE nixbld;"))))))))
     (native-inputs
      (list python-cython-3
-           python-mypy
            python-psycopg-pool
            python-pytest
            python-pytest-asyncio
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index cc84a760e9..fe550d8471 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -4550,7 +4550,6 @@ (define-public uranium
            graphviz
            pkg-config
            python-pytest
-           python-mypy
            python-certifi
            python-twisted))
     (propagated-inputs
@@ -4753,7 +4752,6 @@ (define-public cura
     (build-system qt-build-system)
     (native-inputs
      (list python-certifi
-           python-mypy
            python-pytest
            python-requests))
     (inputs
diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm
index 0d3db31212..6bfe5325ac 100644
--- a/gnu/packages/graphviz.scm
+++ b/gnu/packages/graphviz.scm
@@ -225,7 +225,6 @@ (define-public python-uqbar
     (native-inputs
      (list graphviz
            python-isort
-           python-mypy
            python-pytest
            python-pytest-cov
            python-setuptools
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 350c2d2b39..6fafdac5ef 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -2150,7 +2150,6 @@ (define-public python-imbalanced-learn
     (propagated-inputs (list python-joblib python-numpy python-scikit-learn
                              python-scipy python-threadpoolctl))
     (native-inputs (list python-keras
-                         python-mypy
                          python-pandas
                          python-pytest
                          python-pytest-cov
@@ -5320,7 +5319,6 @@ (define-public python-captum
                          python-flask-compress
                          python-ipython
                          python-ipywidgets
-                         python-mypy
                          python-parameterized
                          python-pytest
                          python-pytest-cov
@@ -5508,7 +5506,6 @@ (define-public python-torchmetrics
      (list python-cloudpickle
            python-fire
            python-mir-eval
-           python-mypy
            python-pandas
            python-psutil
            python-pytest
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index c747b43361..43afe657e4 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -439,7 +439,6 @@ (define-public python-scipy
            '())
        (list python-matplotlib
              python-mpmath
-             python-mypy
              python-numpy
              python-numpydoc
              python-pydata-sphinx-theme
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 8177c63fa2..990228384e 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -564,7 +564,6 @@ (define-public python-huggingface-hub
            python-fastapi
            python-jedi
            python-jinja2
-           python-mypy
            python-numpy
            python-pillow
            python-pydantic
@@ -1216,7 +1215,9 @@ (define-public python-asgiref
                (base32 "146mhkn3zp2bqf7j6r3chdlvfzgs5x1lrnqahsllgjdyl20bshy3"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-mypy python-pytest python-pytest-asyncio python-setuptools
+     (list python-pytest
+           python-pytest-asyncio
+           python-setuptools
            python-wheel))
     (home-page "https://github.com/django/asgiref/")
     (synopsis "ASGI specs, helper code, and adapters")
@@ -10308,7 +10309,6 @@ (define-public python-starsessions
            python-starlette))
     (native-inputs
      (list python-httpx
-           python-mypy
            python-poetry-core
            python-pytest
            python-pytest-asyncio
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 1fe3e020a8..9817da029a 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7589,7 +7589,7 @@ (define-public kalamine
     ;; TODO: Add python-pytest-ruff to native-inputs once it has been
     ;; packaged.
     (native-inputs
-     (list python-hatchling python-mypy python-pytest))
+     (list python-hatchling python-pytest))
     (home-page "https://github.com/OneDeadKey/kalamine")
     (synopsis "Keyboard layout maker")
     (description
@@ -8829,8 +8829,7 @@ (define-public python-pydantic-cli
     (propagated-inputs
      (list python-pydantic))
     (native-inputs
-     (list python-mypy
-           python-pytest))
+     (list python-pytest))
     (home-page "https://github.com/mpkocher/pydantic-cli")
     (synopsis "Turn Pydantic defined data models into CLI tools")
     (description
@@ -27083,7 +27082,6 @@ (define-public python-apispec
     (build-system pyproject-build-system)
     (native-inputs
      (list python-flit-core
-           python-mypy
            python-openapi-spec-validator
            python-pytest))
     (propagated-inputs
@@ -28484,8 +28482,7 @@ (define-public python-typeguard
         (base32 "06y22d1f5dhpyl71wbhsaibig5hvc2v44pw795yb8lxl02fsh8hd"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-mypy
-           python-pytest
+     (list python-pytest
            python-setuptools
            python-setuptools-scm
            python-typing-extensions
@@ -38222,7 +38219,7 @@ (define-public python-verspec
                (base32
                 "07n06wv85fm4vl1ird2mja0823js3x322wgs9gdnq1djjyk4ql64"))))
     (build-system python-build-system)
-    (native-inputs (list python-mypy python-pretend python-pytest))
+    (native-inputs (list python-pretend python-pytest))
     (arguments
      `(#:phases (modify-phases %standard-phases
                   (replace 'check
@@ -39006,7 +39003,7 @@ (define-public python-catalogue
                 "0srdxiil2xys8q1gpc1nvzhvis3a33d8a7amk2i1rlpbg6p36pak"))))
     (build-system python-build-system)
     (native-inputs (list python-pytest))
-    (inputs (list python python-zipp python-typing-extensions python-mypy))
+    (inputs (list python python-zipp python-typing-extensions))
     (home-page "https://github.com/explosion/catalogue")
     (synopsis "Lightweight function registries for your library")
     (description
diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index f77ae9dc16..97951cb510 100644
--- a/gnu/packages/serialization.scm
+++ b/gnu/packages/serialization.scm
@@ -762,7 +762,6 @@ (define-public python-msgspec
     (native-inputs (list python-attrs
                          python-gcovr
                          python-msgpack
-                         python-mypy
                          python-pytest
                          python-setuptools-scm
                          python-versioneer
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index bde357763f..a6872a3f1f 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -2986,8 +2986,7 @@ (define-public python-transient
                         (("==")
                          ">=")))))))
     (native-inputs
-     (list python-mypy
-           python-pyhamcrest
+     (list python-pyhamcrest
            python-setuptools
            python-twine
            python-wheel))
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 27/52] build-system/pyproject: Remove python-isort native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-27-ngraves@ngraves.fr

* gnu/packages/bioinformatics.scm (python-metacells, python-cooler,
  scvelo)
* gnu/packages/databases.scm (aerich)
* gnu/packages/finance.scm (python-trezor)
* gnu/packages/gettext.scm (mdpo)
* gnu/packages/graphviz.scm (python-uqbar)
* gnu/packages/machine-learning.scm (python-pymanopt, python-funsor)
* gnu/packages/mail.scm (python-hyperkitty, postorius)
* gnu/packages/protobuf.scm (python-pure-protobuf)
* gnu/packages/python-web.scm (python-zeep, python-ovh, python-tinycss2)
* gnu/packages/python-xyz.scm (python-archspec)
* gnu/packages/statistics.scm (python-statsmodels)
* gnu/packages/virtualization.scm (python-qemu-qmp)
[native-inputs]: Remove python-isort.
---
 gnu/packages/bioinformatics.scm   | 3 ---
 gnu/packages/databases.scm        | 1 -
 gnu/packages/finance.scm          | 1 -
 gnu/packages/gettext.scm          | 1 -
 gnu/packages/graphviz.scm         | 1 -
 gnu/packages/machine-learning.scm | 4 +---
 gnu/packages/mail.scm             | 2 --
 gnu/packages/protobuf.scm         | 2 +-
 gnu/packages/python-web.scm       | 4 +---
 gnu/packages/python-xyz.scm       | 3 +--
 gnu/packages/statistics.scm       | 1 -
 gnu/packages/virtualization.scm   | 1 -
 12 files changed, 4 insertions(+), 20 deletions(-)

Toggle diff (193 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e139a60bd7..8c9ca0540b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3168,7 +3168,6 @@ (define-public python-metacells
                              python-threadpoolctl
                              python-umap-learn))
     (native-inputs (list python-bumpversion
-                         python-isort
                          python-mypy
                          python-mypy-extensions
                          python-pandas-stubs
@@ -19885,7 +19884,6 @@ (define-public python-cooler
            python-simplejson))
     (native-inputs
      (list python-hatchling
-           python-isort
            python-pytest
            python-pytest-cov))
     ;; Almost all the projects of the Mirnylab are moved under Open2C umbrella
@@ -23979,7 +23977,6 @@ (define-public scvelo
     (propagated-inputs
      (list python-anndata
            python-hnswlib
-           python-isort
            python-igraph
            python-loompy
            python-louvain
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 055bc94e3d..397754521c 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -3459,7 +3459,6 @@ (define-public aerich
      (list poetry
            python-bandit
            python-cryptography
-           python-isort
            python-pydantic
            python-pytest
            python-pytest-asyncio
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index f3be674c01..3af525da18 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -1160,7 +1160,6 @@ (define-public python-trezor
            python-typing-extensions))
     (native-inputs ; Only needed for running the tests
      (list protobuf
-           python-isort
            python-pillow
            python-protobuf
            python-pyqt
diff --git a/gnu/packages/gettext.scm b/gnu/packages/gettext.scm
index 29cdbab915..841d3e0c8b 100644
--- a/gnu/packages/gettext.scm
+++ b/gnu/packages/gettext.scm
@@ -228,7 +228,6 @@ (define-public mdpo
      (list python-bump2version
            python-flake8-implicit-str-concat
            python-flake8-print
-           python-isort
            python-pytest
            python-pytest-cov
            python-sphinx
diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm
index 6bfe5325ac..33ddbeba42 100644
--- a/gnu/packages/graphviz.scm
+++ b/gnu/packages/graphviz.scm
@@ -224,7 +224,6 @@ (define-public python-uqbar
 and not test_sphinx_book_text_broken_strict")))
     (native-inputs
      (list graphviz
-           python-isort
            python-pytest
            python-pytest-cov
            python-setuptools
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 6fafdac5ef..e335ade28f 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -229,8 +229,7 @@ (define-public python-funsor
     (propagated-inputs (list python-makefun python-multipledispatch
                              python-numpy python-opt-einsum
                              python-typing-extensions))
-    (native-inputs (list python-isort
-                         python-nbsphinx
+    (native-inputs (list python-nbsphinx
                          python-pandas
                          python-pillow
                          python-pyro-api
@@ -1143,7 +1142,6 @@ (define-public python-pymanopt
     (propagated-inputs (list python-numpy python-scipy))
     (native-inputs (list python-autograd
                          python-flake8-bugbear
-                         python-isort
                          python-matplotlib
                          python-pytest
                          python-pytest-cov
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index cfda27d7ea..2cb2b0f648 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -3809,7 +3809,6 @@ (define-public python-hyperkitty
            python-django-rest-framework
            python-elasticsearch
            python-flufl-lock
-           python-isort
            python-lxml
            python-mailmanclient
            python-mistune
@@ -3860,7 +3859,6 @@ (define-public postorius
            python-django-mailman3))
     (native-inputs
      (list python-beautifulsoup4
-           python-isort
            python-mock
            python-pdm-backend
            python-pytest
diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm
index 203e4909d6..487c03fa94 100644
--- a/gnu/packages/protobuf.scm
+++ b/gnu/packages/protobuf.scm
@@ -502,7 +502,7 @@ (define-public python-pure-protobuf
         (base32 "15dp5pvazd0jx4wzzh79080ah7hkpd3axh40al9vhzs2hf3v90hx"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-pytest python-pytest-cov python-isort))
+     (list python-pytest python-pytest-cov))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 990228384e..843705539d 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1611,8 +1611,7 @@ (define-public python-ovh
     (build-system pyproject-build-system)
     (arguments (list #:tests? #f))      ; XXX: tests require networking
     (propagated-inputs (list python-requests))
-    (native-inputs (list python-isort
-                         python-pytest
+    (native-inputs (list python-pytest
                          python-pytest-cov
                          python-setuptools
                          python-sphinx
@@ -10136,7 +10135,6 @@ (define-public python-zeep
            python-flake8-blind-except
            python-flake8-debugger
            python-freezegun
-           python-isort
            python-pretend
            python-pytest
            python-pytest-asyncio
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 3259be0f2f..e4cf8aa422 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -395,8 +395,7 @@ (define-public python-archspec
                              python-scikit-learn
                              python-tables
                              python-typing-extensions))
-    (native-inputs (list python-isort
-                         python-poetry-core
+    (native-inputs (list python-poetry-core
                          python-pytest
                          python-pytest-cov))
     (home-page "https://github.com/archspec/archspec")
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 7a02786ab6..0344074366 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2669,7 +2669,6 @@ (define-public python-statsmodels
     (native-inputs
      (list python-colorama
            python-cython
-           python-isort
            python-joblib
            python-matplotlib
            python-pytest
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index a6872a3f1f..d1e2130980 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -2120,7 +2120,6 @@ (define-public python-qemu-qmp
     (native-inputs
      (list python-avocado-framework
            python-flake8
-           python-isort
            python-setuptools
            python-setuptools-scm
            python-wheel))
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 28/52] build-system/pyproject: Remove python-twine native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-28-ngraves@ngraves.fr

* gnu/packages/bioinformatics.scm (python-metacells, python-ngesh,
  python-pyahocorasick)
* gnu/packages/finance.scm (fava)
* gnu/packages/gettext.scm (mdpo)
* gnu/packages/jupyter.scm (python-hatch-jupyter-builder,
  python-papermill)
* gnu/packages/machine-learning.scm (python-linear-operator,
  python-gpytorch)
* gnu/packages/python-check.scm (python-testfixtures)
* gnu/packages/python-web.scm (python-translation-finder,
  python-eventlet, python-transient)
* gnu/packages/python-xyz.scm (python-cftime)
* gnu/packages/terminals.scm (python-halo)
* gnu/packages/virtualization.scm (python-transient)
[native-inputs]: Remove python-twine.
---
 gnu/packages/bioinformatics.scm   | 7 ++-----
 gnu/packages/finance.scm          | 1 -
 gnu/packages/gettext.scm          | 1 -
 gnu/packages/jupyter.scm          | 4 +---
 gnu/packages/machine-learning.scm | 6 ++----
 gnu/packages/python-check.scm     | 2 +-
 gnu/packages/python-web.scm       | 5 ++---
 gnu/packages/python-xyz.scm       | 2 --
 gnu/packages/terminals.scm        | 1 -
 gnu/packages/virtualization.scm   | 1 -
 10 files changed, 8 insertions(+), 22 deletions(-)

Toggle diff (184 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8c9ca0540b..bc813ca711 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3176,7 +3176,6 @@ (define-public python-metacells
                          python-setuptools
                          python-sphinx
                          python-sphinx-rtd-theme
-                         python-twine
                          python-wheel))
     (home-page "https://github.com/tanaylab/metacells.git")
     (synopsis "Single-cell RNA Sequencing Analysis")
@@ -3203,8 +3202,7 @@ (define-public python-ngesh
         (base32 "07sj4x95b5hvx57pw24f80sk4ag4hkg1z6wzym3pzi8n5gn85n1z"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-ete3 python-numpy python-six))
-    (native-inputs (list python-pytest python-twine
-                         python-wheel))
+    (native-inputs (list python-pytest python-wheel))
     (home-page "https://github.com/tresoldi/ngesh")
     (synopsis "Library for phylogenetic tree simulation")
     (description
@@ -7725,8 +7723,7 @@ (define-public python-pyahocorasick
        (sha256
         (base32 "1fsnivwcw56q7lwz41c5kbfvxv0v17mmkx43i2a293l49fxj08j8"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-pytest python-twine python-setuptools
-                         python-wheel))
+    (native-inputs (list python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/WojciechMula/pyahocorasick")
     (synopsis "Library for finding multiple key strings in text")
     (description
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index 3af525da18..30ed44aea9 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -2072,7 +2072,6 @@ (define-public fava
            python-pytest
            python-pytest-cov
            python-setuptools
-           python-twine
            python-types-setuptools
            python-types-simplejson
            python-wheel))
diff --git a/gnu/packages/gettext.scm b/gnu/packages/gettext.scm
index 841d3e0c8b..25f4efe1fc 100644
--- a/gnu/packages/gettext.scm
+++ b/gnu/packages/gettext.scm
@@ -233,7 +233,6 @@ (define-public mdpo
            python-sphinx
            python-sphinx-argparse
            python-sphinx-rtd-theme
-           python-twine
            python-yamllint))
     (propagated-inputs
      (list python-polib python-pymd4c))
diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm
index 8f900d3f88..70c13115de 100644
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -546,8 +546,7 @@ (define-public python-hatch-jupyter-builder
     (native-inputs (list python-pytest
                          python-pytest-cov
                          python-pytest-mock
-                         python-tomli
-                         python-twine))
+                         python-tomli))
     (home-page "https://github.com/jupyterlab/hatch-jupyter-builder")
     (synopsis "Hatch plugin to help build Jupyter packages")
     (description
@@ -1171,7 +1170,6 @@ (define-public python-papermill
                          python-recommonmark
                          python-requests
                          python-setuptools
-                         python-twine
                          python-wheel))
     (home-page "https://github.com/nteract/papermill")
     (synopsis "Parameterize and run Jupyter and nteract Notebooks")
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index e335ade28f..b2d25bae21 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -5889,8 +5889,7 @@ (define-public python-linear-operator
     (native-inputs (list python-flake8-print
                          python-pytest
                          python-setuptools
-                         python-setuptools-scm
-                         python-twine))
+                         python-setuptools-scm))
     (home-page "https://github.com/cornellius-gp/linear_operator/")
     (synopsis "Linear operator implementation")
     (description "LinearOperator is a PyTorch package for abstracting away the
@@ -5919,8 +5918,7 @@ (define-public python-gpytorch
     (native-inputs (list python-flake8-print
                          python-nbval
                          python-pytest
-                         python-setuptools
-                         python-twine))
+                         python-setuptools))
     (home-page "https://gpytorch.ai")
     (synopsis "Implementation of Gaussian Processes in PyTorch")
     (description
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 5bb38e091a..99c4d04019 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -778,7 +778,7 @@ (define-public python-testfixtures
     (native-inputs
      (list python-pytest python-pytest-cov
            ;;("python-pytest-django" ,python-pytest-django)
-           python-twine python-wheel))
+           python-wheel))
     (synopsis "Tests components for Python")
     (description "Testfixtures is a collection of helpers and mock objects that
 are useful when writing automated tests in Python.")
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 843705539d..0a99254f64 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -426,8 +426,7 @@ (define-public python-eventlet
     (native-inputs
      (list python-hatch-vcs
            python-hatchling
-           python-pytest
-           python-twine))
+           python-pytest))
     (propagated-inputs
      (list python-dnspython
            python-greenlet
@@ -7468,7 +7467,7 @@ (define-public python-translation-finder
      (list python-chardet python-pathlib2 python-ruamel.yaml python-six))
     (native-inputs
      (list python-codecov python-codacy-coverage python-pytest-cov
-           python-pytest-runner python-twine))
+           python-pytest-runner))
     (home-page "https://weblate.org/")
     (synopsis "Translation file finder for Weblate")
     (description "This package provides a function to find translation file in
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e4cf8aa422..0b9c0db659 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3729,7 +3729,6 @@ (define-public python-cftime
            python-pytest
            python-setuptools
            python-sphinx
-           python-twine
            python-wheel))
     (home-page "https://unidata.github.io/cftime/")
     (synopsis "Library for time handling")
@@ -33475,7 +33474,6 @@ (define-public python-eliot
            python-sphinx
            python-sphinx-rtd-theme
            python-testtools
-           python-twine
            python-twisted
            python-wheel))
     (home-page "https://github.com/itamarst/eliot/")
diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index 36ad457ca2..de47d67e36 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -1178,7 +1178,6 @@ (define-public python-halo
     (native-inputs
      (list python-nose
            python-setuptools
-           python-twine
            python-wheel))
     (home-page "https://github.com/manrajgrover/halo")
     (synopsis "Python library to display graphical spinners in the terminal")
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index d1e2130980..1d9da88eb6 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -2987,7 +2987,6 @@ (define-public python-transient
     (native-inputs
      (list python-pyhamcrest
            python-setuptools
-           python-twine
            python-wheel))
     (propagated-inputs
      (list python-beautifultable
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 29/52] build-system/pyproject: Remove python-pytest-cov native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-29-ngraves@ngraves.fr

* gnu/packages/astronomy.scm (python-sncosmo, python-jwst, python-wiimatch,
  python-astroml, python-casa-formats-io, python-cdflib, python-poliastro,
  python-tweakwcs)
* gnu/packages/audio.scm (python-resampy, python-librosa, python-pysox)
* gnu/packages/backup.scm (borgmatic)
* gnu/packages/bioinformatics.scm (python-bed-reader, python-liana-py,
  python-metacells, python-pysnptools, python-pairtools, cwltool,
  python-biom-format, python-pyfaidx, python-cooler, python-screed)
* gnu/packages/build-tools.scm (meson-python)
* gnu/packages/check.scm (python-pytest-nunit, python-pytest-enabler,
  python-pytest-perf, python-pyhamcrest)
* gnu/packages/cpp.scm (cpplint)
* gnu/packages/databases.scm (python-redis)
* gnu/packages/dav.scm (vdirsyncer, radicale)
* gnu/packages/django.scm (python-django-redis, python-django-cleanup,
  python-django-extensions)
* gnu/packages/embedded.scm (mbed-tools)
* gnu/packages/engineering.scm (python-scikit-rf)
* gnu/packages/finance.scm (fava)
* gnu/packages/fontutils.scm (psautohint)
* gnu/packages/geo.scm (python-pyogrio, python-geopandas, python-fiona,
  python-cartopy)
* gnu/packages/gettext.scm (mdpo)
* gnu/packages/gpodder.scm (gpodder)
* gnu/packages/graphviz.scm (python-graphviz, python-uqbar)
* gnu/packages/jupyter.scm (python-nbclassic, python-jupyterlab-server,
  python-hatch-jupyter-builder, python-nbclient, python-papermill,
  python-jupyter-packaging, python-jupyter-server, python-jupyterlite-core,
  python-ipydatawidgets)
* gnu/packages/machine-learning.scm (python-pymanopt, python-botorch,
  python-persim, python-scikit-learn-extra, python-imbalanced-learn,
  python-keras-application, python-keras-preprocessing, python-keras,
  python-tensorly, python-pytorch-geometric, python-captum,
  python-torchmetrics)
* gnu/packages/mastodon.scm (python-mastodon-py)
* gnu/packages/maths.scm (python-libensemble)
* gnu/packages/matrix.scm (python-matrix-nio)
* gnu/packages/messaging.scm (zulip-term)
* gnu/packages/music.scm (beets, stargate)
* gnu/packages/networking.scm (gandi.cli)
* gnu/packages/package-management.scm (conda, python-conda-package-handling)
* gnu/packages/patchutils.scm (pwclient)
* gnu/packages/protobuf.scm (python-pure-protobuf)
* gnu/packages/python-check.scm (python-pandas-vet, python-testfixtures,
  python-vcrpy, python-pytest-filter-subpackage, python-atpublic,
  python-sybil, python-vulture)
* gnu/packages/python-compression.scm (python-zipstream-ng,
  python-multivolumefile, python-pybcj, python-bcj-cffi, python-pyppmd,
  python-ppmd-cffi, python-py7zr)
* gnu/packages/python-crypto.scm (python-cryptography, python-trustme,
  python-certauth)
* gnu/packages/python-science.scm (python-scikit-misc,
  python-mpl-scatter-density, python-modin, python-plotnine,
  python-pynetdicom, python-scipy, python-pandaparallel, python-pyts,
  python-usetplot, python-pingouin, python-opt-einsum, python-salib)
* gnu/packages/python-web.scm (python-devpi-process, python-aiohappyeyeballs,
  python-cheroot, python-jsonpickle, python-flask-babel, python-url-normalize,
  python-elasticsearch, python-hupper, python-simple-websocket,
  python-apiron, python-huggingface-hub, python-portend, python-aiosignal,
  python-aiostream, python-ovh, python-cbor2, python-httplib2, parfive,
  python-jose, python-pyscss, python-mechanicalsoup, python-priority,
  hypercorn, python-aioftp, python-oauthlib, python-tinycss,
  python-cssselect2, python-httpcore, python-wsgiprox, python-venusian,
  python-siosocks, python-zeep, gunicorn, python-warcio)
* gnu/packages/python-xyz.scm (python-archspec, python-colorcet, python-echo,
  python-rich-tables, python-babel, python-pymarshal, python-expandvars,
  autokey, python-lsp-jsonrpc, python-pillow, python-property-manager,
  python-cairocffi, python-jupyter-core, python-ipykernel,
  python-pubmed-parser, python-urwid, python-prettytable, python-xdoctest,
  python-waitress, python-rope, python-wcwidth, python-pyproject-api,
  python-async-lru, python-numcodecs, python-dictpath, python-platformdirs,
  python-multipart, python-apprise, python-janus, python-logbook,
  python-affine, python-mdit-py-plugins, python-pint, python-rasterio,
  python-bidict, python-can, dosage, python-contourpy, python-portalocker,
  python-extension-helpers, python-mizani, python-cligj, python-ddlparse,
  python-robotframework-pythonlibcore, python-lsp-server, python-sparse,
  python-pikepdf, python-imageio, python-manimpango,
  python-importlib-resources, python-jaraco-classes, python-jaraco-collections,
  python-jaraco-context, python-jaraco-functools, python-jaraco-test,
  python-jaraco-text, python-ipyparallel, python-three-merge,
  python-seaborn, python-sentry-sdk, python-sniffio, python-get-version,
  python-path, python-pip-run, python-debugpy, python-notebook,
  python-cookiecutter, python-pyqtgraph, python-inflect, python-pymemcache,
  python-natsort, python-mwclient, python-flasgger, python-tempora,
  python-outcome, python-apscheduler, python-iocapture, python-argh,
  python-flit, python-watchdog, python-cmd2, python-inform,
  python-qtsass, python-scikit-build, python-minikanren, python-tablib,
  python-ansicolors, python-shtab, python-scooby, dynaconf, python-pyan3,
  python-numpydoc, python-loguru)
* gnu/packages/rdf.scm (python-rdflib, python-rdflib-6)
* gnu/packages/simulation.scm (python-fenics-dijitso)
* gnu/packages/sphinx.scm (python-sphinx-design, python-sphinx-gallery)
* gnu/packages/statistics.scm (python-patsy, python-rchitect, python-pymc,
  python-emcee, python-rpy2)
* gnu/packages/task-management.scm (todoman)
* gnu/packages/telegram.scm (tgcli)
* gnu/packages/textutils.scm (python-panflute)
* gnu/packages/time.scm (python-arrow, python-tzlocal)
* gnu/packages/vpn.scm (sshuttle)
* gnu/packages/web.scm (anonip, python-tibanna)
* gnu/packages/wm.scm (qtile)
[native-inputs]: Remove python-pytest-cov.
---
 gnu/packages/astronomy.scm          |   9 +-
 gnu/packages/audio.scm              |   5 +-
 gnu/packages/backup.scm             |   1 -
 gnu/packages/bioinformatics.scm     |  16 +--
 gnu/packages/build-tools.scm        |   1 -
 gnu/packages/check.scm              |   5 +-
 gnu/packages/cpp.scm                |   1 -
 gnu/packages/databases.scm          |   1 -
 gnu/packages/dav.scm                |   2 -
 gnu/packages/django.scm             |   3 -
 gnu/packages/embedded.scm           |   1 -
 gnu/packages/engineering.scm        |   1 -
 gnu/packages/fediverse.scm          |   1 -
 gnu/packages/finance.scm            |   1 -
 gnu/packages/fontutils.scm          |   1 -
 gnu/packages/geo.scm                |   4 +-
 gnu/packages/gettext.scm            |   1 -
 gnu/packages/gpodder.scm            |   1 -
 gnu/packages/graphviz.scm           |   2 -
 gnu/packages/jupyter.scm            |  12 +-
 gnu/packages/machine-learning.scm   |  20 +---
 gnu/packages/maths.scm              |   1 -
 gnu/packages/matrix.scm             |   1 -
 gnu/packages/messaging.scm          |   4 +-
 gnu/packages/music.scm              |   2 -
 gnu/packages/networking.scm         |   2 +-
 gnu/packages/package-management.scm |   2 -
 gnu/packages/patchutils.scm         |   2 +-
 gnu/packages/protobuf.scm           |   2 +-
 gnu/packages/python-check.scm       |  10 +-
 gnu/packages/python-compression.scm |  11 +-
 gnu/packages/python-crypto.scm      |   4 +-
 gnu/packages/python-science.scm     |  21 ++--
 gnu/packages/python-web.scm         |  68 ++++--------
 gnu/packages/python-xyz.scm         | 164 ++++++++++------------------
 gnu/packages/rdf.scm                |   4 +-
 gnu/packages/simulation.scm         |   1 -
 gnu/packages/sphinx.scm             |   2 -
 gnu/packages/statistics.scm         |   7 +-
 gnu/packages/task-management.scm    |   1 -
 gnu/packages/telegram.scm           |   1 -
 gnu/packages/textutils.scm          |   1 -
 gnu/packages/time.scm               |   2 -
 gnu/packages/vpn.scm                |   1 -
 gnu/packages/web.scm                |   3 +-
 gnu/packages/wm.scm                 |   1 -
 46 files changed, 117 insertions(+), 290 deletions(-)

Toggle diff (305 lines)diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index b4c29480ac..7384da6452 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1952,7 +1952,7 @@ (define-public python-astroml
              (setenv "HOME" "/tmp"))))))
     (propagated-inputs (list python-astropy python-matplotlib python-numpy
                              python-scikit-learn python-scipy))
-    (native-inputs (list python-pytest-astropy-header python-pytest-cov
+    (native-inputs (list python-pytest-astropy-header python-pytest
                          python-pytest-doctestplus python-pytest-remotedata
                          python-wheel))
     (home-page "https://astroml.org")
@@ -2022,7 +2022,6 @@ (define-public python-casa-formats-io
               (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-pytest-openfiles
            python-setuptools
            python-wheel))
@@ -2096,7 +2095,6 @@ (define-public python-cdflib
     (native-inputs
      (list python-astropy-minimal
            python-pytest
-           python-pytest-cov
            python-pytest-remotedata
            python-setuptools
            python-setuptools-scm
@@ -3422,7 +3420,6 @@ (define-public python-sncosmo
            python-cython
            python-pytest
            python-pytest-astropy
-           python-pytest-cov
            python-setuptools
            python-wheel))
     (home-page "https://sncosmo.readthedocs.org")
@@ -4220,7 +4217,6 @@ (define-public python-jwst
                              python-wiimatch))
     (native-inputs (list python-colorama
                          python-pytest
-                         python-pytest-cov
                          python-pytest-doctestplus
                          python-pytest-openfiles
                          python-requests-mock
@@ -4632,7 +4628,6 @@ (define-public python-poliastro
      (list python-hypothesis
            python-flit-core
            python-pytest
-           python-pytest-cov
            python-pytest-doctestplus
            python-pytest-mpl
            python-pytest-mypy))
@@ -6703,7 +6698,6 @@ (define-public python-tweakwcs
            python-stsci-stimage))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-scipy
            python-setuptools
            python-setuptools-scm
@@ -6827,7 +6821,6 @@ (define-public python-wiimatch
     (build-system pyproject-build-system)
     (propagated-inputs (list python-numpy python-scipy))
     (native-inputs (list python-pytest
-                         python-pytest-cov
                          python-pytest-doctestplus
                          python-setuptools-scm
                          python-wheel))
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 2bb0506ce5..cbec74d438 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -6505,7 +6505,7 @@ (define-public python-pysox
       (propagated-inputs
        (list python-numpy python-typing-extensions))
       (native-inputs
-       (list sox python-pytest python-pytest-cov python-soundfile))
+       (list sox python-pytest python-soundfile))
       (home-page "https://github.com/rabitt/pysox")
       (synopsis "Python wrapper around SoX")
       (description "@code{python-pysox} is a wrapper around the @command{sox}
@@ -6535,7 +6535,7 @@ (define-public python-resampy
     (propagated-inputs
      (list python-numba python-numpy python-scipy python-six))
     (native-inputs
-     (list python-pytest python-pytest-cov python-setuptools python-wheel))
+     (list python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/bmcfee/resampy")
     (synopsis "Efficient signal resampling")
     (description
@@ -6590,7 +6590,6 @@ (define-public python-librosa
      (list python-matplotlib
            python-packaging
            python-pytest
-           python-pytest-cov
            python-resampy
            python-setuptools
            python-wheel))
diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index 13c5590f55..d3e6f7e16d 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -1375,7 +1375,6 @@ (define-public borgmatic
     (native-inputs
      (list python-flexmock
            python-pytest
-           python-pytest-cov
            python-setuptools
            python-wheel))
     (inputs
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bc813ca711..133bee638f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2272,7 +2272,6 @@ (define-public python-bed-reader
               (when tests?
                 (apply invoke "pytest" "-v" #$output test-flags)))))))
     (native-inputs (list python-pytest
-                         python-pytest-cov
                          python-pytest-datadir
                          python-pytest-doctestplus
                          python-recommonmark
@@ -3051,7 +3050,7 @@ (define-public python-liana-py
                              python-tqdm
                              tzdata))
     (native-inputs
-     (list python-poetry-core python-pytest python-pytest-cov))
+     (list python-poetry-core python-pytest))
     (home-page "https://github.com/saezlab/liana-py")
     (synopsis "LIANA is a ligand-receptor analysis framework")
     (description "This is a Ligand-Receptor inference framework.  The
@@ -3172,7 +3171,6 @@ (define-public python-metacells
                          python-mypy-extensions
                          python-pandas-stubs
                          python-pytest
-                         python-pytest-cov
                          python-setuptools
                          python-sphinx
                          python-sphinx-rtd-theme
@@ -3593,7 +3591,6 @@ (define-public python-pysnptools
            python-scipy))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-pytest-datadir
            python-pytest-doctestplus
            python-setuptools
@@ -3879,7 +3876,8 @@ (define-public python-biom-format
            ;;python-scikit-bio ;mutually recursive dependency
            python-scipy))
     (native-inputs
-     (list python-cython python-pytest python-pytest-cov
+     (list python-cython
+           python-pytest
            python-wheel))
     (home-page "https://www.biom-format.org")
     (synopsis "Biological Observation Matrix (BIOM) format utilities")
@@ -3927,7 +3925,6 @@ (define-public python-pairtools
     (native-inputs
      (list python-cython
            python-pytest
-           python-pytest-cov
            python-setuptools
            python-wheel))
     (propagated-inputs
@@ -6620,7 +6617,6 @@ (define-public cwltool
            python-humanfriendly
            python-mock
            python-pytest
-           python-pytest-cov
            python-pytest-mock
            python-pytest-runner
            python-wheel))
@@ -11509,7 +11505,6 @@ (define-public python-screed
     (native-inputs
      (list python-importlib-resources
            python-pytest
-           python-pytest-cov
            python-setuptools
            python-setuptools-scm
            python-setuptools-scm-git-archive
@@ -19830,7 +19825,6 @@ (define-public python-pyfaidx
            python-mock
            python-numpy
            python-pytest
-           python-pytest-cov
            python-wheel))
     (propagated-inputs (list python-setuptools))
     (home-page "http://mattshirley.com")
@@ -19880,9 +19874,7 @@ (define-public python-cooler
            python-scipy
            python-simplejson))
     (native-inputs
-     (list python-hatchling
-           python-pytest
-           python-pytest-cov))
+     (list python-hatchling python-pytest))
     ;; Almost all the projects of the Mirnylab are moved under Open2C umbrella
     (home-page "https://github.com/open2c/cooler")
     (synopsis "Sparse binary format for genomic interaction matrices")
diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm
index 6bf0b2ec67..900ca704e6 100644
--- a/gnu/packages/build-tools.scm
+++ b/gnu/packages/build-tools.scm
@@ -365,7 +365,6 @@ (define-public meson-python
            python-cython-3
            python-gitpython
            python-pytest
-           python-pytest-cov
            python-pytest-mock))
     (home-page "https://github.com/mesonbuild/meson-python")
     (synopsis "Meson-based build backend for Python")
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index da8f42c315..ead9f457c2 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -1871,7 +1871,6 @@ (define-public python-pytest-nunit
     (arguments (list #:tests? #false)) ;no tests included
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-setuptools
            python-wheel
            python-xmlschema))
@@ -2942,7 +2941,6 @@ (define-public python-pytest-enabler
            python-toml))
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
-                         python-pytest-cov
                          python-pytest-flake8
                          python-pytest-mypy
                          python-setuptools
@@ -3115,7 +3113,6 @@ (define-public python-pytest-perf
     (native-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-cov
            python-pytest-enabler
            python-pytest-flake8
            python-pytest-mypy
@@ -3675,7 +3672,7 @@ (define-public python-pyhamcrest
                (base32
                 "05kdzlhs2kvj82pfca13qszszcj6dyrk4b9pbr46x06sq2s4qyls"))))
     (native-inputs                      ;all native inputs are for tests
-     (list python-pytest-cov python-mock python-pytest python-hypothesis))
+     (list python-mock python-pytest python-hypothesis))
     (build-system python-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases
diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index 6c9c70baf4..9d41fd9ea6 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -1349,7 +1349,6 @@ (define-public cpplint
                            (getenv "TMP_PYTHONPATH")))))))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-pytest-runner
            python-setuptools
            python-testfixtures
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 397754521c..e6d29a0457 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -4551,7 +4551,6 @@ (define-public python-redis
      (list python-numpy
            python-pytest
            python-pytest-asyncio-0.23
-           python-pytest-cov
            python-pytest-timeout
            python-setuptools
            python-wheel
diff --git a/gnu/packages/dav.scm b/gnu/packages/dav.scm
index 546118055f..7688c9a994 100644
--- a/gnu/packages/dav.scm
+++ b/gnu/packages/dav.scm
@@ -58,7 +58,6 @@ (define-public radicale
     (build-system pyproject-build-system)
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-pytest-flake8
            python-pytest-isort
            python-setuptools
@@ -151,7 +150,6 @@ (define-public vdirsyncer
            python-trustme
            python-pytest
            python-pytest-asyncio
-           python-pytest-cov
            python-pytest-httpserver
            radicale))
     (inputs
diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index b8c72c55d9..e1b01b3770 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -269,7 +269,6 @@ (define-public python-django-extensions
      (list python-mock
            python-factory-boy
            python-pytest
-           python-pytest-cov
            python-pytest-django
            p

This message was truncated. Download the full message here.

Nicolas Graves wrote 2 weeks ago

[PATCH v4 30/52] gnu: python-django-contact-form: Remove python-pytest-cov native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-30-ngraves@ngraves.fr

* gnu/packages/django.scm (python-django-contact-form):

[native-inputs]: Remove python-pytest-cov.

[build-system]: Upgrade to pyproject-build-system.

[arguments]<#:phases>: Remove coverage tests for check phase.

Change-Id: I4d0fc406401b7e923f7efa084dbe8ea3753e50fc

---

gnu/packages/django.scm | 7 ++-----

1 file changed, 2 insertions(+), 5 deletions(-)

Toggle diff (25 lines)diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index e1b01b3770..6b67b66891 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -888,16 +888,13 @@ (define-public python-django-contact-form
               (sha256
                (base32
                 "1my9hkrylckp5vfqg9b0kncrdlxjnwxll56sdciqn4v19i4wbq1y"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
          (replace 'check
            (lambda _
-             (invoke "coverage" "run" "--source" "contact_form"
-                     "runtests.py"))))))
-    (native-inputs
-     (list python-coverage))
+             (invoke "python" "runtests.py"))))))
     (propagated-inputs
      (list python-django))
     (home-page "https://github.com/ubernostrum/django-contact-form")
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 31/52] gnu: python-dateutil: Remove python-pytest-cov native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-31-ngraves@ngraves.fr

* gnu/packages/time.scm (python-dateutil):

[native-inputs]: Remove python-pytest-cov.

[arguments]<#:phases>: Add remove-pytest-cov-dep phase.

Change-Id: Id82a147d6e40383ecc2661ac896b65b858c181e0

---

gnu/packages/time.scm | 18 ++++++++++++------

1 file changed, 12 insertions(+), 6 deletions(-)

Toggle diff (33 lines)diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm
index 9ed43d1885..5f07e0860a 100644
--- a/gnu/packages/time.scm
+++ b/gnu/packages/time.scm
@@ -277,14 +277,20 @@ (define-public python-dateutil
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags '(list  ; avoid freezegun dependency
-                     "--ignore=dateutil/test/test_utils.py"
-                     "--ignore=dateutil/test/test_rrule.py"
-                     ;; XXX: Fails to get timezone from /etc/localtime.
-                     "--ignore=dateutil/test/test_tz.py")))
+      #:test-flags '(list "dateutil/test" "docs"
+                          ;; avoid freezegun dependency
+                          "--ignore=dateutil/test/test_utils.py"
+                          "--ignore=dateutil/test/test_rrule.py"
+                          ;; XXX: Fails to get timezone from /etc/localtime.
+                          "--ignore=dateutil/test/test_tz.py")
+      #:phases #~(modify-phases %standard-phases
+                   (add-after 'unpack 'remove-pytest-cov-dep
+                     (lambda _
+                       (substitute* "dateutil/test/conftest.py"
+                         (("item\\.add_marker\\(pytest\\.mark\\.no_cover\\)")
+                          "pass")))))))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-setuptools
            python-setuptools-scm
            python-wheel))
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 32/52] build-system/pyproject: Remove python-pytest-isort native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-32-ngraves@ngraves.fr

* gnu/packages/dav.scm (radicale)
* gnu/packages/python-check.scm (python-pytest-isort)
* gnu/packages/python-xyz.scm (python-cairosvg)
[native-inputs]: Remove python-pytest-isort.

python-pytest-isort
---
 gnu/packages/dav.scm          | 1 -
 gnu/packages/python-check.scm | 2 +-
 gnu/packages/python-xyz.scm   | 1 -
 3 files changed, 1 insertion(+), 3 deletions(-)

Toggle diff (39 lines)diff --git a/gnu/packages/dav.scm b/gnu/packages/dav.scm
index 7688c9a994..ff5d8409b0 100644
--- a/gnu/packages/dav.scm
+++ b/gnu/packages/dav.scm
@@ -59,7 +59,6 @@ (define-public radicale
     (native-inputs
      (list python-pytest
            python-pytest-flake8
-           python-pytest-isort
            python-setuptools
            python-waitress
            python-wheel))
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 25fe905afa..8edec4595f 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -1867,7 +1867,7 @@ (define-public python-pytest-pycodestyle
     (propagated-inputs
      (list python-py python-pycodestyle python-pytest))
     (native-inputs
-     (list python-pytest-isort python-setuptools python-wheel))
+     (list python-setuptools python-wheel))
     (home-page "https://github.com/henry0312/pytest-pycodestyle")
     (synopsis "Pytest plugin to run pycodestyle")
     (description "This package provides a plugin to run @code{pycodestyle}
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 5c92b40751..e6c73b0569 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -31603,7 +31603,6 @@ (define-public python-cairosvg
            python-pillow python-tinycss2))
     (native-inputs
      (list python-pytest-flake8
-           python-pytest-isort
            python-pytest-runner
            python-setuptools
            python-wheel))
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 33/52] build-system/pyproject: Remove python-pytest-flake8 native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-33-ngraves@ngraves.fr

* gnu/packages/bioinformatics.scm (python-muon)
* gnu/packages/check.scm (python-pytest-enabler, python-pytest-perf)
* gnu/packages/dav.scm (radicale)
* gnu/packages/debug.scm (c-vise)
* gnu/packages/matrix.scm (python-matrix-nio)
* gnu/packages/python-web.scm (python-mechanicalsoup)
* gnu/packages/python-xyz.scm (python-pyvips, python-dask-image,
  python-importlib-resources, python-jaraco-classes,
  python-jaraco-context, python-jaraco-functools,
  python-jaraco-packaging, python-jaraco-test, python-path,
  python-pip-run, python-tempora, python-cairosvg)
[native-inputs]: Remove python-pytest-flake8.

* gnu/packages/python-check.scm (python-pytest-csv)
[arguments]{test-flags}: Ignore flake8 related test.
[native-inputs]: Remove python-pytest-flake8.
---
 gnu/packages/bioinformatics.scm |  3 +--
 gnu/packages/check.scm          |  2 --
 gnu/packages/dav.scm            |  1 -
 gnu/packages/debug.scm          |  2 +-
 gnu/packages/matrix.scm         |  1 -
 gnu/packages/python-check.scm   |  5 +++--
 gnu/packages/python-web.scm     |  3 +--
 gnu/packages/python-xyz.scm     | 17 ++---------------
 8 files changed, 8 insertions(+), 26 deletions(-)

Toggle diff (209 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 133bee638f..c989e6d4c8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5381,8 +5381,7 @@ (define-public python-muon
                              python-tqdm
                              python-umap-learn))
     (native-inputs (list python-flit-core
-                         python-pytest
-                         python-pytest-flake8))
+                         python-pytest))
     (home-page "https://github.com/scverse/muon")
     (synopsis "Multimodal omics analysis framework")
     (description "muon is a multimodal omics Python framework.")
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index ead9f457c2..0f0278ae22 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2941,7 +2941,6 @@ (define-public python-pytest-enabler
            python-toml))
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
-                         python-pytest-flake8
                          python-pytest-mypy
                          python-setuptools
                          python-setuptools-scm
@@ -3114,7 +3113,6 @@ (define-public python-pytest-perf
      (list python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools
            python-wheel))
diff --git a/gnu/packages/dav.scm b/gnu/packages/dav.scm
index ff5d8409b0..71d12a0ca1 100644
--- a/gnu/packages/dav.scm
+++ b/gnu/packages/dav.scm
@@ -58,7 +58,6 @@ (define-public radicale
     (build-system pyproject-build-system)
     (native-inputs
      (list python-pytest
-           python-pytest-flake8
            python-setuptools
            python-waitress
            python-wheel))
diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm
index 5580b4eaf4..59d17f2623 100644
--- a/gnu/packages/debug.scm
+++ b/gnu/packages/debug.scm
@@ -255,7 +255,7 @@ (define-public c-vise
        (file-name (git-file-name name version))))
     (build-system cmake-build-system)
     (native-inputs
-     (list flex python-pytest python-pytest-flake8))
+     (list flex python-pytest))
     (inputs
      (list bash-minimal clang llvm unifdef
            python python-pebble python-psutil python-chardet))
diff --git a/gnu/packages/matrix.scm b/gnu/packages/matrix.scm
index 970093d345..e7c1468da4 100644
--- a/gnu/packages/matrix.scm
+++ b/gnu/packages/matrix.scm
@@ -200,7 +200,6 @@ (define-public python-matrix-nio
            python-pytest-aiohttp
            python-pytest-asyncio
            python-pytest-benchmark
-           python-pytest-flake8
            python-setuptools
            python-wheel))
     (propagated-inputs
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 8edec4595f..03be7db63e 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -673,9 +673,10 @@ (define-public python-pytest-csv
         (base32
          "17518f2fn5l98lyk9p8r7215c1whi61imzrh6ahrmcksr8w0zz04"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list #:test-flags '(list "--ignore=tests/test_flake8.py")))
     (native-inputs
-     (list python-pytest-flake8
-           python-pytest-xdist
+     (list python-pytest-xdist
            python-setuptools
            python-tabulate
            python-wheel))
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index fc519d660a..bdad225b4c 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -2319,8 +2319,7 @@ (define-public python-mechanicalsoup
     (propagated-inputs
      (list python-beautifulsoup4 python-lxml python-requests python-six))
     (native-inputs
-     (list python-pytest-flake8
-           python-pytest-httpbin
+     (list python-pytest-httpbin
            python-pytest-mock
            python-pytest-runner
            python-requests-mock
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e6c73b0569..a17b20e822 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -11992,7 +11992,6 @@ (define-public python-pyvips
     (native-inputs
      (list python-pyperf
            python-pytest
-           python-pytest-flake8
            python-pytest-runner))
     (inputs
      (list glib vips))
@@ -12747,7 +12746,6 @@ (define-public python-importlib-resources
      (list python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools-57
            python-setuptools-scm))
@@ -12895,7 +12893,6 @@ (define-public python-jaraco-classes
     (native-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools
            python-setuptools-scm
@@ -12986,7 +12983,6 @@ (define-public python-jaraco-context
     (native-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools
            python-setuptools-scm
@@ -13019,7 +13015,6 @@ (define-public python-jaraco-functools
      (list python-jaraco-classes
            python-pytest
            python-pytest-checkdocs
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools
            python-setuptools-scm
@@ -13049,7 +13044,6 @@ (define-public python-jaraco-packaging
     (propagated-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-flake8
            python-rst.linker
            python-setuptools
            python-setuptools-scm
@@ -17853,7 +17847,6 @@ (define-public python-path
                python-pytest
                python-pytest-checkdocs
                python-pytest-enabler
-               python-pytest-flake8
                python-pytest-mypy)))
     (properties (alist-delete 'hidden?
                               (package-properties
@@ -17957,7 +17950,6 @@ (define-public python-pip-run
                python-pytest
                python-pytest-checkdocs
                python-pytest-enabler
-               python-pytest-flake8
                python-pytest-mypy)))
     (properties (alist-delete 'hidden? (package-properties
                                         python-pip-run-bootstrap)))))
@@ -22563,7 +22555,6 @@ (define-public python-inflect
                          python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-flake8
                          python-pytest-mypy
                          ;; For the version number
                          python-setuptools-scm
@@ -27834,7 +27825,6 @@ (define-public python-tempora
            python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-flake8
            python-pytest-freezegun
            python-pytest-mypy
            python-setuptools-scm
@@ -30508,7 +30498,7 @@ (define-public python-dask-image
                              python-scipy
                              python-tifffile))
     (native-inputs
-     (list python-pytest-flake8 python-pytest))
+     (list python-pytest))
     (home-page "https://github.com/dask/dask-image")
     (synopsis "Distributed image processing")
     (description "This is a package for image processing with Dask arrays.
@@ -31602,10 +31592,7 @@ (define-public python-cairosvg
      (list python-cairocffi python-cssselect2 python-defusedxml
            python-pillow python-tinycss2))
     (native-inputs
-     (list python-pytest-flake8
-           python-pytest-runner
-           python-setuptools
-           python-wheel))
+     (list python-pytest-runner python-setuptools python-wheel))
     (home-page "https://cairosvg.org/")
     (synopsis "SVG to PDF/PS/PNG converter based on Cairo")
     (description "CairoSVG is a SVG converter based on Cairo.  It can export
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 34/52] build-system/pyproject: Remove python-pytest-mypy inputs.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-34-ngraves@ngraves.fr

* gnu/packages/astronomy.scm (python-poliastro)

[native-inputs]: Remove python-pytest-mypy.

* gnu/packages/check.scm (python-pytest-perf)[native-inputs]: Remove

python-pytest-mypy.

* gnu/packages/python-web.scm (python-portend)[native-inputs]: Remove

python-pytest-mypy.

* gnu/packages/python-xyz.scm (python-importlib-resources,

python-jaraco-classes, python-jaraco-collections,

python-jaraco-context, python-jaraco-functools, python-jaraco-test,

python-path, python-pip-run, python-inflect, python-tempora,

python-portalocker)[native-inputs]: Remove python-pytest-mypy.

---

gnu/packages/astronomy.scm | 3 +--

gnu/packages/check.scm | 1 -

gnu/packages/python-web.scm | 1 -

gnu/packages/python-xyz.scm | 15 ++-------------

4 files changed, 3 insertions(+), 17 deletions(-)

Toggle diff (136 lines)diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 7384da6452..2cea636e1b 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4629,8 +4629,7 @@ (define-public python-poliastro
            python-flit-core
            python-pytest
            python-pytest-doctestplus
-           python-pytest-mpl
-           python-pytest-mypy))
+           python-pytest-mpl))
     (propagated-inputs
      (list python-astropy
            python-astroquery
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 0f0278ae22..8c157d91c1 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -3113,7 +3113,6 @@ (define-public python-pytest-perf
      (list python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-mypy
            python-setuptools
            python-wheel))
     (propagated-inputs
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index bdad225b4c..4e68aa47ea 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -699,7 +699,6 @@ (define-public python-portend
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-mypy
                          python-setuptools
                          python-wheel))
     (home-page "https://github.com/jaraco/portend")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index a17b20e822..b42c954233 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -5657,7 +5657,6 @@ (define-public python-portalocker
                 "0lawjm736vs86wlnxc3qqh37l11z0yx81xq3dmrw33m86kaq2bh3"))))
     (build-system pyproject-build-system)
     (native-inputs (list python-pytest
-                         python-pytest-mypy
                          python-pytest-timeout
                          python-redis
                          python-setuptools
@@ -12746,7 +12745,6 @@ (define-public python-importlib-resources
      (list python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-mypy
            python-setuptools-57
            python-setuptools-scm))
     (propagated-inputs
@@ -12893,7 +12891,6 @@ (define-public python-jaraco-classes
     (native-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-mypy
            python-setuptools
            python-setuptools-scm
            python-wheel))
@@ -12925,7 +12922,6 @@ (define-public python-jaraco-collections
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-mypy
                          python-setuptools
                          python-wheel))
     (home-page "https://github.com/jaraco/jaraco.collections")
@@ -12983,7 +12979,6 @@ (define-public python-jaraco-context
     (native-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-mypy
            python-setuptools
            python-setuptools-scm
            python-wheel))
@@ -13015,7 +13010,6 @@ (define-public python-jaraco-functools
      (list python-jaraco-classes
            python-pytest
            python-pytest-checkdocs
-           python-pytest-mypy
            python-setuptools
            python-setuptools-scm
            python-wheel))
@@ -13107,7 +13101,6 @@ (define-public python-jaraco-text
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-mypy
                          python-setuptools
                          python-wheel))
     (home-page "https://github.com/jaraco/jaraco.text")
@@ -17846,8 +17839,7 @@ (define-public python-path
                python-pygments
                python-pytest
                python-pytest-checkdocs
-               python-pytest-enabler
-               python-pytest-mypy)))
+               python-pytest-enabler)))
     (properties (alist-delete 'hidden?
                               (package-properties
                                python-path-bootstrap)))))
@@ -17949,8 +17941,7 @@ (define-public python-pip-run
                python-pygments
                python-pytest
                python-pytest-checkdocs
-               python-pytest-enabler
-               python-pytest-mypy)))
+               python-pytest-enabler)))
     (properties (alist-delete 'hidden? (package-properties
                                         python-pip-run-bootstrap)))))
 
@@ -22555,7 +22546,6 @@ (define-public python-inflect
                          python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-mypy
                          ;; For the version number
                          python-setuptools-scm
                          python-setuptools
@@ -27826,7 +27816,6 @@ (define-public python-tempora
            python-pytest-checkdocs
            python-pytest-enabler
            python-pytest-freezegun
-           python-pytest-mypy
            python-setuptools-scm
            python-types-freezegun
            python-types-pytz
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 39/52] build-system/pyproject: Remove python-mypy native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-39-ngraves@ngraves.fr

---
 gnu/packages/bioinformatics.scm | 2 --
 gnu/packages/check.scm          | 1 -
 gnu/packages/databases.scm      | 3 +--
 gnu/packages/finance.scm        | 1 -
 gnu/packages/matrix.scm         | 1 -
 gnu/packages/openstack.scm      | 1 -
 gnu/packages/python-check.scm   | 8 ++------
 gnu/packages/python-crypto.scm  | 1 -
 gnu/packages/python-science.scm | 3 +--
 gnu/packages/python-web.scm     | 2 --
 gnu/packages/python-xyz.scm     | 7 ++-----
 11 files changed, 6 insertions(+), 24 deletions(-)

Toggle diff (223 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c989e6d4c8..5fd6958735 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3167,7 +3167,6 @@ (define-public python-metacells
                              python-threadpoolctl
                              python-umap-learn))
     (native-inputs (list python-bumpversion
-                         python-mypy
                          python-mypy-extensions
                          python-pandas-stubs
                          python-pytest
@@ -6348,7 +6347,6 @@ (define-public python-schema-salad
     (native-inputs
      (list python-black
            python-cachecontrol
-           python-mypy
            python-pytest
            python-pytest-runner
            python-setuptools
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 8c157d91c1..c0b6f3e0af 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2823,7 +2823,6 @@ (define-public python-crosshair
     (native-inputs
      (list python-icontract ;optional
            python-importlib-metadata
-           python-mypy
            python-numpy
            python-pytest
            python-pytest-xdist))
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index e6d29a0457..cb198c411a 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -4141,8 +4141,7 @@ (define-public python-aiosqlite
                           (lambda* (#:key tests? #:allow-other-keys)
                             (when tests?
                               (invoke "python" "-m" "aiosqlite.tests")))))))
-    (native-inputs (list python-flit-core
-                         python-mypy))
+    (native-inputs (list python-flit-core))
     (home-page "https://github.com/jreese/aiosqlite")
     (synopsis
      "Asyncio bridge for sqlite3")
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index eb676592b3..ddc9954d8e 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -2068,7 +2068,6 @@ (define-public fava
            python-werkzeug))
     (native-inputs
      (list python-babel
-           python-mypy
            python-pytest
            python-setuptools
            python-types-setuptools
diff --git a/gnu/packages/matrix.scm b/gnu/packages/matrix.scm
index e7c1468da4..e503d17b91 100644
--- a/gnu/packages/matrix.scm
+++ b/gnu/packages/matrix.scm
@@ -193,7 +193,6 @@ (define-public python-matrix-nio
            python-hpack
            python-hyperframe
            python-hypothesis
-           python-mypy
            python-mypy-extensions
            python-poetry-core
            python-pytest
diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index 84696a586f..2b74994cc5 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -552,7 +552,6 @@ (define-public python-oslo.context
     (native-inputs
      (list python-fixtures
            python-hacking
-           python-mypy
            python-oslotest
            python-pbr
            python-stestr))
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 03be7db63e..7a8ff17175 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -585,8 +585,7 @@ (define-public python-green
               (when tests?
                 (apply invoke "python" "-m" "green" test-flags)))))))
     (native-inputs
-     (list python-mypy
-           python-setuptools
+     (list python-setuptools
            python-testtools
            python-wheel))
     (propagated-inputs
@@ -814,7 +813,6 @@ (define-public python-icontract
     (native-inputs
      (list python-astor
            python-asyncstdlib
-           python-mypy
            python-numpy
            python-setuptools
            python-typeguard
@@ -2620,7 +2618,6 @@ (define-public python-nptyping
     (native-inputs
      (list python-beartype
            python-feedparser
-           python-mypy
            python-pandas
            python-pytest
            python-setuptools
@@ -3113,8 +3110,7 @@ (define-public python-sybil
         (sha256
          (base32 "0r491k91fi2nb0kdd6di8cb2kxcvsk1xzw3sgwsxhhg4qynsp3bi"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-mypy
-                         python-myst-parser
+    (native-inputs (list python-myst-parser
                          python-pytest
                          python-pyyaml
                          python-seedir
diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm
index eb6fdd5227..0dda3fb774 100644
--- a/gnu/packages/python-crypto.scm
+++ b/gnu/packages/python-crypto.scm
@@ -584,7 +584,6 @@ (define-public python-cryptography
            python-cffi
            python-click
            python-cryptography-vectors
-           python-mypy
            python-pretend
            python-pytest
            python-pytest-benchmark
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index b5269bf5a4..e3ccbfed06 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -3953,8 +3953,7 @@ (define-public python-pynetdicom
                          python-pytest-xdist
                          python-sphinx
                          python-sphinx-rtd-theme))
-    (propagated-inputs (list python-mypy
-                             python-numpydoc
+    (propagated-inputs (list python-numpydoc
                              python-pydicom
                              python-pyfakefs
                              python-sqlalchemy))
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 97b9263499..149daf6d88 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -8855,7 +8855,6 @@ (define-public python-sanic
            python-chardet
            python-cryptography
            python-docutils
-           python-mypy
            python-pygments
            python-pytest
            python-pytest-benchmark
@@ -9878,7 +9877,6 @@ (define-public python-scrapy
            python-zope-interface))
     (native-inputs
      (list nss-certs-for-test
-           python-mypy
            python-pexpect
            python-pytest
            python-pytest-xdist
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 4dd1f92e05..a938a05bde 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -9475,7 +9475,6 @@ (define-public python-numpy
            meson-python
            pkg-config
            python-hypothesis
-           python-mypy
            python-pytest
            python-pytest-xdist
            python-setuptools
@@ -9554,7 +9553,6 @@ (define-public python-numpy-2
            ninja
            pkg-config
            python-hypothesis
-           python-mypy
            python-pytest
            python-pytest-xdist
            python-setuptools
@@ -9796,7 +9794,6 @@ (define-public python-multiscale-spatial-image
            python-nbmake
            python-pooch
            python-pytest
-           python-pytest-mypy
            python-urllib3
            python-zarr))
     (home-page "https://github.com/spatial-image/multiscale-spatial-image")
@@ -13356,7 +13353,6 @@ (define-public python-traitlets
     (native-inputs
      (list python-argcomplete
            python-hatchling
-           python-mypy
            python-pytest
            python-pytest-mock
            python-pytest-mypy-testing))
@@ -14998,7 +14994,6 @@ (define-public python-seaborn
            python-ipykernel
            python-nbconvert
            python-numpydoc
-           python-mypy
            python-pytest
            python-pytest-xdist
            python-pyyaml))
@@ -28431,6 +28426,8 @@ (define-public python-typeguard
        (sha256
         (base32 "06y22d1f5dhpyl71wbhsaibig5hvc2v44pw795yb8lxl02fsh8hd"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list #:test-flags ''("--ignore=tests/mypy")))
     (native-inputs
      (list python-pytest
            python-setuptools
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 40/52] build-system/pyproject: Add option #:use-pytest-plugin?

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-40-ngraves@ngraves.fr

In the very rare cases where our plugin actually breaks a test, adding

a flag is more convenient than replacing the phase.

* guix/build-system/pyproject.scm (pyproject-build): Add option

use-pytest-plugin?

* guix/build/pyproject-build-system.scm (check): Add and use option

use-pytest-plugin?

* gnu/packages/check.scm (python-coverage,

python-pytest-mypy)[arguments]{use-pytest-plugin}: Set to #f to fix

tests.

* gnu/packages/python-check.scm (python-pytest-flake8)[arguments]:

Likewise.

---

gnu/packages/check.scm | 6 +++++-

gnu/packages/python-check.scm | 1 +

guix/build-system/pyproject.scm | 2 ++

guix/build/pyproject-build-system.scm | 9 ++++++---

4 files changed, 14 insertions(+), 4 deletions(-)

Toggle diff (85 lines)diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index c0b6f3e0af..c817a18631 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2497,6 +2497,8 @@ (define-public python-coverage
          "--deselect=tests/test_filereporter.py::FileReporterTest::test_zipfile"
          ;; XXX: Checking coverage for too much files, not only the target one.
          "--deselect=tests/test_oddball.py::DoctestTest::test_doctest")
+      ;; This is one of the rare cases where our plugin causes a test to fail.
+      #:use-pytest-plugin? #f
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-pyproject
@@ -2994,7 +2996,9 @@ (define-public python-pytest-mypy
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags #~(list "--numprocesses" "auto")))
+      #:use-pytest-plugin? #f
+      #:test-flags #~(list "--numprocesses"
+                           (number->string (parallel-job-count)))))
     (native-inputs
      (list python-pexpect
            python-pytest-xdist
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 7a8ff17175..7cedb111ad 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -1704,6 +1704,7 @@ (define-public python-pytest-flake8
         (base32
          "1rhz7mxcg7x9dbabfcjai3zxikfgw7az07m4ddf92bg35ib3byw8"))))
     (build-system pyproject-build-system)
+    (arguments (list #:use-pytest-plugin? #f))
     (native-inputs
      (list python-pytest
            python-setuptools
diff --git a/guix/build-system/pyproject.scm b/guix/build-system/pyproject.scm
index bdf8f440ac..1cd38ce349 100644
--- a/guix/build-system/pyproject.scm
+++ b/guix/build-system/pyproject.scm
@@ -93,6 +93,7 @@ (define private-keywords
 (define* (pyproject-build name inputs
                           #:key source
                           (tests? #t)
+                          (use-pytest-plugin? #t)
                           (configure-flags ''(@))
                           (backend-path #f)
                           (build-backend #f)
@@ -125,6 +126,7 @@ (define build
                  #:test-backend #$test-backend
                  #:test-flags #$test-flags
                  #:tests? #$tests?
+                 #:use-pytest-plugin? #$use-pytest-plugin?
                  #:phases #$(if (pair? phases)
                                 (sexp->gexp phases)
                                 phases)
diff --git a/guix/build/pyproject-build-system.scm b/guix/build/pyproject-build-system.scm
index 2df9f2f479..a96ec05ad6 100644
--- a/guix/build/pyproject-build-system.scm
+++ b/guix/build/pyproject-build-system.scm
@@ -231,7 +231,8 @@ (define-syntax-rule (with-guix-pytest-plugin inputs exp ...)
   "Evaluate EXP in a context where the Guix pytest plugin is added."
   (call-with-guix-pytest-plugin inputs (lambda () exp ...)))
 
-(define* (check #:key inputs tests? test-backend test-flags #:allow-other-keys)
+(define* (check #:key inputs tests? test-backend test-flags use-pytest-plugin?
+                #:allow-other-keys)
   "Run the test suite of a given Python package."
   (if tests?
       ;; Unfortunately with PEP 517 there is no common method to specify test
@@ -254,8 +255,10 @@ (define* (check #:key inputs tests? test-backend test-flags #:allow-other-keys)
         (format #t "Using ~a~%" use-test-backend)
         (match use-test-backend
           ('pytest
-           (with-guix-pytest-plugin inputs
-             (apply invoke pytest "-vv" test-flags)))
+           (if use-pytest-plugin?
+               (with-guix-pytest-plugin inputs
+                 (apply invoke pytest "-vv" test-flags))
+               (apply invoke pytest "-vv" test-flags)))
           ('nose
            (apply invoke nosetests "-v" test-flags))
           ('nose2
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 43/52] build-system/pyproject: Remove python-mypy-extensions native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-43-ngraves@ngraves.fr

---

gnu/packages/bioinformatics.scm | 1 -

gnu/packages/web.scm | 3 +--

2 files changed, 1 insertion(+), 3 deletions(-)

Toggle diff (28 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5fd6958735..f815bac9b2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3167,7 +3167,6 @@ (define-public python-metacells
                              python-threadpoolctl
                              python-umap-learn))
     (native-inputs (list python-bumpversion
-                         python-mypy-extensions
                          python-pandas-stubs
                          python-pytest
                          python-setuptools
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 61c5775e43..8393f55a2a 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -9656,8 +9656,7 @@ (define-public archivebox
            python-crontab
            python-dateparser
            python-django-extensions
-           python-django-3.1.14
-           python-mypy-extensions))
+           python-django-3.1.14))
     (native-inputs
      (list python-wheel))
     (synopsis "Self-hosted Web archiving")
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 45/52] build-system/pyproject: Remove python-pip native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-45-ngraves@ngraves.fr

---
 gnu/packages/bioinformatics.scm |  2 +-
 gnu/packages/databases.scm      |  1 -
 gnu/packages/python-science.scm |  1 -
 gnu/packages/python-web.scm     |  4 +---
 gnu/packages/python-xyz.scm     | 15 ++++-----------
 gnu/packages/shells.scm         |  1 -
 gnu/packages/web.scm            |  1 -
 7 files changed, 6 insertions(+), 19 deletions(-)

Toggle diff (153 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f815bac9b2..e421f78440 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7669,7 +7669,7 @@ (define-public python-illumina-utils
     (build-system pyproject-build-system)
     (arguments (list #:tests? #false))  ;there are none
     (propagated-inputs (list python-matplotlib python-numpy python-levenshtein))
-    (native-inputs (list python-setuptools python-wheel python-pip))
+    (native-inputs (list python-setuptools python-wheel))
     (home-page "https://github.com/meren/illumina-utils")
     (synopsis "Library and scripts to work with Illumina paired-end data")
     (description
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index cb198c411a..b5b8246bca 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -5795,7 +5795,6 @@ (define-public datasette
      (list nss-certs-for-test
            python-beautifulsoup4
            python-cogapp
-           python-pip
            python-pytest
            python-pytest-asyncio
            python-pytest-runner
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index e3ccbfed06..023decd507 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -551,7 +551,6 @@ (define-public python-scikit-build-core
                          python-hatch-vcs
                          python-hatchling
                          python-numpy
-                         python-pip
                          python-pypa-build
                          python-pytest
                          python-pytest-subprocess
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 149daf6d88..230de4f5a3 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -2039,7 +2039,6 @@ (define-public httpie
            python-defusedxml
            python-importlib-metadata
            python-multidict
-           python-pip
            python-pygments
            python-requests
            python-requests-toolbelt
@@ -4485,8 +4484,7 @@ (define-public python-requests
            python-idna
            python-urllib3))
     (native-inputs
-     (list python-pip
-           python-pytest
+     (list python-pytest
            python-pytest-mock
            python-setuptools
            python-wheel))
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 155a69fc10..c7e8199f30 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -5749,8 +5749,7 @@ (define-public python-extension-helpers
            python-setuptools-scm
            python-tomli
            python-setuptools
-           python-wheel
-           python-pip))
+           python-wheel))
     (home-page "https://extension-helpers.readthedocs.io")
     (synopsis "Astropy ecosystem utilities for building and installing packages")
     (description
@@ -19460,8 +19459,7 @@ (define-public python-argparse-manpage
          "1nq4sq1zk1xzdsqq61hd27jhj978ys136aba1zjg02x1g0c0cg11"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-pip python-pytest python-setuptools python-tomli
-           python-wheel))
+     (list python-pytest python-setuptools python-tomli python-wheel))
     (home-page "https://github.com/praiskup/argparse-manpage")
     (synopsis "Build manual page from Python's ArgumentParser object")
     (description
@@ -22992,7 +22990,6 @@ (define-public poetry
            python-keyring
            python-packaging
            python-pexpect
-           python-pip
            python-pkginfo
            python-platformdirs
            python-poetry-core
@@ -23315,8 +23312,7 @@ (define-public python-lazy-object-proxy
         (base32 "0sdc92bbzy6slcl432j04mr131cy8n0many26ppm4fpl8mnpn93q"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-pip
-           python-setuptools
+     (list python-setuptools
            python-setuptools-scm
            python-wheel))
     (home-page "https://github.com/ionelmc/python-lazy-object-proxy")
@@ -25931,7 +25927,6 @@ (define-public python-isort
            python-hypothesmith
            python-libcst-minimal
            python-natsort
-           python-pip
            python-poetry-core
            python-pylama
            python-pypa-build
@@ -26661,8 +26656,7 @@ (define-public python-rfc3986-validator
         (base32 "0mfh82r37ma5n54n8ibnqvmwr3j3f2ixqfjfmv1rwfqvjbkvsi1x"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-pip
-           python-pytest
+     (list python-pytest
            python-pytest-runner
            python-rfc3987
            python-setuptools
@@ -34322,7 +34316,6 @@ (define-public python-pypandoc
      (list (texlive-updmap.cfg
             (list texlive-xpatch texlive-lm
                   texlive-xcolor))
-           python-pip
            python-poetry-core
            python-setuptools))
     (inputs (list pandoc python-pandocfilters))
diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm
index 6f830d54aa..7763c2729b 100644
--- a/gnu/packages/shells.scm
+++ b/gnu/packages/shells.scm
@@ -620,7 +620,6 @@ (define-public xonsh
                    (setenv "HOME" "/tmp"))))))
     (native-inputs
      (list git-minimal
-           python-pip
            python-pyte
            python-pytest
            python-pytest-mock
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 8393f55a2a..f433dc6dc8 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -5262,7 +5262,6 @@ (define-public python-lambda-4dn
      (list python-boto3
            python-botocore
            python-docutils
-           python-pip
            python-six
            python-virtualenv))
     (home-page "https://github.com/4dn-dcic/python-lambda")
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 46/52] build-system/pyproject: Remove python-pre-commit native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-46-ngraves@ngraves.fr

---

gnu/packages/python-check.scm | 3 +--

gnu/packages/python-xyz.scm | 2 --

2 files changed, 1 insertion(+), 4 deletions(-)

Toggle diff (36 lines)diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 7cedb111ad..9e4cb841cd 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -2291,8 +2291,7 @@ (define-public python-pytest-qt
     (propagated-inputs
      (list python-pluggy python-pyqt python-pytest))
     (native-inputs
-     (list python-pre-commit
-           python-setuptools
+     (list python-setuptools
            python-setuptools-scm
            python-wheel))
     (home-page "https://github.com/pytest-dev/pytest-qt")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index c7e8199f30..c0f047aebc 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -11391,7 +11391,6 @@ (define-public python-pillow-heif
                          python-defusedxml
                          python-numpy
                          python-packaging
-                         python-pre-commit
                          python-pympler
                          python-setuptools
                          python-pytest
@@ -13465,7 +13464,6 @@ (define-public python-jupyter-core
     (propagated-inputs (list python-platformdirs python-traitlets))
     (native-inputs (list python-hatchling
                          python-pip
-                         python-pre-commit
                          python-pytest
                          python-pytest-timeout))
     ;; This package provides the `jupyter` binary and thus also exports the
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 47/52] gnu: python-django-ldap: Remove uneeded native-inputs.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-47-ngraves@ngraves.fr

* gnu/packages/django.scm (python-django-ldap)[native-inputs]: Remove
python-pypa-build, python-pip.
---
 gnu/packages/django.scm | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

Toggle diff (18 lines)diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index 6b67b66891..3924a237a2 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -1550,10 +1550,7 @@ (define-public python-django-auth-ldap
                      (invoke "pip" "--no-cache-dir" "--no-input"
                              "install" "--no-deps" "--prefix" #$output whl)))))))
     (native-inputs
-     (list openldap python-wheel python-setuptools-scm python-toml
-
-           ;; These can be removed after <https://bugs.gnu.org/46848>.
-           python-pypa-build python-pip))
+     (list openldap python-wheel python-setuptools-scm python-toml))
     (propagated-inputs
      (list python-django python-ldap))
     (home-page "https://github.com/django-auth-ldap/django-auth-ldap")
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 48/52] gnu: python-docstring-to-markdown: Remove uneeded native-inputs.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-48-ngraves@ngraves.fr

* gnu/packages/python-xyz.scm (python-docstring-to-markdown)
[native-inputs]: Remove python-pytest-cov, python-pytest-flake8.
[arguments]: Remove field.
---
 gnu/packages/python-xyz.scm | 10 ----------
 1 file changed, 10 deletions(-)

Toggle diff (25 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index c0f047aebc..c4c174bbbe 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1836,18 +1836,8 @@ (define-public python-docstring-to-markdown
        (sha256
         (base32 "0gdpabnyl1kyy0cjrnph6xl4fyhgim50a1amsaqq3hahki6i2ip1"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'reduce-test-coverage-since-failing
-            (lambda _
-              (substitute* "setup.cfg"
-                (("(^.*cov.*$|^.*flake8.*$)") "")))))))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
-           python-pytest-flake8
            python-setuptools
            python-wheel))
     (home-page "https://github.com/python-lsp/docstring-to-markdown")
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 35/52] build-system/pyproject: Stop hiding options.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-35-ngraves@ngraves.fr

* gnu/packages/pdf.scm (python-pydyf, weasyprint)[arguments]
<#:test-flags>: Remove arguments hiding coverage options.

* gnu/packages/python-crypto.scm (python-keyring)
[arguments]<#:test-flags>: Remove arguments hiding coverage options.

* gnu/packages/python-web.scm (python-asgi-lifespan,
python-openapi-schema-validator, python-openapi-spec-validator,
python-openapi-core)[arguments]<#:test-flags>: Remove arguments hiding
coverage options.
(python-openapi-schema-validator, python-openapi-spec-validator)
[arguments]<#:phases>: Remove 'remove-coverage-pytest-options phase.
(python-cssselect2)[arguments]: Remove uneeded field.
(python-quart)[arguments]: Remove uneeded field.
(python-jsonpickle)[arguments]<#:test-flags>: Remove uneeded
test-flags.

* gnu/packages/python-xyz.scm (python-cattrs)
[arguments]<#:phases>: Remove arguments hiding coverage options.
(python-blessed)[arguments]: Remove uneeded field.

python-pytest-cov remove option
---
 gnu/packages/pdf.scm           |  6 +----
 gnu/packages/python-crypto.scm |  1 -
 gnu/packages/python-web.scm    | 42 +++-------------------------------
 gnu/packages/python-xyz.scm    |  8 +------
 4 files changed, 5 insertions(+), 52 deletions(-)

Toggle diff (159 lines)diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm
index ce63306c07..7308b0c661 100644
--- a/gnu/packages/pdf.scm
+++ b/gnu/packages/pdf.scm
@@ -805,9 +805,6 @@ (define-public python-pydyf
        (sha256
         (base32 "18q43g5d9455msipcgd5fvnh8m4a2rz189slzfg80yycjw66rshs"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:test-flags #~'("-c" "/dev/null")))
     (propagated-inputs (list python-pillow))
     (native-inputs
      (list ghostscript
@@ -1669,8 +1666,7 @@ (define-public weasyprint
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags #~(list "-c" "/dev/null"
-                           "-n" (number->string (parallel-job-count)))
+      #:test-flags #~(list "-n" (number->string (parallel-job-count)))
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-library-paths
diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm
index 674092b1cc..eb6fdd5227 100644
--- a/gnu/packages/python-crypto.scm
+++ b/gnu/packages/python-crypto.scm
@@ -268,7 +268,6 @@ (define-public python-keyring
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags '(list "-c" "/dev/null") ;avoid extra test dependencies
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'check 'workaround-test-failure
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 4e68aa47ea..97b9263499 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1267,8 +1267,7 @@ (define-public python-asgi-lifespan
     (arguments
      (list
       #:test-flags
-      '(list "-c" "/dev/null"           ;ignore coverage-related options
-             "-k"
+      '(list "-k"
              (string-append
               ;; XXX: Some tests fail because of "Exceptions from Trio nursery"
               "not (test_lifespan_manager[trio-None-None-StartupFailed]"
@@ -2269,10 +2268,7 @@ (define-public python-jsonpickle
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags
-      ;; Prevent running the flake8 and black pytest plugins, which only tests
-      ;; style and frequently causes harmless failures.
-      '(list "-o" "addopts=''" "tests")
+      #:test-flags '(list "tests")
       #:phases
       '(modify-phases %standard-phases
          (add-before 'check 'pre-check
@@ -3024,10 +3020,6 @@ (define-public python-openapi-schema-validator
       '(list "-k" "not test_array_prefixitems_invalid")
       #:phases
       #~(modify-phases %standard-phases
-          (add-after 'unpack 'remove-coverage-pytest-options
-            (lambda _
-              (substitute* "pyproject.toml"
-                (("^--cov.*") ""))))
           ;; See https://github.com/python-openapi/openapi-schema-validator/issues/204
           (add-after 'unpack 'relax-requirements
             (lambda _
@@ -3071,13 +3063,7 @@ (define-public python-openapi-spec-validator
      (list
       ;; These tests attempt to fetch resources from the Internet
       #:test-flags '(list "--ignore-glob=tests/integration/validation/**"
-                          "-k" "not example")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'remove-coverage-pytest-options
-            (lambda _
-              (substitute* "pyproject.toml"
-                (("^--cov.*") "")))))))
+                          "-k" "not example")))
     (native-inputs
      (list python-poetry-core
            python-pytest))
@@ -3116,9 +3102,6 @@ (define-public python-openapi-core
      (list
       #:test-flags
       '(list "tests/unit"
-             ;; Ignore Pytest configuration in setup.cfg that adds
-             ;; unwanted flake8 and coverage options.
-             "-c" "/dev/null"
              "-k" "not test_chars_valid")))
     (native-inputs (list python-django
                          python-falcon
@@ -7114,17 +7097,6 @@ (define-public python-cssselect2
        (sha256
         (base32 "1j2fcr217rsvkipsg6zjq03rl64rxnvb5hqqpx0dv58fhspvkywk"))))
     (build-system pyproject-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'disable-linters
-           ;; Their check fails; none of our business.
-           (lambda _
-             (substitute* '("setup.py" "pyproject.toml")
-               (("'pytest-flake8',") "")
-               (("'pytest-isort',") "")
-               (("--flake8") "")
-               (("--isort") "")))))))
     (propagated-inputs
      (list python-tinycss2))
     (native-inputs
@@ -9758,14 +9730,6 @@ (define-public python-quart
        (sha256
         (base32 "1h5ifv8g9dc9m07vj4v7dfalam83v38545d845vvgys1gan1pscd"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'remove-coverage-pytest-options
-            (lambda _
-              (substitute* "pyproject.toml"
-                (("--no-cov-on-fail") "")))))))
     (native-inputs
      (list python-poetry-core
            python-pytest
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index b42c954233..b2cad47edf 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -22866,9 +22866,7 @@ (define-public python-cattrs
               (substitute* "pyproject.toml"
                 ;; Fix version string
                 (("dynamic = \\[\"version\"\\]")
-                 (string-append "version = \"" #$version "\""))
-                ;; Just run pytest with no frills
-                (("addopts = \"-l.*") ""))))
+                 (string-append "version = \"" #$version "\"")))))
           ;; XXX Our python-hypothesis package is too old.
           (add-after 'unpack 'compatibility
             (lambda _
@@ -33914,10 +33912,6 @@ (define-public python-blessed
          ;; Don't get hung up on Windows test failures.
          '(delete-file "blessed/win_terminal.py"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list
-      ;; Avoid python-pytest-coverage
-      #:test-flags '(list "-c /dev/null")))
     (propagated-inputs (list python-six python-wcwidth))
     (native-inputs (list python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/jquast/blessed")
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 49/52] gnu: python-translation-finder: Remove python coverage native-inputs.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-49-ngraves@ngraves.fr

* gnu/packages/python-web.scm (python-translation-finder)
[native-inputs]: Remove python-codecov, python-codacy-coverage,
python-pytest-cov.
---
 gnu/packages/python-web.scm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

Toggle diff (16 lines)diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 230de4f5a3..2d45ac04ba 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -7415,8 +7415,7 @@ (define-public python-translation-finder
     (propagated-inputs
      (list python-chardet python-pathlib2 python-ruamel.yaml python-six))
     (native-inputs
-     (list python-codecov python-codacy-coverage python-pytest-cov
-           python-pytest-runner))
+     (list python-codacy-coverage python-pytest-runner))
     (home-page "https://weblate.org/")
     (synopsis "Translation file finder for Weblate")
     (description "This package provides a function to find translation file in
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 50/52] gnu: python-pymanopt: Remove python-flake8-bugbear native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-50-ngraves@ngraves.fr

* gnu/packages/machine-learning.scm (python-pymanopt)[native-input]:
Remove python-flake8-bugbear.
---
 gnu/packages/machine-learning.scm | 1 -
 1 file changed, 1 deletion(-)

Toggle diff (14 lines)diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 8cbd16a3c7..6a034ea23c 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1140,7 +1140,6 @@ (define-public python-pymanopt
                ((",!=1.12\\.\\*") "")))))))
     (propagated-inputs (list python-numpy python-scipy))
     (native-inputs (list python-autograd
-                         python-flake8-bugbear
                          python-matplotlib
                          python-pytest
                          python-setuptools
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 52/52] gnu: gunicorn: Migrate 'check phase to pyproject-build-system.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-52-ngraves@ngraves.fr

* gnu/packages/python-web.scm (gunicorn)[arguments]
{phases}: Remove 'check phase and migrate its flags to...
{test-flags}: ...here.
---
 gnu/packages/python-web.scm | 16 +++++-----------
 1 file changed, 5 insertions(+), 11 deletions(-)

Toggle diff (35 lines)diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 2d45ac04ba..9495210d04 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -7200,23 +7200,17 @@ (define-public gunicorn
     (outputs '("out" "doc"))
     (build-system pyproject-build-system)
     (arguments
-     `(#:phases
+     `(#:test-flags
+       ;; Disable the geventlet tests because eventlet uses dnspython, which
+       ;; does not work in the build container due to lack of /etc/resolv.conf
+       '("--ignore=tests/workers/test_geventlet.py")
+       #:phases
        (modify-phases %standard-phases
          (add-after 'build 'build-doc
            (lambda _
              (invoke "make" "-C" "docs" "PAPER=a4" "html" "info")
              (delete-file "docs/build/texinfo/Makefile")
              (delete-file "docs/build/texinfo/Gunicorn.texi")))
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (if tests?
-                 (begin
-                   (invoke "pytest" "-vv"
-                           ;; Disable the geventlet tests because eventlet uses
-                           ;; dnspython, which does not work in the build
-                           ;; container due to lack of /etc/resolv.conf, etc.
-                           "--ignore=tests/workers/test_geventlet.py"))
-                 (format #t "test suite not run~%"))))
          (add-after 'install 'install-doc
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((doc (string-append (assoc-ref outputs "doc")
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 51/52] gnu: python-loguru: Remove python-pytest-mypy-plugins.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-51-ngraves@ngraves.fr

* gnu/packages/python-xyz.scm (python-loguru)
[arguments]: Add in {test-flags} to skip the concerned test file.
[native-inputs]: Remove python-pytest-mypy-plugins.
---
 gnu/packages/python-xyz.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

Toggle diff (21 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index c4c174bbbe..c8ccb422d2 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -35035,11 +35035,12 @@ (define-public python-loguru
       #~(list"--numprocesses" (number->string (parallel-job-count))
              ;; All of these fail with: error: Cannot find implementation or
              ;; library stub for module named "loguru"
-             "--ignore=tests/typesafety/test_logger.yml")))
+             "--ignore=tests/typesafety/test_logger.yml"
+             ;; Removes mypy dependency
+             "--ignore=tests/test_type_hinting.py")))
     (native-inputs
      (list python-freezegun
            python-pytest
-           python-pytest-mypy-plugins
            python-pytest-xdist
            python-setuptools
            python-wheel))
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 36/52] gnu: python-linear-operator: Remove python-flake8-print native-input

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-36-ngraves@ngraves.fr

* gnu/packages/machine-learning.scm (python-linear-operator):

[native-inputs]: Remove pytest-flake8-print.

Change-Id: Iba2670b47e479c20a3f4ae1c703ad9fe815e3764

---

gnu/packages/machine-learning.scm | 3 +--

1 file changed, 1 insertion(+), 2 deletions(-)

Toggle diff (16 lines)diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index b27d4f4f23..8cbd16a3c7 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -5877,8 +5877,7 @@ (define-public python-linear-operator
                              python-pytorch
                              python-scipy
                              python-typeguard))
-    (native-inputs (list python-flake8-print
-                         python-pytest
+    (native-inputs (list python-pytest
                          python-setuptools
                          python-setuptools-scm))
     (home-page "https://github.com/cornellius-gp/linear_operator/")
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 37/52] gnu: multidict: Remove python-pytest-cov native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-37-ngraves@ngraves.fr

* gnu/packages/python-xyz.scm (multidict)
[native-inputs]: Remove python-pytest-cov.
[arguments]{phases}: Add 'avoid-pytest-cov-preload phase.
---
 gnu/packages/python-xyz.scm | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

Toggle diff (23 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index b2cad47edf..881d07045e 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -10943,9 +10943,15 @@ (define-public python-multidict
         (base32
          "0jlgjpclkh5g6vr1danl6alz0cza2jlzdqh3q03d4s8ckfzjxbi2"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list #:phases #~(modify-phases %standard-phases
+                        (add-after 'unpack 'avoid-pytest-cov-preload
+                          (lambda _
+                            (substitute* "pytest.ini"
+                              (("-p pytest_cov") "")))))))
     (propagated-inputs (list python-typing-extensions))
     (native-inputs
-     (list python-pytest python-pytest-cov python-setuptools python-wheel))
+     (list python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/aio-libs/multidict/")
     (synopsis "Multidict implementation")
     (description "Multidict is dict-like collection of key-value pairs
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 38/52] gnu: python-isort: Remove python-black native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-38-ngraves@ngraves.fr

* gnu/packages/python-xyz.scm (python-isort)
[native-inputs]: Remove python-black.
[arguments]: Adapt {test-flags} accordingly.
---
 gnu/packages/python-xyz.scm | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

Toggle diff (39 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 881d07045e..4dd1f92e05 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -25908,15 +25908,15 @@ (define-public python-isort
      (list
       #:test-flags
       #~(list "tests/unit/"
-              "-k" (string-join
-                    (list
-                     "not test_gitignore"
-                     ;; See <https://github.com/PyCQA/isort/issues/2234>.
-                     "test_isort_should_warn_on_empty_custom_config_issue_1433"
-                     ;; Fails because of an unexpected linebreak.
-                     "test_black_pyi_file")
-                    " and not ")
-              "--ignore=tests/unit/test_deprecated_finders.py")
+              "-k"
+              (string-join
+               (list
+                "not test_gitignore"
+                ;; See <https://github.com/PyCQA/isort/issues/2234>.
+                "test_isort_should_warn_on_empty_custom_config_issue_1433")
+               " and not ")
+              "--ignore=tests/unit/test_deprecated_finders.py"
+              "--ignore=tests/unit/profiles/test_black.py")
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'install 'install-example-plugins
@@ -25935,7 +25935,6 @@ (define-public python-isort
                        "install"  "--user" "--no-deps" example-whls)))))))
     (native-inputs
      (list python-colorama
-           python-black
            python-hypothesmith
            python-libcst-minimal
            python-natsort
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 42/52] build-system/pyproject: Remove python-check-manifest native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-42-ngraves@ngraves.fr

* guix/import/pypi.scm (pypi-ignored-inputs): Add "check-manifest".

* gnu/packages/jupyter.scm (python-papermill)
* gnu/packages/python-xyz.scm (python-pillow, python-mercantile)
* gnu/packages/time.scm (python-tzlocal)
[native-inputs]: Remove python-check-manifest.
---
 gnu/packages/jupyter.scm    | 1 -
 gnu/packages/python-xyz.scm | 6 ++----
 gnu/packages/time.scm       | 3 +--
 guix/import/pypi.scm        | 2 +-
 4 files changed, 4 insertions(+), 8 deletions(-)

Toggle diff (65 lines)diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm
index 8ce856f128..62f028077f 100644
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -1151,7 +1151,6 @@ (define-public python-papermill
                          python-boto3
                          python-botocore
                          python-bumpversion
-                         python-check-manifest
                          python-ipython
                          python-ipywidgets
                          python-moto
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index a938a05bde..155a69fc10 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -11338,9 +11338,7 @@ (define-public python-pillow
                (add-installed-pythonpath inputs outputs)
                (invoke "python" "selftest.py" "--installed")
                (invoke "python" "-m" "pytest" "-vv")))))))
-    (native-inputs (list python-check-manifest
-                         python-coverage
-                         python-defusedxml
+    (native-inputs (list python-defusedxml
                          python-markdown2
                          python-olefile
                          python-packaging
@@ -31436,7 +31434,7 @@ (define-public python-mercantile
     (build-system python-build-system)
     (propagated-inputs (list python-click))
     (native-inputs
-     (list python-check-manifest python-hypothesis python-pytest))
+     (list python-hypothesis python-pytest))
     (home-page "https://github.com/mapbox/mercantile")
     (synopsis "Web mercator XYZ tile utilities")
     (description "The mercantile module provides @code{ul(xtile, ytile, zoom)}
diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm
index 5f07e0860a..310b1ce5cb 100644
--- a/gnu/packages/time.scm
+++ b/gnu/packages/time.scm
@@ -454,8 +454,7 @@ (define-public python-tzlocal
     (propagated-inputs
      (list python-tzdata))
     (native-inputs
-     (list python-check-manifest
-           python-pytest
+     (list python-pytest
            python-pytest-mock))
     (home-page "https://github.com/regebro/tzlocal")
     (synopsis "Local timezone information for Python")
diff --git a/guix/import/pypi.scm b/guix/import/pypi.scm
index a49ab1e429..2e3ea6403d 100644
--- a/guix/import/pypi.scm
+++ b/guix/import/pypi.scm
@@ -87,7 +87,7 @@ (define pypi-ignored-inputs
         "tox" ; test wrapper for other environments
         "codecov" "coverage"  ; coverage
         "black" "isort" "pycodestyle" "pep8"  ; style
-        "pyflakes" "flake8" "pylint" "mypy"  ; style+lint
+        "check-manifest" "pyflakes" "flake8" "pylint" "mypy"  ; style+lint
         "coveralls" "twine"  ; upload integration tools
         "pytest-isort" "pytest-flake8" "pytest-cov" "pytest-black"
         "pytest-pep8" "pytest-mypy" "pytest-pep8" "pre-commit"))  ; variants
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 44/52] gnu: python-matrix-nio: Remove python-mypy-extension native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-44-ngraves@ngraves.fr

* gnu/packages/matrix.scm (python-matrix-nio)[native-inputs]: Remove
python-mypy-extension.
---
 gnu/packages/matrix.scm | 1 -
 1 file changed, 1 deletion(-)

Toggle diff (14 lines)diff --git a/gnu/packages/matrix.scm b/gnu/packages/matrix.scm
index e503d17b91..1a090c05a7 100644
--- a/gnu/packages/matrix.scm
+++ b/gnu/packages/matrix.scm
@@ -193,7 +193,6 @@ (define-public python-matrix-nio
            python-hpack
            python-hyperframe
            python-hypothesis
-           python-mypy-extensions
            python-poetry-core
            python-pytest
            python-pytest-aiohttp
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v4 41/52] gnu: python-pixell: Update to 0.28.1.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250226031112.15843-41-ngraves@ngraves.fr

See https://github.com/simonsobs/pixell/issues/291for the reasons
behind the patch.

* gnu/packages/astronomy.scm (python-pixell): Update to 0.28.1.
[source]: Switch to git-fetch. Add patch.
[propagated-inputs]: Remove python-cython, python-coveralls.
* gnu/packages/patches/python-pixell-avoid-dependency-propagation.patch
New file.
* gnu/local.mk: Add patch.
---
 gnu/local.mk                                    |  1 +
 gnu/packages/astronomy.scm                      | 15 +++++++++------
 ...on-pixell-avoid-dependency-propagation.patch | 17 +++++++++++++++++
 3 files changed, 27 insertions(+), 6 deletions(-)
 create mode 100644 gnu/packages/patches/python-pixell-avoid-dependency-propagation.patch

Toggle diff (73 lines)diff --git a/gnu/local.mk b/gnu/local.mk
index fba21df72e..78792312d2 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -2003,6 +2003,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-matplotlib-fix-legend-loc-best-test.patch	\
   %D%/packages/patches/python-random2-getrandbits-test.patch		\
   %D%/packages/patches/python-pillow-use-zlib-1.3.patch	\
+  %D%/packages/patches/python-pixell-avoid-dependency-propagation.patch	\
   %D%/packages/patches/python-pydocstyle-add-support-for-pep701.patch	\
   %D%/packages/patches/python-pyreadstat-link-libiconv.patch	\
   %D%/packages/patches/python-sip-include-dirs.patch	\
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 2cea636e1b..4804e74a81 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3045,13 +3045,18 @@ (define-public python-mapsims
 (define-public python-pixell
   (package
     (name "python-pixell")
-    (version "0.28.0")
+    (version "0.28.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "pixell" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/simonsobs/pixell")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "11xd0ld329vr3spg5nzszn0bxzahnvkrh2akkd7qff33ndf75hkk"))))
+        (base32 "0p3pndy04n0hd352gjgwpqafp9sm1iq6c45pj745z1cswaf2lmc8"))
+       (patches (search-patches
+                 "python-pixell-avoid-dependency-propagation.patch"))))
     (build-system pyproject-build-system)
     (native-inputs
      (list gfortran
@@ -3062,8 +3067,6 @@ (define-public python-pixell
            python-pytest))
     (propagated-inputs
      (list python-astropy
-           python-coveralls
-           python-cython ; check why it needs in installation
            python-dateutil
            python-ducc0
            python-h5py
diff --git a/gnu/packages/patches/python-pixell-avoid-dependency-propagation.patch b/gnu/packages/patches/python-pixell-avoid-dependency-propagation.patch
new file mode 100644
index 0000000000..52c27bad6f
--- /dev/null
+++ b/gnu/packages/patches/python-pixell-avoid-dependency-propagation.patch
@@ -0,0 +1,17 @@
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -22,14 +22,10 @@
+     'h5py>=2.7',
+     'scipy>=1.0',
+     'python_dateutil>=2.7',
+-    'cython',
+     'healpy>=1.13',
+     'matplotlib>=2.0',
+     'pyyaml>=5.0',
+     'Pillow>=5.3.0, != 10.4.0',
+-    'pytest-cov>=2.6',
+-    'coveralls>=1.5',
+-    'pytest>=4.6',
+     'ducc0>=0.36.0',
+     'numba>=0.54.0'
+ ]
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 01/48] gnu: Remove python-pytest-pep8.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-2-ngraves@ngraves.fr

This package is outdated.

* gnu/packages/check.scm (python-pytest-pep8): Delete variable.
(python-pytest-flakes)[native-inputs]: Remove python-pytest-pep8.
* gnu/packages/machine-learning.scm (python-keras,
python-keras-applications)[native-inputs]: Remove python-pytest-pep8.
---
 gnu/packages/check.scm            | 33 -------------------------------
 gnu/packages/machine-learning.scm |  3 +--
 2 files changed, 1 insertion(+), 35 deletions(-)

Toggle diff (67 lines)diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index f131a0be01..baa3a2f4c3 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -3090,39 +3090,6 @@ (define-public python-pytest-mypy-testing
 expression this allows you to check mypys type interference.")
     (license (list license:expat license:asl2.0))))
 
-(define-public python-pytest-pep8
-  (package
-    (name "python-pytest-pep8")
-    (version "1.0.6")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "pytest-pep8" version))
-              (sha256
-               (base32
-                "06032agzhw1i9d9qlhfblnl3dw5hcyxhagn7b120zhrszbjzfbh3"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:tests? #f ; Fails with recent pytest and pep8. See upstream issues #8 and #12.
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-dependencies
-           (lambda _
-             (substitute* "setup.py"
-               (("'pytest-cache', ") ""))))  ; Included in recent pytest
-         (replace 'check
-            (lambda* (#:key tests? inputs outputs #:allow-other-keys)
-              (when tests?
-                (add-installed-pythonpath inputs outputs)
-                (invoke "pytest" "-v")))))))
-    (native-inputs
-     (list python-pytest))
-    (propagated-inputs
-     (list python-pep8))
-    (home-page "https://bitbucket.org/pytest-dev/pytest-pep8")
-    (synopsis "Py.test plugin to check PEP8 requirements")
-    (description "Pytest plugin for checking PEP8 compliance.")
-    (license license:expat)))
-
 (define-public python-pytest-perf
   (package
     (name "python-pytest-perf")
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 1a007520a4..c051974244 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -3903,7 +3903,7 @@ (define-public python-keras-applications
     (propagated-inputs
      (list python-h5py python-numpy))
     (native-inputs
-     (list python-pytest python-pytest-cov python-pytest-pep8
+     (list python-pytest python-pytest-cov
            python-pytest-xdist))
     (home-page "https://github.com/keras-team/keras-applications")
     (synopsis "Reference implementations of popular deep learning models")
@@ -4073,7 +4073,6 @@ (define-public python-keras
            python-pandas
            python-pytest
            python-pytest-cov
-           python-pytest-pep8
            python-pytest-timeout
            python-pytest-xdist
            python-pyux
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 python-team 00/48] Removing unwanted native-inputs.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-1-ngraves@ngraves.fr

/!\ I rebased the patch series on the current origin/master
(fc4795d7d2), so that we can merge it before the patch series itself /!\

Hopefully the last revision of this patch series :)

Nicolas Graves (48):
  gnu: Remove python-pytest-pep8.
  gnu: Remove python-pep8.
  guix: import: pypi: Ignore pypi-ignored-inputs.
  build-system/pyproject: Ignore unwanted pytest flags.
  build-system/pyproject: Remove python-black inputs.
  build-system/pyproject: Remove python-pylint native-input.
  build-system/pyproject: Remove python-flake8 inputs.
  build-system/pyproject: Remove python-coverage input.
  build-system/pyproject: Remove python-coverage native-input.
  build-system/pyproject: Remove python-pytest-black native-input.
  gnu: python-cram: Remove python-coverage native-input.
  gnu: u-boot-tools: Remove python-coverage native-input.
  gnu: python-aiosqlite: Remove python-coverage native-input.
  gnu: python-openid: Remove python-coverage native-input.
  build-system/pyproject: Remove python-coveralls native-input.
  build-system/pyproject: Remove python-pycodestyle native-input.
  gnu: python-re-assert: Remove python-covdefaults native-input.
  build-system/pyproject: Remove python-covdefaults native-input.
  build-system/pyproject: Remove python-codecov native-input.
  build-system/pyproject: Remove python-tox native-input.
  build-system/pyproject: Remove python-mypy native-input.
  gnu: python-immutables: Remove python-mypy native-input.
  build-system/pyproject: Remove python-isort native-input.
  build-system/pyproject: Remove python-twine native-input.
  build-system/pyproject: Remove python-pytest-cov native-input.
  gnu: python-django-contact-form: Remove python-pytest-cov
    native-input.
  gnu: python-dateutil: Remove python-pytest-cov native-input.
  build-system/pyproject: Remove python-pytest-isort native-input.
  build-system/pyproject: Remove python-pytest-flake8 native-input.
  build-system/pyproject: Remove python-pytest-mypy inputs.
  build-system/pyproject: Stop hiding options.
  gnu: python-linear-operator: Remove python-flake8-print native-input
  gnu: multidict: Remove python-pytest-cov native-input.
  gnu: python-isort: Remove python-black native-input.
  build-system/pyproject: Remove python-mypy native-input.
  build-system/pyproject: Add option #:use-pytest-plugin?
  gnu: python-pixell: Update to 0.28.1.
  build-system/pyproject: Remove python-check-manifest native-input.
  build-system/pyproject: Remove python-mypy-extensions native-input.
  gnu: python-matrix-nio: Remove python-mypy-extension native-input.
  build-system/pyproject: Remove python-pip native-input.
  build-system/pyproject: Remove python-pre-commit native-input.
  gnu: python-django-ldap: Remove uneeded native-inputs.
  gnu: python-docstring-to-markdown: Remove uneeded native-inputs.
  gnu: python-translation-finder: Remove python coverage native-inputs.
  gnu: python-pymanopt: Remove python-flake8-bugbear native-input.
  gnu: python-loguru: Remove python-pytest-mypy-plugins.
  gnu: gunicorn: Migrate 'check phase to pyproject-build-system.

 gnu/local.mk                                  |   1 +
 gnu/packages/android.scm                      |   6 +-
 gnu/packages/astronomy.scm                    |  41 +-
 gnu/packages/audio.scm                        |   5 +-
 gnu/packages/backup.scm                       |   1 -
 gnu/packages/bioinformatics.scm               |  59 +-
 gnu/packages/bootloaders.scm                  |  17 +-
 gnu/packages/build-tools.scm                  |   1 -
 gnu/packages/check.scm                        |  57 +-
 gnu/packages/cpp.scm                          |   4 +-
 gnu/packages/databases.scm                    |  13 +-
 gnu/packages/dav.scm                          |   4 -
 gnu/packages/debug.scm                        |   2 +-
 gnu/packages/django.scm                       |  23 +-
 gnu/packages/ebook.scm                        |   1 -
 gnu/packages/embedded.scm                     |   1 -
 gnu/packages/engineering.scm                  |   7 +-
 gnu/packages/fediverse.scm                    |   1 -
 gnu/packages/finance.scm                      |   9 +-
 gnu/packages/fontutils.scm                    |   1 -
 gnu/packages/games.scm                        |   1 -
 gnu/packages/geo.scm                          |   7 +-
 gnu/packages/gettext.scm                      |   4 -
 gnu/packages/gpodder.scm                      |   4 +-
 gnu/packages/graph.scm                        |   6 +-
 gnu/packages/graphviz.scm                     |   5 -
 gnu/packages/jupyter.scm                      |  24 +-
 gnu/packages/logging.scm                      |   2 +-
 gnu/packages/machine-learning.scm             |  70 +--
 gnu/packages/mail.scm                         |   2 -
 gnu/packages/maths.scm                        |   1 -
 gnu/packages/matrix.scm                       |   4 -
 gnu/packages/messaging.scm                    |   6 +-
 gnu/packages/mp3.scm                          |   3 +-
 gnu/packages/music.scm                        |   9 +-
 gnu/packages/networking.scm                   |   2 +-
 gnu/packages/openstack.scm                    |   7 +-
 gnu/packages/package-management.scm           |   8 +-
 ...-pixell-avoid-dependency-propagation.patch |  17 +
 gnu/packages/patchutils.scm                   |   2 +-
 gnu/packages/pdf.scm                          |   6 +-
 gnu/packages/potassco.scm                     |   3 +-
 gnu/packages/protobuf.scm                     |   4 +-
 gnu/packages/python-check.scm                 |  40 +-
 gnu/packages/python-compression.scm           |  25 +-
 gnu/packages/python-crypto.scm                |   6 +-
 gnu/packages/python-science.scm               |  39 +-
 gnu/packages/python-web.scm                   | 220 ++------
 gnu/packages/python-xyz.scm                   | 517 ++++++------------
 gnu/packages/radio.scm                        |   4 +-
 gnu/packages/rdf.scm                          |   4 +-
 gnu/packages/serialization.scm                |   1 -
 gnu/packages/shells.scm                       |   1 -
 gnu/packages/simulation.scm                   |   3 -
 gnu/packages/sphinx.scm                       |   2 -
 gnu/packages/statistics.scm                   |  18 +-
 gnu/packages/syndication.scm                  |   8 +-
 gnu/packages/task-management.scm              |   1 -
 gnu/packages/telegram.scm                     |   4 +-
 gnu/packages/terminals.scm                    |  16 +-
 gnu/packages/textutils.scm                    |   4 -
 gnu/packages/time.scm                         |  23 +-
 gnu/packages/version-control.scm              |   2 -
 gnu/packages/virtualization.scm               |   7 +-
 gnu/packages/vpn.scm                          |   2 -
 gnu/packages/web.scm                          |   8 +-
 gnu/packages/wm.scm                           |   2 -
 gnu/packages/xml.scm                          |   2 +-
 guix/build-system/pyproject.scm               |   2 +
 guix/build/pyproject-build-system.scm         | 102 +++-
 guix/import/pypi.scm                          |  21 +-
 guix/lint.scm                                 |  10 +-
 tests/pypi.scm                                |   3 +-
 73 files changed, 524 insertions(+), 1024 deletions(-)
 create mode 100644 gnu/packages/patches/python-pixell-avoid-dependency-propagation.patch

-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 03/48] guix: import: pypi: Ignore pypi-ignored-inputs.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-4-ngraves@ngraves.fr

* guix/import/pypi.scm (pypi-ignored-inputs): New variable.

(compute-inputs): Use it.

* tests/pypi.scm (parse-requires.txt): Add ignored input to test the

feature.

* guix/lint.scm (check-inputs-should-be-native): Adapt list.

(check-inputs-should-not-be-an-input-at-all): Use pypi-ignored-list.

Change-Id: I774e526c5a090026e778ee44049637174a1dca95

---

guix/import/pypi.scm | 21 ++++++++++++++++++---

guix/lint.scm | 10 ++++++----

tests/pypi.scm | 3 ++-

3 files changed, 26 insertions(+), 8 deletions(-)

Toggle diff (117 lines)diff --git a/guix/import/pypi.scm b/guix/import/pypi.scm
index 4af02dd250..a49ab1e429 100644
--- a/guix/import/pypi.scm
+++ b/guix/import/pypi.scm
@@ -14,6 +14,7 @@
 ;;; Copyright © 2022 Vivien Kraus <vivien@planete-kraus.eu>
 ;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2022 Hartmut Goebel <h.goebel@crazy-compilers.com>
+;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -62,6 +63,7 @@ (define-module (guix import pypi)
   #:use-module (guix upstream)
   #:use-module ((guix licenses) #:prefix license:)
   #:export (%pypi-base-url
+            pypi-ignored-inputs
             parse-requires.txt
             parse-wheel-metadata
             specification->requirement-name
@@ -78,6 +80,18 @@ (define %pypi-base-url
   ;; Base URL of the PyPI API.
   (make-parameter "https://pypi.org/pypi/"))
 
+(define pypi-ignored-inputs
+  ;; This list contains packages that are useful for development or quality
+  ;; testing, but that most of the time are not necessary to have as an input.
+  (list "argparse"  ; native
+        "tox" ; test wrapper for other environments
+        "codecov" "coverage"  ; coverage
+        "black" "isort" "pycodestyle" "pep8"  ; style
+        "pyflakes" "flake8" "pylint" "mypy"  ; style+lint
+        "coveralls" "twine"  ; upload integration tools
+        "pytest-isort" "pytest-flake8" "pytest-cov" "pytest-black"
+        "pytest-pep8" "pytest-mypy" "pytest-pep8" "pre-commit"))  ; variants
+
 (define non-empty-string-or-false
   (match-lambda
     ("" #f)
@@ -464,9 +478,10 @@ (define (compute-inputs source-url wheel-url archive)
   "Given the SOURCE-URL and WHEEL-URL of an already downloaded ARCHIVE, return
 the corresponding list of <upstream-input> records."
   (define (requirements->upstream-inputs deps type)
-    (filter-map (match-lambda
-                  ("argparse" #f)
-                  (name (upstream-input
+    (filter-map (lambda (name)
+                  (if (member name pypi-ignored-inputs)
+                      #f
+                      (upstream-input
                          (name name)
                          (downstream-name (python->package-name name))
                          (type type))))
diff --git a/guix/lint.scm b/guix/lint.scm
index d54db725b5..caa4f63f88 100644
--- a/guix/lint.scm
+++ b/guix/lint.scm
@@ -73,6 +73,7 @@ (define-module (guix lint)
                                     hg-reference-url)
   #:autoload   (guix bzr-download) (bzr-reference?
                                     bzr-reference-url)
+  #:use-module ((guix import pypi) #:select (pypi-ignored-inputs))
   #:use-module (guix import stackage)
   #:use-module (ice-9 match)
   #:use-module (ice-9 regex)
@@ -588,14 +589,12 @@ (define (check-inputs-should-be-native package)
             "m4"
             "qttools-5"
             "yasm" "nasm" "fasm"
-            "python-coverage"
             "python-cython"
             "python-docutils"
             "python-mock"
             "python-nose"
             "python-pbr"
             "python-pytest"
-            "python-pytest-cov"
             "python-setuptools-scm"
             "python-sphinx"
             "scdoc"
@@ -617,8 +616,11 @@ (define (check-inputs-should-be-native package)
 (define (check-inputs-should-not-be-an-input-at-all package)
   ;; Emit a warning if some inputs of PACKAGE are likely to should not be
   ;; an input at all.
-  (let ((input-names '("python-pip"
-                       "python-pre-commit")))
+  (let ((input-names (append
+                      '("python-pip"
+                       "python-pre-commit")
+                      (map (cut string-append "python-" <>)
+                           pypi-ignored-inputs))))
     (map (lambda (input)
            (make-warning
             package
diff --git a/tests/pypi.scm b/tests/pypi.scm
index 3fbce1786f..f848325ad7 100644
--- a/tests/pypi.scm
+++ b/tests/pypi.scm
@@ -97,6 +97,7 @@ (define test-requires.txt "\
 
 [test]
 pytest (>=2.5.0)
+pytest-cov  # read but ignored
 ")
 
 ;; Beaker contains only optional dependencies.
@@ -258,7 +259,7 @@ (define-syntax-rule (with-pypi responses body ...)
   (map specification->requirement-name test-specifications))
 
 (test-equal "parse-requires.txt"
-  (list '("foo" "bar") '("pytest"))
+  (list '("foo" "bar") '("pytest" "pytest-cov"))
   (mock ((ice-9 ports) call-with-input-file
          call-with-input-string)
         (parse-requires.txt test-requires.txt)))
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 04/48] build-system/pyproject: Ignore unwanted pytest flags.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-5-ngraves@ngraves.fr

* guix/build/pyproject-build-system.scm : Ignore unwanted pytest flags.

Change-Id: Ib9f1602e5af11227e5b7ce124f0f9be4fa2b78e4

---

guix/build/pyproject-build-system.scm | 99 ++++++++++++++++++++++++++-

1 file changed, 96 insertions(+), 3 deletions(-)

Toggle diff (137 lines)diff --git a/guix/build/pyproject-build-system.scm b/guix/build/pyproject-build-system.scm
index 947d240114..2df9f2f479 100644
--- a/guix/build/pyproject-build-system.scm
+++ b/guix/build/pyproject-build-system.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2021 Lars-Dominik Braun <lars@6xq.net>
 ;;; Copyright © 2022 Marius Bakke <marius@gnu.org>
+;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -35,7 +36,8 @@ (define-module (guix build pyproject-build-system)
             add-installed-pythonpath
             site-packages
             python-version
-            pyproject-build))
+            pyproject-build
+            with-guix-pytest-plugin))
 
 ;;; Commentary:
 ;;;
@@ -142,7 +144,94 @@ (define* (build #:key outputs build-backend backend-path configure-flags #:allow
      wheel-dir
      config-settings)))
 
-(define* (check #:key tests? test-backend test-flags #:allow-other-keys)
+(define pytest-default-ignore-alist
+  '(("cov" . ("--cov" "--cov-reset" "--cov-report" "--cov-config"
+              "--no-cov-on-fail" "--no-cov" "--cov-fail-under"
+              "--cov-append" "--cov-branch" "--cov-context"))
+    ("mypy" . ("--mypy" "--mypy-config-file" "--mypy-ignore-missing-imports"))
+    ("isort" . ("--isort"))
+    ("flake8" . ("--flake8"))
+    ("black" . ("--black"))
+    ("flakes" . ("--flakes"))
+    ("pep8" . ("--pep8"))))
+
+(define (pytest-ignore-flags-plugin flags)
+  "This function converts an list of flags into a string that can
+  be instantiated as a python pytest plugin."
+  (format #f "\
+import pytest
+
+def pytest_addoption(parser):
+    group = parser.getgroup('guix','Guix ignored options')
+    options = [~{~s, ~}]
+    for option in options:
+        group.addoption(option, action='append', nargs='?')"
+          flags))
+
+(define (call-with-guix-pytest-plugin inputs thunk)
+  "This function emulates command line options provided by pytest plugins in
+the absence of the plugins defining these options.
+
+This is done by selecting absent plugins, gettings their flags defined in
+PYTEST-DEFAULT-IGNORE-ALIST, and generating the plugin from there with
+PYTEST-IGNORE-FLAGS-PLUGIN."
+  (let* ((former-path (getenv "PYTHONPATH"))
+         (input-names
+          (map car
+               (filter (match-lambda
+                         ((name . _)
+                          (if (string-prefix? "python-pytest-" name)
+                              name
+                              #f))
+                         ( _ #f))
+                       inputs)))
+         (filtered-flags
+          (filter identity
+                  (append-map
+                   (match-lambda
+                     ((group . flags)
+                      (if (member (string-append "python-pytest-" group)
+                                  input-names)
+                          (list #f)
+                          flags))
+                     (_ (list #f)))
+                   pytest-default-ignore-alist)))
+         (dir (string-append
+               (if (access? (dirname (getcwd)) W_OK)
+                   (dirname (getcwd))
+                   ;; fallback if we're already out-of-source
+                   (getcwd))
+               "/.guix-pytest")))
+    (dynamic-wind
+      (lambda ()
+        (setenv "PYTHONPATH"
+                (string-append
+                 (if former-path
+                     (string-append former-path ":")
+                     "")
+                 dir))
+        (setenv "PYTEST_PLUGINS"
+                (string-append
+                 (if (getenv "PYTEST_PLUGINS")
+                     (string-append former-path ",")
+                     "")
+                 "pytest_guix_plugin"))
+        (mkdir-p dir)
+        (with-output-to-file (string-append dir "/__init__.py")
+          (lambda _ (display "")))
+        (with-output-to-file (string-append dir "/pytest_guix_plugin.py")
+          (lambda _
+            (display (pytest-ignore-flags-plugin filtered-flags)))))
+      thunk
+      (lambda ()
+        (setenv "PYTHONPATH" former-path)
+        (unsetenv "PYTEST_PLUGINS")))))
+
+(define-syntax-rule (with-guix-pytest-plugin inputs exp ...)
+  "Evaluate EXP in a context where the Guix pytest plugin is added."
+  (call-with-guix-pytest-plugin inputs (lambda () exp ...)))
+
+(define* (check #:key inputs tests? test-backend test-flags #:allow-other-keys)
   "Run the test suite of a given Python package."
   (if tests?
       ;; Unfortunately with PEP 517 there is no common method to specify test
@@ -165,7 +254,8 @@ (define* (check #:key tests? test-backend test-flags #:allow-other-keys)
         (format #t "Using ~a~%" use-test-backend)
         (match use-test-backend
           ('pytest
-           (apply invoke pytest "-vv" test-flags))
+           (with-guix-pytest-plugin inputs
+             (apply invoke pytest "-vv" test-flags)))
           ('nose
            (apply invoke nosetests "-v" test-flags))
           ('nose2
@@ -386,3 +476,6 @@ (define* (pyproject-build #:key inputs (phases %standard-phases)
   (apply python:python-build #:inputs inputs #:phases phases args))
 
 ;;; pyproject-build-system.scm ends here
+;;; Local Variables:
+;;; eval: (put 'with-guix-pytest-plugin 'scheme-indent-function 1)
+;;; End:
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 02/48] gnu: Remove python-pep8.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-3-ngraves@ngraves.fr

* gnu/packages/python-xyz.scm (python-pep8): Delete variable.
(python-cliapp, python-ttystatus)[native-inputs]: Remove python-pep8.
* gnu/packages/radio.scm (chirp)[native-inputs]: Remove python-pep8.
---
 gnu/packages/python-xyz.scm | 27 ++-------------------------
 gnu/packages/radio.scm      |  1 -
 2 files changed, 2 insertions(+), 26 deletions(-)

Toggle diff (66 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 0cb681f401..33e58fb205 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -15790,29 +15790,6 @@ (define-public python-sentry-sdk
 application monitoring and error tracking software.")
     (license license:bsd-2)))
 
-(define-public python-pep8
-  ;; This package has been renamed to ‘pycodestyle’ and is no longer updated.
-  ;; Its last release (1.7.1) adds only a scary warning to this effect, breaking
-  ;; some dependents' test suites, and nothing more.
-  (package
-    (name "python-pep8")
-    (version "1.7.0")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "pep8" version))
-        (sha256
-          (base32
-           "002rkl4lsn6x2mxmf8ar00l0m8i3mzrc6pnzz77blyksmpsxa4x1"))
-        (patches (search-patches "python-pep8-stdlib-tokenize-compat.patch"))))
-    (build-system python-build-system)
-    (home-page "https://pep8.readthedocs.org/")
-    (synopsis "Python style guide checker")
-    (description
-     "This tools checks Python code against some of the style conventions in
-PEP 8.")
-    (license license:expat)))
-
 (define-public python-pep8-naming
   (package
     (name "python-pep8-naming")
@@ -25906,7 +25883,7 @@ (define-public python-cliapp
        ;; fails due to deprecation warnings, etc.
        #:tests? #f))
     (native-inputs
-     (list python-coverage-test-runner python-pep8))
+     (list python-coverage-test-runner))
     (propagated-inputs
      (list python-pyaml))
     (home-page "https://liw.fi/cliapp/")
@@ -25932,7 +25909,7 @@ (define-public python-ttystatus
        (file-name (git-file-name name version))))
     (build-system python-build-system)
     (native-inputs
-     (list python-coverage-test-runner python-pep8))
+     (list python-coverage-test-runner))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index cda2f1907c..d2c8bee76b 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -3272,7 +3272,6 @@ (define-public chirp
       (native-inputs
        (list python-mock
              python-mox3
-             python-pep8
              python-pytest
              python-pytest-mock
              python-pyyaml
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 05/48] build-system/pyproject: Remove python-black inputs.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-6-ngraves@ngraves.fr

* gnu/packages/bioinformatics.scm (python-doubletdetection,
python-liana-py, python-metacells, python-ngesh, scvelo)
* gnu/packages/databases.scm (datasette)
* gnu/packages/finance.scm (python-trezor)
* gnu/packages/graph.scm (python-graphtools)
* gnu/packages/jupyter.scm (python-papermill)
* gnu/packages/machine-learning.scm (python-funsor,
python-imbalanced-learn, python-hyperopt, python-captum)
* gnu/packages/python-check.scm (python-vcrpy)
* gnu/packages/python-web.scm (python-ovh, python-openai,
* gnu/packages/python-science.scm (python-scikit-survival)
python-starsessions-for-pytorch-lightning)
* gnu/packages/python-xyz.scm (python-archspec, python-pydantic-cli,
python-imageio, python-update-checker, python-eliot,
python-minikanren)
* gnu/packages/virtualization.scm (python-transient)
[native-inputs]: Remove python-black.

* gnu/packages/python-xyz.scm (ptpython,
python-get-version)[propagated-inputs]: Remove python-black.
---
 gnu/packages/bioinformatics.scm   | 16 +++++-----------
 gnu/packages/databases.scm        |  1 -
 gnu/packages/finance.scm          |  1 -
 gnu/packages/graph.scm            |  1 -
 gnu/packages/jupyter.scm          |  1 -
 gnu/packages/machine-learning.scm | 10 +++-------
 gnu/packages/python-science.scm   |  3 +--
 gnu/packages/python-web.scm       |  8 +++-----
 gnu/packages/python-xyz.scm       | 19 ++++++-------------
 gnu/packages/virtualization.scm   |  3 +--
 10 files changed, 19 insertions(+), 44 deletions(-)

Toggle diff (287 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6f4c5053b6..00dc20e8b6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2824,8 +2824,7 @@ (define-public python-doubletdetection
            python-scipy
            python-tqdm))
     (native-inputs
-     (list python-black
-           python-flake8
+     (list python-flake8
            python-poetry-core
            python-pytest))
     (home-page "https://github.com/JonathanShor/DoubletDetection")
@@ -3053,10 +3052,7 @@ (define-public python-liana-py
                              python-tqdm
                              tzdata))
     (native-inputs
-     (list python-black
-           python-poetry-core
-           python-pytest
-           python-pytest-cov))
+     (list python-poetry-core python-pytest python-pytest-cov))
     (home-page "https://github.com/saezlab/liana-py")
     (synopsis "LIANA is a ligand-receptor analysis framework")
     (description "This is a Ligand-Receptor inference framework.  The
@@ -3172,8 +3168,7 @@ (define-public python-metacells
                              python-scipy
                              python-threadpoolctl
                              python-umap-learn))
-    (native-inputs (list python-black
-                         python-bumpversion
+    (native-inputs (list python-bumpversion
                          python-flake8
                          python-isort
                          python-mypy
@@ -3213,7 +3208,7 @@ (define-public python-ngesh
         (base32 "07sj4x95b5hvx57pw24f80sk4ag4hkg1z6wzym3pzi8n5gn85n1z"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-ete3 python-numpy python-six))
-    (native-inputs (list python-black python-flake8 python-pytest python-twine
+    (native-inputs (list python-flake8 python-pytest python-twine
                          python-wheel))
     (home-page "https://github.com/tresoldi/ngesh")
     (synopsis "Library for phylogenetic tree simulation")
@@ -24057,8 +24052,7 @@ (define-public scvelo
            python-umap-learn
            pybind11))
     (native-inputs
-     (list python-black
-           python-flake8
+     (list python-flake8
            python-hypothesis
            python-pytest
            python-setuptools-scm
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 3f0a7435d5..fd77fa940c 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -5801,7 +5801,6 @@ (define-public datasette
     (native-inputs
      (list nss-certs-for-test
            python-beautifulsoup4
-           python-black
            python-cogapp
            python-pip
            python-pytest
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index bb1234ebd9..9805679597 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -1160,7 +1160,6 @@ (define-public python-trezor
            python-typing-extensions))
     (native-inputs ; Only needed for running the tests
      (list protobuf
-           python-black
            python-isort
            python-pillow
            python-protobuf
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index f29a71c0d7..75ebbff2db 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -482,7 +482,6 @@ (define-public python-graphtools
     (native-inputs
      (list util-linux ;for lscpu
            python-anndata
-           python-black
            python-coverage
            python-coveralls
            python-nose
diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm
index 6c2f549583..f47d8de295 100644
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -1157,7 +1157,6 @@ (define-public python-papermill
                              python-tenacity
                              python-tqdm))
     (native-inputs (list python-attrs
-                         python-black
                          python-boto3
                          python-botocore
                          python-bumpversion
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index c051974244..8609ea81bf 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -229,8 +229,7 @@ (define-public python-funsor
     (propagated-inputs (list python-makefun python-multipledispatch
                              python-numpy python-opt-einsum
                              python-typing-extensions))
-    (native-inputs (list python-black
-                         python-flake8
+    (native-inputs (list python-flake8
                          python-isort
                          python-nbsphinx
                          python-pandas
@@ -2154,8 +2153,7 @@ (define-public python-imbalanced-learn
                               (getcwd)))))))
     (propagated-inputs (list python-joblib python-numpy python-scikit-learn
                              python-scipy python-threadpoolctl))
-    (native-inputs (list python-black
-                         python-flake8
+    (native-inputs (list python-flake8
                          python-keras
                          python-mypy
                          python-pandas
@@ -2594,8 +2592,7 @@ (define-public python-hyperopt
            python-six
            python-tqdm))
     (native-inputs
-     (list python-black
-           python-nose
+     (list python-nose
            python-pymongo
            python-pytest
            python-wheel))
@@ -5325,7 +5322,6 @@ (define-public python-captum
      (list python-matplotlib python-numpy python-pytorch python-tqdm))
     (native-inputs (list jupyter
                          python-annoy
-                         python-black
                          python-flake8
                          python-flask
                          python-flask-compress
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index ae6d40cec2..508b819cf9 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -888,8 +888,7 @@ (define-public python-scikit-survival
              python-scikit-learn
              python-scipy))
       (native-inputs
-       (list python-black
-             python-pypa-build
+       (list python-pypa-build
              python-coverage
              python-cython-3
              python-packaging
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 3ab0180fb3..17c36189f7 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1604,8 +1604,7 @@ (define-public python-ovh
     (build-system pyproject-build-system)
     (arguments (list #:tests? #f))      ; XXX: tests require networking
     (propagated-inputs (list python-requests))
-    (native-inputs (list python-black
-                         python-coverage
+    (native-inputs (list python-coverage
                          python-flake8
                          python-isort
                          python-pytest
@@ -3014,7 +3013,7 @@ (define-public python-openai
  and not test_file_cli")))
     (propagated-inputs (list python-aiohttp python-requests python-tqdm
                              python-typing-extensions))
-    (native-inputs (list python-black python-pytest python-pytest-asyncio
+    (native-inputs (list python-pytest python-pytest-asyncio
                          python-pytest-mock python-setuptools python-wheel))
     (home-page "https://github.com/openai/openai-python")
     (synopsis "Python client library for the OpenAI API")
@@ -10322,8 +10321,7 @@ (define-public python-starsessions
            python-itsdangerous
            python-starlette))
     (native-inputs
-     (list python-black
-           python-flake8
+     (list python-flake8
            python-httpx
            python-mypy
            python-poetry-core
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 33e58fb205..e348dc9b6b 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -396,8 +396,7 @@ (define-public python-archspec
                              python-scikit-learn
                              python-tables
                              python-typing-extensions))
-    (native-inputs (list python-black
-                         python-flake8
+    (native-inputs (list python-flake8
                          python-isort
                          python-poetry-core
                          python-pylint
@@ -8879,8 +8878,7 @@ (define-public python-pydantic-cli
     (propagated-inputs
      (list python-pydantic))
     (native-inputs
-     (list python-black
-           python-mypy
+     (list python-mypy
            python-pytest))
     (home-page "https://github.com/mpkocher/pydantic-cli")
     (synopsis "Turn Pydantic defined data models into CLI tools")
@@ -12028,8 +12026,7 @@ (define-public python-imageio
     (propagated-inputs
      (list python-imageio-ffmpeg python-numpy python-pillow python-tifffile))
     (native-inputs
-     (list python-black
-           python-flake8
+     (list python-flake8
            python-fsspec
            python-pytest
            python-pytest-cov
@@ -17596,7 +17593,6 @@ (define-public python-get-version
     (propagated-inputs
      (list python-pygments
            python-pytest
-           python-pytest-black
            python-pytest-cov
            python-setuptools
            python-testpath))
@@ -23847,8 +23843,7 @@ (define-public ptpython
     (arguments
      `(#:tests? #f)) ;there are no tests
     (propagated-inputs
-     (list python-appdirs python-black python-jedi python-prompt-toolkit
-           python-pygments))
+     (list python-appdirs python-jedi python-prompt-toolkit python-pygments))
     (home-page "https://github.com/jonathanslenders/ptpython")
     (synopsis "Python Read-Eval-Print-Loop with nice IDE-like features")
     (description
@@ -29234,7 +29229,7 @@ (define-public python-update-checker
         (base32 "04yb5a9mi45ax50m2m0ih6gdvkk1j7gfmy83dd58i1f59axlabba"))))
     (build-system python-build-system)
     (propagated-inputs (list python-requests))
-    (native-inputs (list python-black python-flake8 python-pytest))
+    (native-inputs (list python-flake8 python-pytest))
     (home-page "https://github.com/bboe/update_checker")
     (synopsis "Python module that will check for package updates")
     (description "This package provides a Python module that will check for
@@ -33566,8 +33561,7 @@ (define-public python-eliot
     (propagated-inputs
      (list python-boltons python-orjson python-pyrsistent python-zope-interface))
     (native-inputs
-     (list python-black
-           python-coverage
+     (list python-coverage
            python-flake8
            python-hypothesis
            python-pytest
@@ -36878,7 +36872,6 @@ (define-public python-minikanren
            python-pytest
            python-pytest-cov
            python-pylint
-           python-black
            python-sympy
            python-versioneer
            python-coverage))
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index 9ab65e6c6c..cc0346297e 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -2987,8 +2987,7 @@ (define-public python-transient
                         (("==")
                          ">=")))))))
     (native-inputs
-     (list python-black
-           python-mypy
+     (list python-mypy
            python-pyhamcrest
            python-setuptools
            python-twine
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 11/48] gnu: python-cram: Remove python-coverage native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-12-ngraves@ngraves.fr

* gnu/packages/python-xyz.scm (python-cram):
  [native-inputs]: Remove python-coverage.
  [build-system]: Move to pyproject-build-system.
  [arguments]<#:phases>: Adapt check and patch-source phases
  to coverage removal.

Change-Id: I83fafcdcfbc977f9d3e3411d01d23d9a0e120ec6
---
 gnu/packages/python-xyz.scm | 16 ++++------------
 1 file changed, 4 insertions(+), 12 deletions(-)

Toggle diff (36 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index c7468c1beb..fc49715718 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -16443,25 +16443,17 @@ (define-public python-cram
                ;; causes the line showing the default shell to break into two
                ;; lines, but the test expects a single line...
                (("env\\['COLUMNS'\\] = '80'")
-                "env['COLUMNS'] = '160'"))
-
-             (substitute* "Makefile"
-               ;; Recent versions of python-coverage have caused the test
-               ;; coverage to decrease (as of version 0.7).  Allow that.
-               (("--fail-under=100")
-                "--fail-under=90"))
-
-             #t))
+                "env['COLUMNS'] = '160'"))))
          (replace 'check
            ;; The test phase uses the built library and executable.
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (add-installed-pythonpath inputs outputs)
              (setenv "PATH" (string-append (getenv "PATH") ":"
                                            (assoc-ref outputs "out") "/bin"))
-             (invoke "make" "test"))))))
-    (build-system python-build-system)
+             (invoke "make" "quicktest"))))))
+    (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage python-setuptools python-wheel which))
+     (list python-setuptools python-wheel which))
     (synopsis "Simple testing framework for command line applications")
     (description
      "Cram is a functional testing framework for command line applications.
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 09/48] build-system/pyproject: Remove python-coverage native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-10-ngraves@ngraves.fr

* gnu/packages/jupyter.scm (python-nbclassic, python-papermill)
* gnu/packages/openstack.scm (python-hacking, python-oslo.context)
* gnu/packages/python-check.scm (python-pytest-testmon)
* gnu/packages/python-science.scm (python-scikit-survival, python-modin,
  python-pynetdicom)
* gnu/packages/python-web.scm (python-aioitertools, python-python3-saml,
  python-zope-i18n-messageid, python-rangehttpserver, python-http-ece,
  python-zeep)
* gnu/packages/python-xyz.scm (python-argopt, python-case, python-pypugjs,
  python-repoze-lru, python-lsp-jsonrpc, python-pillow-heif,
  python-legacy-api-wrap, python-waitress, python-gevent, python-twisted,
  python-mamba, python-bagit, python-typer, python-numcodecs, python-diceware,
  python-param)
* gnu/packages/statistics.scm (python-radian)
[native-inputs]: Remove python-coverage.
---
 gnu/packages/jupyter.scm        |  4 +---
 gnu/packages/openstack.scm      |  6 ++----
 gnu/packages/python-check.scm   |  3 +--
 gnu/packages/python-science.scm |  3 ---
 gnu/packages/python-web.scm     | 13 +++++--------
 gnu/packages/python-xyz.scm     | 32 +++++++++++---------------------
 gnu/packages/statistics.scm     |  3 +--
 7 files changed, 21 insertions(+), 43 deletions(-)

Toggle diff (311 lines)diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm
index 70d894939c..a9f57b2ccc 100644
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -81,8 +81,7 @@ (define-public python-nbclassic
                              python-terminado
                              python-tornado-6
                              python-traitlets))
-    (native-inputs (list python-coverage
-                         python-nbval
+    (native-inputs (list python-nbval
                          python-jupyter-packaging
                          python-pytest
                          python-pytest-cov
@@ -1162,7 +1161,6 @@ (define-public python-papermill
                          python-bumpversion
                          python-check-manifest
                          python-codecov
-                         python-coverage
                          python-ipython
                          python-ipywidgets
                          python-moto
diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index ac283bd019..84696a586f 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -153,8 +153,7 @@ (define-public python-hacking
     (propagated-inputs
      (list python-flake8))
     (native-inputs
-     (list python-coverage
-           python-ddt
+     (list python-ddt
            python-eventlet
            python-fixtures
            python-setuptools
@@ -551,8 +550,7 @@ (define-public python-oslo.context
     (propagated-inputs
      (list python-debtcollector))
     (native-inputs
-     (list python-coverage
-           python-fixtures
+     (list python-fixtures
            python-hacking
            python-mypy
            python-oslotest
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index ebfdd7312e..27abc67c58 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -1651,8 +1651,7 @@ (define-public python-pytest-testmon
     (build-system pyproject-build-system)
     (arguments (list #:tests? #false)) ;there are none
     (native-inputs
-     (list python-coverage
-           python-pytest
+     (list python-pytest
            python-setuptools
            python-wheel))
     (home-page "https://github.com/tarpas/pytest-testmon")
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 508b819cf9..2e643f1740 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -889,7 +889,6 @@ (define-public python-scikit-survival
              python-scipy))
       (native-inputs
        (list python-pypa-build
-             python-coverage
              python-cython-3
              python-packaging
              python-pytest
@@ -3055,7 +3054,6 @@ (define-public python-modin
            python-s3fs))
     (native-inputs
      (list python-boto3
-           python-coverage
            python-jinja2
            python-lxml
            python-matplotlib
@@ -4061,7 +4059,6 @@ (define-public python-pynetdicom
                     " and not test_pr_level_series"
                     " and not test_scp_cancelled"))))
     (native-inputs (list python-codespell
-                         python-coverage
                          python-poetry-core
                          python-pytest
                          python-pytest-cov
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 6281ca5c8c..70830bb672 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -903,8 +903,7 @@ (define-public python-aioitertools
     (arguments (list #:tests? #false))
     (propagated-inputs (list python-typing-extensions))
     (native-inputs
-     (list python-coverage
-           python-flake8
+     (list python-flake8
            python-flit-core
            python-mypy
            python-pytest
@@ -1577,8 +1576,7 @@ (define-public python-python3-saml
               (setenv "LD_LIBRARY_PATH"
                       (dirname (search-input-file inputs "lib/libxmlsec1-openssl.so.1.2.37"))))))))
     (propagated-inputs (list python-isodate python-lxml python-xmlsec))
-    (native-inputs (list python-coverage
-                         python-flake8
+    (native-inputs (list python-flake8
                          python-freezegun
                          python-poetry-core
                          python-pytest
@@ -3987,7 +3985,7 @@ (define-public python-zope-i18nmessageid
         (base32 "14mx62khys82p2gmmf3m40x4jmvcz3rndvl6qik2n2qfp13n7ds7"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage python-setuptools
+     (list python-setuptools
            python-wheel python-zope-testrunner))
     (propagated-inputs
      (list python-six))
@@ -8217,7 +8215,7 @@ (define-public python-rangehttpserver
        (sha256
         (base32 "1dx533fsbq1mbz3by7qkm5bh2c253nwvm8214pqbwbfq07kqkwf2"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-coverage python-coveralls python-pytest
+    (native-inputs (list python-coveralls python-pytest
                          python-setuptools python-wheel))
     (home-page "https://github.com/danvk/RangeHTTPServer")
     (synopsis "SimpleHTTPServer with support for range requests")
@@ -8577,7 +8575,7 @@ (define-public python-http-ece
     (propagated-inputs
      (list python-cryptography))
     (native-inputs
-     (list python-coverage python-mock python-nose))
+     (list python-mock python-nose))
     (home-page "https://github.com/web-push-libs/encrypted-content-encoding")
     (synopsis "Encrypted Content Encoding for HTTP")
     (description
@@ -10134,7 +10132,6 @@ (define-public python-zeep
            python-requests-toolbelt))
     (native-inputs
      (list nss-certs-for-test
-           python-coverage
            python-flake8
            python-flake8-blind-except
            python-flake8-debugger
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index d49b153b5f..dfebaf96a3 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1408,7 +1408,7 @@ (define-public python-argopt
               "0ybs7kkp0cpl8zn1lvf7481xhssg1bbhh5la2cjzdm5yibashyxa"))))
    (build-system python-build-system)
    (native-inputs
-    (list python-coverage python-nose python-setuptools ; Won't build without this.
+    (list python-nose python-setuptools ; Won't build without this.
           python-setuptools-scm))
    (propagated-inputs
     (list python-toml python-flake8))
@@ -4690,8 +4690,6 @@ (define-public python-case
     (build-system python-build-system)
     (propagated-inputs
      (list python-mock python-nose python-six))
-    (native-inputs
-     (list python-coverage))
     (home-page "https://github.com/celery/case")
     (synopsis "Unittest utilities and convenience methods")
     (description
@@ -7214,8 +7212,7 @@ (define-public python-pypugjs
                        ;; pyramid is outdated and pyramid-mako is unpackaged.
                        (substitute* "setup.cfg"
                          (("'(pyramid|pyramid-mako)[^']*',") "")))))))
-    (native-inputs (list python-coverage
-                         python-django
+    (native-inputs (list python-django
                          python-jinja2
                          python-flake8
                          python-flask
@@ -7825,7 +7822,7 @@ (define-public python-repoze-lru
         (base32 "0xzz1aw2smy8hdszrq8yhnklx6w1r1mf55061kalw3iq35gafa84"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage python-nose python-setuptools python-wheel))
+     (list python-nose python-setuptools python-wheel))
     (home-page "https://www.repoze.org")
     (synopsis "Tiny LRU cache implementation and decorator")
     (description
@@ -8690,8 +8687,7 @@ (define-public python-lsp-jsonrpc
          "04n95h0cqnsrdyh1gv0abh2i5ynyrq2wfqpppx9djp7mxr9y9226"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage
-           python-pycodestyle
+     (list python-pycodestyle
            python-pyflakes
            python-pytest
            python-pytest-cov
@@ -11463,7 +11459,6 @@ (define-public python-pillow-heif
     (inputs (list libheif))
     (propagated-inputs (list python-pillow))
     (native-inputs (list opencv         ; for opencv-python
-                         python-coverage
                          python-defusedxml
                          python-numpy
                          python-packaging
@@ -17688,8 +17683,7 @@ (define-public python-legacy-api-wrap
          "1d5jyd8d2wxm6y0s39wwqw87gdm4zqlbyz78cf3yqbrim1xdch4w"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage
-           python-hatch-vcs
+     (list python-hatch-vcs
            python-hatchling
            python-pytest))
     (home-page "https://github.com/flying-sheep/legacy-api-wrap")
@@ -20815,7 +20809,7 @@ (define-public python-waitress
      ;; https://github.com/Pylons/waitress/issues/443
      (list #:test-flags #~(list "-k" "not test_service_port")))
     (native-inputs
-     (list python-coverage python-pytest python-pytest-cov
+     (list python-pytest python-pytest-cov
            python-setuptools python-wheel))
     (home-page "https://github.com/Pylons/waitress")
     (synopsis "Waitress WSGI server")
@@ -22309,7 +22303,6 @@ (define-public python-gevent
      (list python-greenlet python-zope-event python-zope-interface))
     (native-inputs
      (list python-cffi
-           python-coverage
            python-cython
            python-dnspython
            python-idna
@@ -22412,7 +22405,6 @@ (define-public python-twisted
            python-zope-interface))
     (native-inputs
      (list glibc-utf8-locales ;for OpenTestLogTests.test_utf8
-           python-coverage
            python-hatch-fancy-pypi-readme
            python-hatchling
            python-httpx
@@ -26105,7 +26097,7 @@ (define-public python-mamba
     (build-system python-build-system)
     (arguments `(#:tests? #f))  ; No test
     (propagated-inputs
-     (list python-clint python-coverage))
+     (list python-clint))
     (home-page "https://nestorsalceda.com/mamba/")
     (synopsis "Test runner for Python")
     (description
@@ -26869,7 +26861,7 @@ (define-public python-bagit
           "1m6y04qmig0b5hzb35lnaw3d2yfydb7alyr1579yblvgs3da6j7j"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-setuptools-scm python-coverage python-mock))
+     (list python-setuptools-scm python-mock))
     (home-page "https://libraryofcongress.github.io/bagit-python/")
     (synopsis "Create and validate BagIt packages")
     (description "Bagit is a Python library and command line utility for working
@@ -28529,7 +28521,7 @@ (define-public python-typer
     (propagated-inputs
      (list python-click))
     (native-inputs
-     (list python-coverage python-flit python-pytest python-rich
+     (list python-flit python-pytest python-rich
            python-shellingham))
     (home-page "https://github.com/tiangolo/typer")
     (synopsis "Typer builds CLI based on Python type hints")
@@ -29916,8 +29908,7 @@ (define-public python-numcodecs
      (list c-blosc lz4 zlib
            `(,zstd "lib")))
     (propagated-inputs
-     (list python-coverage
-           python-google-crc32c
+     (list python-google-crc32c
            python-importlib-metadata
            python-msgpack
            python-numpy
@@ -33715,7 +33706,7 @@ (define-public python-diceware
          "0klb0ysybzlh2wihvir82hgq62v0jjmlcqklwajyms7c0p529yby"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-coverage python-pytest python-pytest-runner))
+     (list python-pytest python-pytest-runner))
     (home-page "https://github.com/ulif/diceware/")
     (synopsis "Generates memorable passphrases")
     (description "This package generates passphrases by concatenating words
@@ -34810,7 +34801,6 @@ (define-public python-param
     (build-system pyproject-build-system)
     (native-inputs
      (list python-cloudpickle
-           python-coverage
            python-hatchling
            python-hatch-vcs
            python-ipython
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 736b90b384..7a02786ab6 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -7208,8 +7208,7 @@ (define-public python-radian
                        (setenv "HOME" "/tmp"))))))
     (propagated-inputs (list python-prompt-toolkit python-pygments
                              python-rchitect))
-    (native-inputs (list python-coverage
-                         python-pexpect
+    (native-inputs (list python-pexpect
                          python-ptyprocess
                          python-pyte
                          python-pytest
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 06/48] build-system/pyproject: Remove python-pylint native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-7-ngraves@ngraves.fr

* gnu/packages/bioinformatics.scm (python-metacells)
* gnu/packages/games.scm (open-adventure)
* gnu/packages/machine-learning.scm (python-ml-collections)
* gnu/packages/potassco.scm (python-clingraph)
* gnu/packages/python-xyz.scm (python-archspec, python-lsp-jsonrpc,
python-lsp-server, python-mediapy, python-minikanren)
* gnu/packages/syndication.scm (rtv, tuir)
* gnu/packages/terminals.scm (python-halo, python-log-symbols,
python-spinners)
* gnu/packages/virtualization.scm (python-qemu-qmp)
[native-inputs]: Remove python-pylint.
---
 gnu/packages/bioinformatics.scm   | 1 -
 gnu/packages/games.scm            | 1 -
 gnu/packages/machine-learning.scm | 3 +--
 gnu/packages/potassco.scm         | 3 +--
 gnu/packages/python-xyz.scm       | 5 -----
 gnu/packages/syndication.scm      | 2 --
 gnu/packages/terminals.scm        | 3 ---
 gnu/packages/virtualization.scm   | 1 -
 8 files changed, 2 insertions(+), 17 deletions(-)

Toggle diff (158 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 00dc20e8b6..1a0ae8918e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3174,7 +3174,6 @@ (define-public python-metacells
                          python-mypy
                          python-mypy-extensions
                          python-pandas-stubs
-                         python-pylint
                          python-pytest
                          python-pytest-cov
                          python-setuptools
diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 546c513de0..47566c8df1 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -7856,7 +7856,6 @@ (define-public open-adventure
              cppcheck
              libedit
              pkg-config
-             python-pylint
              python-pyyaml
              python-wrapper)
        (if (supported-package? ruby-asciidoctor)
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 8609ea81bf..480e534823 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -379,8 +379,7 @@ (define-public python-ml-collections
       #:test-flags '(list "--pyargs" "ml_collections/config_dict/tests")))
     (propagated-inputs
      (list python-absl-py python-pyyaml))
-    (native-inputs (list python-pylint
-                         python-pytest
+    (native-inputs (list python-pytest
                          python-pytest-xdist
                          python-flit-core))
     (home-page "https://github.com/google/ml_collections")
diff --git a/gnu/packages/potassco.scm b/gnu/packages/potassco.scm
index 43e56ec8bf..7c3fe2e309 100644
--- a/gnu/packages/potassco.scm
+++ b/gnu/packages/potassco.scm
@@ -697,8 +697,7 @@ (define-public python-clingraph
                              python-jsonschema
                              python-networkx
                              python-setuptools))
-    (native-inputs (list dot2tex graphviz python-pylint python-pytest
-                         python-wheel))
+    (native-inputs (list dot2tex graphviz python-pytest python-wheel))
     (home-page "https://github.com/potassco/clingraph")
     (synopsis "Visualizer for graphs defined as logic programs")
     (description
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e348dc9b6b..f2c5f7fa63 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -399,7 +399,6 @@ (define-public python-archspec
     (native-inputs (list python-flake8
                          python-isort
                          python-poetry-core
-                         python-pylint
                          python-pytest
                          python-pytest-cov))
     (home-page "https://github.com/archspec/archspec")
@@ -5107,7 +5106,6 @@ (define-public python-mediapy
                              python-pillow))
     (native-inputs
      (list python-flit-core
-           python-pylint
            python-pytest
            python-pytest-xdist))
     (home-page "https://github.com/google/mediapy")
@@ -8706,7 +8704,6 @@ (define-public python-lsp-jsonrpc
      (list python-coverage
            python-pycodestyle
            python-pyflakes
-           python-pylint
            python-pytest
            python-pytest-cov
            python-setuptools
@@ -9082,7 +9079,6 @@ (define-public python-lsp-server
            python-matplotlib
            python-numpy
            python-pandas
-           python-pylint
            python-pytest
            python-rope
            python-setuptools
@@ -36871,7 +36867,6 @@ (define-public python-minikanren
            python-pydocstyle
            python-pytest
            python-pytest-cov
-           python-pylint
            python-sympy
            python-versioneer
            python-coverage))
diff --git a/gnu/packages/syndication.scm b/gnu/packages/syndication.scm
index f717cbb3af..fc563a657f 100644
--- a/gnu/packages/syndication.scm
+++ b/gnu/packages/syndication.scm
@@ -501,7 +501,6 @@ (define-public rtv
            python-coveralls
            python-coverage
            python-mock
-           python-pylint
            python-pytest
            python-vcrpy))
     (home-page "https://github.com/michael-lazar/rtv")
@@ -545,7 +544,6 @@ (define-public tuir
      (list python-coverage
            python-coveralls
            python-mock
-           python-pylint
            python-pytest
            python-setuptools
            python-vcrpy
diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index 9fdd378cf2..b9dd12803d 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -1178,7 +1178,6 @@ (define-public python-halo
     (native-inputs
      (list python-coverage
            python-nose
-           python-pylint
            python-setuptools
            python-tox
            python-twine
@@ -1211,7 +1210,6 @@ (define-public python-log-symbols
     (native-inputs
      (list python-coverage
            python-nose
-           python-pylint
            python-setuptools
            python-tox
            python-wheel))
@@ -1245,7 +1243,6 @@ (define-public python-spinners
     (native-inputs
      (list python-coverage
            python-nose
-           python-pylint
            python-setuptools
            python-tox
            python-wheel))
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index cc0346297e..bde357763f 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -2121,7 +2121,6 @@ (define-public python-qemu-qmp
      (list python-avocado-framework
            python-flake8
            python-isort
-           python-pylint
            python-setuptools
            python-setuptools-scm
            python-wheel))
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 10/48] build-system/pyproject: Remove python-pytest-black native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-11-ngraves@ngraves.fr

* gnu/packages/check.scm (python-pytest-perf, python-pytest-enabler)
[native-inputs]: Remove python-pytest-black.

* gnu/packages/python-web.scm (python-portend)[native-inputs]:
Remove python-pytest-black.
---
 gnu/packages/check.scm      | 2 --
 gnu/packages/python-web.scm | 1 -
 gnu/packages/python-xyz.scm | 9 ---------
 3 files changed, 12 deletions(-)

Toggle diff (110 lines)diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 4263329559..e6aa4d6de6 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2944,7 +2944,6 @@ (define-public python-pytest-enabler
            python-jaraco-functools
            python-toml))
     (native-inputs (list python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-cov
                          python-pytest-flake8
@@ -3118,7 +3117,6 @@ (define-public python-pytest-perf
                            "and not upstream_url"))))
     (native-inputs
      (list python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-cov
            python-pytest-enabler
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 70830bb672..8dd8a58217 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -702,7 +702,6 @@ (define-public python-portend
     (propagated-inputs (list python-tempora))
     ;; TODO: Add python-pytest-ruff to native-inputs once it has been packaged.
     (native-inputs (list python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-cov
                          python-pytest-enabler
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index dfebaf96a3..c7468c1beb 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -12820,7 +12820,6 @@ (define-public python-importlib-resources
                      (string-append (getcwd) "/_custom_build")))))))
     (native-inputs
      (list python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-cov
            python-pytest-enabler
@@ -12971,7 +12970,6 @@ (define-public python-jaraco-classes
       #:test-flags '(list "-k" "not project")))
     (native-inputs
      (list python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-cov
            python-pytest-flake8
@@ -13005,7 +13003,6 @@ (define-public python-jaraco-collections
     ;; TODO: Add python-pytest-ruff to native-inputs once it has been
     ;; packaged.
     (native-inputs (list python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-cov
                          python-pytest-enabler
@@ -13066,7 +13063,6 @@ (define-public python-jaraco-context
            #:test-flags '(list "-k" "not project")))
     (native-inputs
      (list python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-cov
            python-pytest-flake8
@@ -13101,7 +13097,6 @@ (define-public python-jaraco-functools
     (native-inputs
      (list python-jaraco-classes
            python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-cov
            python-pytest-flake8
@@ -13196,7 +13191,6 @@ (define-public python-jaraco-text
     ;; TODO: Add python-pytest-ruff to native-inputs once it has been
     ;; packaged.
     (native-inputs (list python-pytest
-                         python-pytest-black
                          python-pytest-checkdocs
                          python-pytest-cov
                          python-pytest-enabler
@@ -17945,7 +17939,6 @@ (define-public python-path
                python-packaging
                python-pygments
                python-pytest
-               python-pytest-black
                python-pytest-checkdocs
                python-pytest-cov
                python-pytest-enabler
@@ -18051,7 +18044,6 @@ (define-public python-pip-run
        (append python-nbformat
                python-pygments
                python-pytest
-               python-pytest-black
                python-pytest-checkdocs
                python-pytest-cov
                python-pytest-enabler
@@ -27923,7 +27915,6 @@ (define-public python-tempora
     (native-inputs
      (list python-freezegun
            python-pytest
-           python-pytest-black
            python-pytest-checkdocs
            python-pytest-cov
            python-pytest-enabler
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 07/48] build-system/pyproject: Remove python-flake8 inputs.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-8-ngraves@ngraves.fr

* gnu/packages/bioinformatics.scm (python-doubletdetection,
python-biom-format, python-metacells, python-ngesh)
* gnu/packages/ebook.scm (calibre)
* gnu/packages/engineering.scm (python-scikit-rf)
* gnu/packages/finance.scm (python-mt-940)
* gnu/packages/geo.scm (python-geopy)
* gnu/packages/gettext.scm (python-mdpo)
* gnu/packages/graph.scm (python-pygsp)
* gnu/packages/graphviz.scm (python-uqbar)
* gnu/packages/machine-learning.scm (python-funsor,
python-imbalanced-learn, python-captum, python-pymanopt,
python-pyro-api, python-pyro-ppl, python-linear-operator,
python-gpytorch)
* gnu/packages/python-web.scm (python-ovh, python-furl,
python-httplib2, python-http-ece, python-woob,
python-starsessions-for-pytorch-lightning)
* gnu/packages/python-xyz.scm (python-archspec, python-colorful,
python-pymd4c, python-flasgger, python-imageio,
python-importlib-ressources, python-seaborn, python-inflect,
python-yq, python-update-checker, python-eliot, python-dateparser,
python-jinja2-cli, python-verspec, python-mike,
python-simple-websocket)
* gnu/packages/simulation.scm (python-dolfin-adjoint)
* gnu/packages/statistics.scm (python-statsmodels)
* gnu/packages/vpn.scm (sshuttle)
* gnu/packages/wm.scm (qtile)
* gnu/packages/textutils.scm (python-panflute)
[native-inputs]: Remove python-flake8.

* gnu/packages/music.scm (python-mutagen):
  [arguments]<#:test-flags>: Ignore flake8 quality tests.
  [native-inputs]: Remove python-flake8.

* gnu/packages/protobuf.scm (python-pure-protobuf):
  [arguments]<#:phases>: Remove flake8 invocation from check phase.
  [native-inputs]: Remove python-flake8.
---
 gnu/packages/bioinformatics.scm   | 10 +++-------
 gnu/packages/ebook.scm            |  1 -
 gnu/packages/engineering.scm      |  1 -
 gnu/packages/finance.scm          |  4 +---
 gnu/packages/gettext.scm          |  1 -
 gnu/packages/graph.scm            |  3 +--
 gnu/packages/graphviz.scm         |  1 -
 gnu/packages/machine-learning.scm | 15 ++++-----------
 gnu/packages/music.scm            |  4 ++--
 gnu/packages/protobuf.scm         |  4 +---
 gnu/packages/python-web.scm       | 15 ++++-----------
 gnu/packages/python-xyz.scm       | 31 ++++++++++++-------------------
 gnu/packages/simulation.scm       |  1 -
 gnu/packages/statistics.scm       |  1 -
 gnu/packages/textutils.scm        |  1 -
 gnu/packages/vpn.scm              |  1 -
 gnu/packages/wm.scm               |  1 -
 17 files changed, 28 insertions(+), 67 deletions(-)

Toggle diff (423 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1a0ae8918e..bda5ab3a8f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2824,8 +2824,7 @@ (define-public python-doubletdetection
            python-scipy
            python-tqdm))
     (native-inputs
-     (list python-flake8
-           python-poetry-core
+     (list python-poetry-core
            python-pytest))
     (home-page "https://github.com/JonathanShor/DoubletDetection")
     (synopsis
@@ -3169,7 +3168,6 @@ (define-public python-metacells
                              python-threadpoolctl
                              python-umap-learn))
     (native-inputs (list python-bumpversion
-                         python-flake8
                          python-isort
                          python-mypy
                          python-mypy-extensions
@@ -3207,7 +3205,7 @@ (define-public python-ngesh
         (base32 "07sj4x95b5hvx57pw24f80sk4ag4hkg1z6wzym3pzi8n5gn85n1z"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-ete3 python-numpy python-six))
-    (native-inputs (list python-flake8 python-pytest python-twine
+    (native-inputs (list python-pytest python-twine
                          python-wheel))
     (home-page "https://github.com/tresoldi/ngesh")
     (synopsis "Library for phylogenetic tree simulation")
@@ -3923,7 +3921,6 @@ (define-public python-biom-format
     (propagated-inputs
      (list python-anndata
            python-click
-           python-flake8
            python-future
            python-h5py
            python-numpy
@@ -24051,8 +24048,7 @@ (define-public scvelo
            python-umap-learn
            pybind11))
     (native-inputs
-     (list python-flake8
-           python-hypothesis
+     (list python-hypothesis
            python-pytest
            python-setuptools-scm
            python-wheel))
diff --git a/gnu/packages/ebook.scm b/gnu/packages/ebook.scm
index 46ec951916..75e14801dd 100644
--- a/gnu/packages/ebook.scm
+++ b/gnu/packages/ebook.scm
@@ -156,7 +156,6 @@ (define-public calibre
     (native-inputs
      (list bash-minimal
            pkg-config
-           python-flake8
            python-pyqt-builder
            qtbase-5                     ; for qmake
            xdg-utils))
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index 8ca3b87ff2..3882a35d6b 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -2965,7 +2965,6 @@ (define-public python-scikit-rf
                              python-qtpy
                              python-scipy))
     (native-inputs (list python-coverage
-                         python-flake8
                          python-nbval
                          python-networkx
                          python-pytest
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index 9805679597..f3be674c01 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -2310,9 +2310,7 @@ (define-public python-mt-940
                         ;; Remove custom --cov flags.
                         (delete-file "pytest.ini")
                         (invoke "pytest" "-vv")))))))
-    (native-inputs (list python-flake8
-                         python-pytest
-                         python-pyyaml))
+    (native-inputs (list python-pytest python-pyyaml))
     (home-page "https://mt940.readthedocs.io/")
     (synopsis "Python parser for MT940-encoded SWIFT data")
     (description
diff --git a/gnu/packages/gettext.scm b/gnu/packages/gettext.scm
index 7862c296bd..29cdbab915 100644
--- a/gnu/packages/gettext.scm
+++ b/gnu/packages/gettext.scm
@@ -226,7 +226,6 @@ (define-public mdpo
     (build-system python-build-system)
     (native-inputs
      (list python-bump2version
-           python-flake8
            python-flake8-implicit-str-concat
            python-flake8-print
            python-isort
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 75ebbff2db..57c4bd05ed 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -570,8 +570,7 @@ (define-public python-pygsp
                 "")))))))
     (propagated-inputs (list python-numpy python-scikit-image python-scipy))
     (native-inputs
-     (list python-coverage python-coveralls python-flake8
-           python-pytest))
+     (list python-coverage python-coveralls python-pytest))
     (home-page "https://github.com/epfl-lts2/pygsp")
     (synopsis "Graph Signal Processing in Python")
     (description "The PyGSP is a Python package to ease signal processing on
diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm
index defd53df73..0d3db31212 100644
--- a/gnu/packages/graphviz.scm
+++ b/gnu/packages/graphviz.scm
@@ -224,7 +224,6 @@ (define-public python-uqbar
 and not test_sphinx_book_text_broken_strict")))
     (native-inputs
      (list graphviz
-           python-flake8
            python-isort
            python-mypy
            python-pytest
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 480e534823..65cb08e2f3 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -229,8 +229,7 @@ (define-public python-funsor
     (propagated-inputs (list python-makefun python-multipledispatch
                              python-numpy python-opt-einsum
                              python-typing-extensions))
-    (native-inputs (list python-flake8
-                         python-isort
+    (native-inputs (list python-isort
                          python-nbsphinx
                          python-pandas
                          python-pillow
@@ -1143,7 +1142,6 @@ (define-public python-pymanopt
                ((",!=1.12\\.\\*") "")))))))
     (propagated-inputs (list python-numpy python-scipy))
     (native-inputs (list python-autograd
-                         python-flake8
                          python-flake8-bugbear
                          python-isort
                          python-matplotlib
@@ -2152,8 +2150,7 @@ (define-public python-imbalanced-learn
                               (getcwd)))))))
     (propagated-inputs (list python-joblib python-numpy python-scikit-learn
                              python-scipy python-threadpoolctl))
-    (native-inputs (list python-flake8
-                         python-keras
+    (native-inputs (list python-keras
                          python-mypy
                          python-pandas
                          python-pytest
@@ -5321,7 +5318,6 @@ (define-public python-captum
      (list python-matplotlib python-numpy python-pytorch python-tqdm))
     (native-inputs (list jupyter
                          python-annoy
-                         python-flake8
                          python-flask
                          python-flask-compress
                          python-ipython
@@ -5842,8 +5838,7 @@ (define-public python-pyro-api
     (build-system python-build-system)
     (arguments '(#:tests? #false)) ;requires pyro
     (native-inputs
-     (list python-flake8
-           python-ipython
+     (list python-ipython
            python-pytest
            python-sphinx
            python-sphinx-rtd-theme))
@@ -5900,8 +5895,7 @@ (define-public python-linear-operator
                              python-pytorch
                              python-scipy
                              python-typeguard))
-    (native-inputs (list python-flake8
-                         python-flake8-print
+    (native-inputs (list python-flake8-print
                          python-pytest
                          python-setuptools
                          python-setuptools-scm
@@ -5932,7 +5926,6 @@ (define-public python-gpytorch
                              python-scikit-learn
                              python-scipy))
     (native-inputs (list python-coverage
-                         python-flake8
                          python-flake8-print
                          python-nbval
                          python-pytest
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index bf47489d34..7d28ef4b58 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -4116,6 +4116,7 @@ (define-public python-mutagen
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags '(list "--ignore=tests/quality/test_flake8.py")
        #:phases
        #~(modify-phases %standard-phases
            (add-before 'check 'remove-hypothesis-deadlines
@@ -4126,8 +4127,7 @@ (define-public python-mutagen
                  (("( +)@given" all spaces)
                   (string-append spaces "@settings(deadline=None)\n" all))))))))
     (native-inputs
-     (list python-flake8
-           python-hypothesis
+     (list python-hypothesis
            python-pytest
            python-setuptools
            python-wheel))
diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm
index 9d81b1c508..203e4909d6 100644
--- a/gnu/packages/protobuf.scm
+++ b/gnu/packages/protobuf.scm
@@ -502,7 +502,7 @@ (define-public python-pure-protobuf
         (base32 "15dp5pvazd0jx4wzzh79080ah7hkpd3axh40al9vhzs2hf3v90hx"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-flake8 python-pytest python-pytest-cov python-isort))
+     (list python-pytest python-pytest-cov python-isort))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
@@ -510,8 +510,6 @@ (define-public python-pure-protobuf
            (lambda _
              (invoke "pytest" "--cov-report" "term-missing" "--cov"
                      "pure_protobuf")
-             (invoke "flake8" "pure_protobuf" "tests"
-                     "--ignore=F541")
              (invoke "isort" "-rc" "-c" "pure_protobuf" "tests"))))))
     (home-page "https://pypi.org/project/pure-protobuf/")
     (synopsis "Protobuf implementation using dataclasses")
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 17c36189f7..c654f3f13d 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1605,7 +1605,6 @@ (define-public python-ovh
     (arguments (list #:tests? #f))      ; XXX: tests require networking
     (propagated-inputs (list python-requests))
     (native-inputs (list python-coverage
-                         python-flake8
                          python-isort
                          python-pytest
                          python-pytest-cov
@@ -1921,8 +1920,6 @@ (define-public python-furl
     (build-system python-build-system)
     (propagated-inputs
      (list python-six python-orderedmultidict))
-    (native-inputs
-     (list python-flake8))
     (home-page "https://github.com/gruns/furl")
     (synopsis "URL manipulation in Python")
     (description "Furl provides an easy-to-use alternative to the
@@ -1955,7 +1952,6 @@ (define-public python-httplib2
                  (("==") ">=")))))))
     (native-inputs
      (list python-cryptography
-           python-flake8
            python-future
            python-mock
            python-pytest
@@ -8583,7 +8579,7 @@ (define-public python-http-ece
     (propagated-inputs
      (list python-cryptography))
     (native-inputs
-     (list python-coverage python-flake8 python-mock python-nose))
+     (list python-coverage python-mock python-nose))
     (home-page "https://github.com/web-push-libs/encrypted-content-encoding")
     (synopsis "Encrypted Content Encoding for HTTP")
     (description
@@ -9048,8 +9044,7 @@ (define-public python-simple-websocket
      ;; Requires Internet access to resolve example.com
      (list #:test-flags '(list "--ignore=tests/test_client.py")))
     (propagated-inputs (list python-wsproto))
-    (native-inputs (list python-flake8
-                         python-pytest
+    (native-inputs (list python-pytest
                          python-pytest-cov
                          python-setuptools
                          python-tox
@@ -9660,8 +9655,7 @@ (define-public python-woob
            python-six
            python-unidecode))
     (native-inputs
-     (list python-coverage python-flake8 python-nose python-selenium
-           python-xunitparser))
+     (list python-coverage python-nose python-selenium python-xunitparser))
     (home-page "https://woob.tech/")
     (synopsis "Woob, Web Outside Of Browsers")
     (description "Woob is a collection of applications able to interact with
@@ -10321,8 +10315,7 @@ (define-public python-starsessions
            python-itsdangerous
            python-starlette))
     (native-inputs
-     (list python-flake8
-           python-httpx
+     (list python-httpx
            python-mypy
            python-poetry-core
            python-pytest
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f2c5f7fa63..52f7ebde3f 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -396,8 +396,7 @@ (define-public python-archspec
                              python-scikit-learn
                              python-tables
                              python-typing-extensions))
-    (native-inputs (list python-flake8
-                         python-isort
+    (native-inputs (list python-isort
                          python-poetry-core
                          python-pytest
                          python-pytest-cov))
@@ -1555,8 +1554,7 @@ (define-public python-colorful
         (base32 "0kyy9qhvrb5m9h8xmri7c88i0k1g5qc7017anw39gx44an7mn33y"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage python-flake8 python-pytest python-setuptools
-           python-wheel))
+     (list python-coverage python-pytest python-setuptools python-wheel))
     (propagated-inputs
      (list python-colorama))
     (home-page "http://github.com/timofurrer/colorful")
@@ -2926,7 +2924,7 @@ (define-public python-pymd4c
     (inputs
      (list md4c))
     (native-inputs
-     (list python-flake8 python-pkgconfig pkg-config))
+     (list python-pkgconfig pkg-config))
     (home-page "https://github.com/dominickpastore/pymd4c")
     (synopsis "Python bindings for MD4C")
     (description
@@ -12022,8 +12020,7 @@ (define-public python-imageio
     (propagated-inputs
      (list python-imageio-ffmpeg python-numpy python-pillow python-tifffile))
     (native-inputs
-     (list python-flake8
-           python-fsspec
+     (list python-fsspec
            python-pytest
            python-pytest-cov
            python-setuptools
@@ -12837,8 +12834,7 @@ (define-public python-importlib-resources
              (setenv "PYTHONPATH"
                      (string-append (getcwd) "/_custom_build")))))))
     (native-inputs
-     (list python-flake8
-           python-pytest
+     (list python-pytest
            python-pytest-black
            python-pytest-checkdocs
            python-pytest-cov
@@ -15110,8 +15106,7 @@ (define-public python-seaborn
            python-scipy
            python-statsmodels))
     (native-inputs
-     (list python-flake8
-           python-flit-core
+     (list python-flit-core
            python-ipykernel
            python-nbconvert
            python-numpydoc
@@ -28217,7 +28212,7 @@ (define-public python-yq
     (inputs
      (list python-argcomplete python-pyyaml python-xmltodict python-toml jq))
     (native-inputs
-     (list python-coverage python-flake8 python-setuptools-scm python-wheel))
+     (list python-coverage python-setuptools-scm python-wheel))
     (home-page "https://github.com/kislyuk/yq")
     (synopsis "Command-line YAML/XML processor")
     (description
@@ -29225,7 +29220,7 @@ (define-public python-update-checker
         (base32 "04yb5a9mi45ax50m2m0ih6gdvkk1j7gfmy83dd58i1f59axlabba"))))
     (build-system python-build-system)
     (propagated-inputs (list python-requests))
-    (native-inputs (list python-flake8 python-pytest))
+    (native-inputs (list python-pytest))
     (home-page "https://github.com/bboe/update_checker")
     (synopsis "Python module that will check for package updates")
     (description "This package provides a Python module that will check for
@@ -33558,7 +33553,6 @@ (define-public python-eliot
      (list python-boltons python-orjson python-pyrsistent python-zope-interface))
     (native-inputs
      (list python-coverage
-           python-flake8
            python-hypothesis
            python-pytest
            python-pytest-xdist
@@ -34346,7 +34340,7 @@ (define-public python-dateparser
      (list python-dateutil python-pytz python-regex python-ruamel.yaml
            python-tzlocal))
     (native-inputs
-     (list python-flake8 python-pytest python-parameterized tzdata-for-tests
+     (list python-pytest python-parameterized tzdata-for-tests
            python-setuptools python-wheel))
     (arguments
      `(#:phases
@@ -35772,8 +35766,7 @@ (define-public python-jinja2-cli
     (propagated-inputs
      (list python-jinja2))
     (native-inputs
-     (list python-flake8
-           python-jinja2
+     (list python-jinja2
            python-pytest
            python-setuptools
            python-wheel))
@@ -38326,7 +38319,7 @@ (define-public python-verspec
                (base32
                 "07n06wv85fm4vl1ird2mja0823js3x322wgs9gdnq1djjyk4ql64"))))
     (build-system python-build-system)
-    (native-inputs (list python-coverage python-flake8 python-mypy
+    (native-inputs (list python-coverage python-mypy
                          python-pretend python-pytest))
     (arguments
      `(#:phases (modify-phases %standard-

This message was truncated. Download the full message here.

Nicolas Graves wrote 2 weeks ago

[PATCH v5 12/48] gnu: u-boot-tools: Remove python-coverage native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-13-ngraves@ngraves.fr

* gnu/packages/bootloaders.scm (u-boot-tools):

[native-inputs]: Remove python-coverage.

[arguments]<#:phases>: Adapt patch phase.

Change-Id: I94394544079197b4a3f8c53cc0b3d78d1f5dc8be

---

gnu/packages/bootloaders.scm | 17 ++++-------------

1 file changed, 4 insertions(+), 13 deletions(-)

Toggle diff (44 lines)diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm
index 01497678cd..6c4e4f70f5 100644
--- a/gnu/packages/bootloaders.scm
+++ b/gnu/packages/bootloaders.scm
@@ -834,8 +834,7 @@ (define-public u-boot-tools
     (name "u-boot-tools")
     (native-inputs
      (modify-inputs (package-native-inputs u-boot)
-       (prepend python-coverage
-                python-filelock
+       (prepend python-filelock
                 python-pycryptodomex
                 python-pytest
                 python-pytest-xdist)))
@@ -851,14 +850,6 @@ (define-public u-boot-tools
                (("/bin/false") (which "false")))
              (substitute* "tools/dtoc/fdt_util.py"
                (("'cc'") "'gcc'"))
-             (substitute* "tools/u_boot_pylib/test_util.py"
-               ;; python3-coverage is simply called coverage in guix.
-               (("python3-coverage") "coverage")
-
-               ;; Don't require 100% coverage since it's brittle and can
-               ;; fail with newer versions of coverage or dependencies.
-               (("raise ValueError\\('Test coverage failure'\\)")
-                "print('Continuing anyway since Guix does not care :O')"))
              (substitute* "test/run"
                ;; Make it easier to find test failures.
                (("#!/bin/bash") "#!/bin/bash -x")
@@ -871,9 +862,9 @@ (define-public u-boot-tools
                 "# run_test \"sandbox_noinst\"")
                (("run_test \"sandbox_vpl\"")
                 "# run_test \"sandbox_vpl\"")
-               ;; FIXME: code coverage not working
-               (("run_test \"binman code coverage\"")
-                "# run_test \"binman code coverage\"")
+               ;; Disable code coverage tests.
+               (("run_test \"(\\w+) code coverage\"" all)
+                (string-append "# " all))
                ;; This test would require internet access.
                (("\\./tools/buildman/buildman") (which "true")))
              (substitute* "test/py/tests/test_sandbox_exit.py"
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 13/48] gnu: python-aiosqlite: Remove python-coverage native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-14-ngraves@ngraves.fr

* gnu/packages/databases.scm (python-aiosqlite):

[arguments]<#:phases>: Adapt check phase.

[native-inputs]: Remove python-coverage.

Change-Id: I165d174426022f0603223e3def91ffe280f15899

---

gnu/packages/databases.scm | 5 +----

1 file changed, 1 insertion(+), 4 deletions(-)

Toggle diff (19 lines)diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index fd77fa940c..3b8d1d9d23 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -4141,11 +4141,8 @@ (define-public python-aiosqlite
                         (replace 'check
                           (lambda* (#:key tests? #:allow-other-keys)
                             (when tests?
-                              (invoke "python" "-m" "coverage" "run" "-m"
-                                      "aiosqlite.tests")
-                              (invoke "python" "-m" "coverage" "report")))))))
+                              (invoke "python" "-m" "aiosqlite.tests")))))))
     (native-inputs (list python-flit-core
-                         python-coverage
                          python-mypy))
     (home-page "https://github.com/jreese/aiosqlite")
     (synopsis
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 08/48] build-system/pyproject: Remove python-coverage input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-9-ngraves@ngraves.fr

* gnu/packages/astronomy.scm (python-asdf-astropy,
python-poliastro)
* gnu/packages/bioinformatics.scm (python-ega-download-client,
python-scikit-bio, python-cooler)
* gnu/packages/check.scm (python-pytest-randomly,
python-pytest-flakes, python-aiounittest)
* gnu/packages/cpp.scm (cpplint)
* gnu/packages/django.scm (python-django-haystack)
* gnu/packages/engineering.scm (python-scikit-rf)
* gnu/packages/geo.scm (python-geopy)
* gnu/packages/gpodder.scm (gpodder)
* gnu/packages/graph.scm (python-graphtools, python-pygsp)
* gnu/packages/jupyter.scm (python-jupyter-packaging)
* gnu/packages/machine-learning.scm (onnx, onnx-optimizer,
python-lightning-utilities, python-pytorch-lightning,
python-torchmetrics, python-gpytorch)
* gnu/packages/music.scm (python-pylast)
* gnu/packages/package-management.scm (python-anaconda-client, conda)
* gnu/packages/python-check.scm (python-vcrpy,
python-re-assert)
* gnu/packages/python-compression.scm (python-multivolumefile,
python-pybcj, python-bcj-cffi, python-pyppmd, python-ppmd-cffi,
python-py7zr)
* gnu/packages/python-web.scm (python-ovh, python-zope-interface,
python-zope-hookable, python-url, python-transaction, python-sanic,
python-woob, python-flask-combo-jsonapi)
* gnu/packages/python-xyz.scm (python-affine, python-colorful,
python-lunr, python-mdit-py-plugins, python-bidict, python-sh,
python-can, python-jsonargparse, python-pyjwt,
python-virtualenv-clone, python-pikepdf, python-tasklogger,
python-notebook, python-structlog, binwalk, python-argcomplete,
python-attrs, python-yq, python-stone, python-identify,
python-nodeenv, python-forbiddenfruit, python-eliot,
python-pem, python-scikit-build, python-minikanren, python-verspec,
python-mike)
* gnu/packages/simulation.scm (python-dolfin-adjoint)
* gnu/packages/statistics.scm (python-emcee, python-rpy2)
* gnu/packages/syndication.scm (rtv, tuir)
* gnu/packages/terminals.scm (python-halo, python-log-symbols,
python-spinners)
* gnu/packages/textutils.scm (python-panflute)
* gnu/packages/version-control.scm (pre-commit)
* gnu/packages/web.scm (python-httpretty)
* gnu/packages/xml.scm (python-xmltodict)
[native-inputs]: Remove python-coverage.

* gnu/packages/android.scm (python-androguard):
  [native-inputs]: Remove python-coverage.
  [arguments]<#:phases>: Adapt 'check phase replacement.
---
 gnu/packages/android.scm            |  6 ++--
 gnu/packages/astronomy.scm          |  6 ++--
 gnu/packages/bioinformatics.scm     |  8 ++---
 gnu/packages/check.scm              |  7 ++--
 gnu/packages/cpp.scm                |  3 +-
 gnu/packages/django.scm             |  3 +-
 gnu/packages/engineering.scm        |  3 +-
 gnu/packages/gpodder.scm            |  3 +-
 gnu/packages/graph.scm              |  3 +-
 gnu/packages/jupyter.scm            |  2 +-
 gnu/packages/machine-learning.scm   | 12 ++-----
 gnu/packages/music.scm              |  3 +-
 gnu/packages/package-management.scm |  6 ++--
 gnu/packages/python-check.scm       |  2 +-
 gnu/packages/python-compression.scm | 14 +++-----
 gnu/packages/python-web.scm         | 18 ++++------
 gnu/packages/python-xyz.scm         | 55 ++++++++++-------------------
 gnu/packages/simulation.scm         |  1 -
 gnu/packages/statistics.scm         |  6 ++--
 gnu/packages/syndication.scm        |  4 +--
 gnu/packages/terminals.scm          |  9 ++---
 gnu/packages/textutils.scm          |  1 -
 gnu/packages/version-control.scm    |  1 -
 gnu/packages/web.scm                |  1 -
 gnu/packages/xml.scm                |  2 +-
 25 files changed, 59 insertions(+), 120 deletions(-)

Toggle diff (415 lines)diff --git a/gnu/packages/android.scm b/gnu/packages/android.scm
index bafca18abe..58d3815d2a 100644
--- a/gnu/packages/android.scm
+++ b/gnu/packages/android.scm
@@ -1076,11 +1076,9 @@ (define-public python-androguard
          (replace 'check
            ;; Adapted from .travis.yml
            (lambda _
-             (invoke "nosetests" "--with-coverage" "--with-timer"
-                     "--timer-top-n" "50"))))))
+             (invoke "nosetests" "--with-timer" "--timer-top-n" "50"))))))
     (native-inputs
-     (list python-codecov python-coverage python-mock python-nose
-           python-nose-timer))
+     (list python-codecov python-mock python-nose python-nose-timer))
     (propagated-inputs
      (list python-asn1crypto
            python-colorama
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index a3aedac986..8c47e7c61c 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1729,8 +1729,7 @@ (define-public python-asdf-astropy
           (add-before 'check 'set-home-env
             (lambda _ (setenv "HOME" "/tmp"))))))
     (native-inputs
-     (list python-coverage
-           python-h5py
+     (list python-h5py
            python-pandas
            python-pytest
            python-pytest-astropy
@@ -4630,8 +4629,7 @@ (define-public python-poliastro
             (lambda _
               (setenv "HOME" "/tmp"))))))
     (native-inputs
-     (list python-coverage
-           python-hypothesis
+     (list python-hypothesis
            python-mypy
            python-flit-core
            python-pytest
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bda5ab3a8f..12a18cbf80 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3701,8 +3701,7 @@ (define-public python-ega-download-client
     (propagated-inputs (list python-htsget python-psutil python-requests
                              python-tqdm python-urllib3))
     (native-inputs
-     (list python-coverage
-           python-mock
+     (list python-mock
            python-pyfakefs
            python-pytest
            python-responses
@@ -6462,7 +6461,7 @@ (define-public python-scikit-bio
            python-requests
            python-scipy))
     (native-inputs
-     (list python-coverage python-pytest))
+     (list python-pytest))
     (home-page "https://scikit-bio.org")
     (synopsis "Data structures, algorithms and educational resources for bioinformatics")
     (description
@@ -19937,8 +19936,7 @@ (define-public python-cooler
            python-scipy
            python-simplejson))
     (native-inputs
-     (list python-coverage
-           python-hatchling
+     (list python-hatchling
            python-isort
            python-pytest
            python-pytest-cov))
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index baa3a2f4c3..4263329559 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -1972,8 +1972,7 @@ (define-public python-pytest-randomly
                          "not reordered "
                          "and not test_it_runs_before_stepwise "
                          "and not test_entrypoint_injection"))))))))
-    (native-inputs (list python-coverage
-                         python-factory-boy
+    (native-inputs (list python-factory-boy
                          python-faker
                          python-numpy
                          python-pytest-xdist))
@@ -3162,7 +3161,7 @@ (define-public python-pytest-flakes
       #:test-flags
       '(list "-k" "not test_syntax_error")))
     (native-inputs
-     (list python-coverage python-pytest python-setuptools python-wheel))
+     (list python-pytest python-setuptools python-wheel))
     (propagated-inputs
      (list python-pyflakes))
     (home-page "https://github.com/fschulze/pytest-flakes")
@@ -4194,7 +4193,7 @@ (define-public python-aiounittest
                       #t)))))
     (propagated-inputs (list python-wrapt))
     (native-inputs
-     (list python-coverage python-nose))
+     (list python-nose))
     (home-page
      "https://github.com/kwarunek/aiounittest")
     (synopsis "Test asyncio code more easily")
diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index a456bf3b51..21aa13b73c 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -1399,8 +1399,7 @@ (define-public cpplint
                    (setenv "GUIX_PYTHONPATH"
                            (getenv "TMP_PYTHONPATH")))))))
     (native-inputs
-     (list python-coverage
-           python-pytest
+     (list python-pytest
            python-pytest-cov
            python-pytest-runner
            python-setuptools
diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index cb9df0d2df..1a66dc8b0b 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -510,8 +510,7 @@ (define-public python-django-haystack
      (list python-django python-packaging))
     ;; (inputs (list gdal)) ; it's optional, tests fail when provided
     (native-inputs
-     (list python-coverage
-           python-dateutil
+     (list python-dateutil
            python-geopy
            python-pysolr
            python-requests
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index 3882a35d6b..cc84a760e9 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -2964,8 +2964,7 @@ (define-public python-scikit-rf
                              python-pyqtgraph
                              python-qtpy
                              python-scipy))
-    (native-inputs (list python-coverage
-                         python-nbval
+    (native-inputs (list python-nbval
                          python-networkx
                          python-pytest
                          python-pytest-cov
diff --git a/gnu/packages/gpodder.scm b/gnu/packages/gpodder.scm
index c3e1c9b496..57e14ee93f 100644
--- a/gnu/packages/gpodder.scm
+++ b/gnu/packages/gpodder.scm
@@ -65,7 +65,6 @@ (define-public gpodder
     (build-system python-build-system)
     (native-inputs
      (list intltool
-           python-coverage
            python-minimock
            python-pytest
            python-pytest-cov
@@ -169,7 +168,7 @@ (define-public python-mygpoclient
          "05hmjdb73m7vl6lzvh58bnliy4227pv8hprwfka0bg19cnvgpyf5"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-coverage python-minimock python-nose python-pytest))
+     (list python-minimock python-nose python-pytest))
     (arguments
      '(#:phases
        (modify-phases %standard-phases
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 57c4bd05ed..a11667b678 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -482,7 +482,6 @@ (define-public python-graphtools
     (native-inputs
      (list util-linux ;for lscpu
            python-anndata
-           python-coverage
            python-coveralls
            python-nose
            python-nose2
@@ -570,7 +569,7 @@ (define-public python-pygsp
                 "")))))))
     (propagated-inputs (list python-numpy python-scikit-image python-scipy))
     (native-inputs
-     (list python-coverage python-coveralls python-pytest))
+     (list python-coveralls python-pytest))
     (home-page "https://github.com/epfl-lts2/pygsp")
     (synopsis "Graph Signal Processing in Python")
     (description "The PyGSP is a Python package to ease signal processing on
diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm
index f47d8de295..70d894939c 100644
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -519,7 +519,7 @@ (define-public python-jupyter-packaging
      (list python-deprecation python-packaging python-setuptools
            python-tomlkit python-wheel))
     (native-inputs
-     (list python-pypa-build python-coverage python-pytest
+     (list python-pypa-build python-pytest
            python-pytest-cov python-pytest-mock))
     (home-page "https://jupyter.org")
     (synopsis "Jupyter packaging utilities")
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 65cb08e2f3..2caa64cc08 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1589,7 +1589,6 @@ (define args
       (list cmake-minimal
             googletest
             pybind11
-            python-coverage
             python-fb-re2
             python-parameterized
             python-pytest
@@ -1667,8 +1666,7 @@ (define-public onnx-optimizer
                              " and not test_fuse_transpose")))))))))
     (native-inputs
      (append
-      (list cmake-minimal python-pytest python-pytest-runner
-            python-coverage)
+      (list cmake-minimal python-pytest python-pytest-runner)
       (filter
        (lambda (pkg)
          (member (or (%current-target-system)
@@ -5279,8 +5277,7 @@ (define-public python-lightning-utilities
                 "016zikn39apig3y6xyipw34w0w02c73z483radddbf68ivpjgz3r"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage
-           python-setuptools
+     (list python-setuptools
            python-wheel))
     (propagated-inputs
      (list python-importlib-metadata
@@ -5471,7 +5468,6 @@ (define-public python-pytorch-lightning
       (native-inputs
        (list python-aiohttp
              python-cloudpickle
-             python-coverage
              python-flaky
              python-pympler
              python-pytest
@@ -5509,7 +5505,6 @@ (define-public python-torchmetrics
            python-lightning-utilities))
     (native-inputs
      (list python-cloudpickle
-           python-coverage
            python-fire
            python-mir-eval
            python-mypy
@@ -5925,8 +5920,7 @@ (define-public python-gpytorch
                              python-mpmath
                              python-scikit-learn
                              python-scipy))
-    (native-inputs (list python-coverage
-                         python-flake8-print
+    (native-inputs (list python-flake8-print
                          python-nbval
                          python-pytest
                          python-setuptools
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 7d28ef4b58..ae2afb8441 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -4229,8 +4229,7 @@ (define-public python-pylast
     ;; https://github.com/pylast/pylast/issues/105
     (arguments '(#:tests? #f))
     (native-inputs
-     (list python-coverage python-pytest python-flaky python-pyyaml
-           python-setuptools-scm))
+     (list python-pytest python-flaky python-pyyaml python-setuptools-scm))
     (home-page "https://github.com/pylast/pylast")
     (synopsis "Python interface to Last.fm and Libre.fm")
     (description "A Python interface to Last.fm and other API-compatible
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 7b3756d0aa..7605e4073d 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -1107,8 +1107,7 @@ (define-public python-anaconda-client
            python-requests
            python-setuptools))
     (native-inputs
-     (list python-coverage
-           python-dateutil
+     (list python-dateutil
            python-freezegun
            python-mock
            python-pillow
@@ -1296,8 +1295,7 @@ (define-public conda
            ;; XXX: This is dragged in by libarchive and is needed at runtime.
            zstd))
     (native-inputs
-     (list python-coverage
-           python-flaky
+     (list python-flaky
            python-pytest-cov
            python-pytest-timeout
            python-pytest-xprocess
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index c969499521..ebfdd7312e 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -1625,7 +1625,7 @@ (define-public python-re-assert
            (lambda _
              (invoke "pytest" "-vv"))))))
     (native-inputs
-     (list python-covdefaults python-coverage python-pytest))
+     (list python-covdefaults python-pytest))
     (propagated-inputs
      (list python-regex))
     (home-page "https://github.com/asottile/re-assert")
diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm
index 5b994d408f..dfe819733e 100644
--- a/gnu/packages/python-compression.scm
+++ b/gnu/packages/python-compression.scm
@@ -163,7 +163,6 @@ (define-public python-multivolumefile
     (build-system pyproject-build-system)
     (native-inputs
      (list python-setuptools-scm
-           python-coverage
            python-coveralls
            python-hypothesis
            python-pyannotate
@@ -306,8 +305,7 @@ (define-public python-pybcj
     (build-system pyproject-build-system)
     (propagated-inputs (list python-importlib-metadata))
     (native-inputs
-     (list python-coverage
-           python-hypothesis
+     (list python-hypothesis
            python-pytest
            python-pytest-cov
            python-setuptools-scm
@@ -340,8 +338,7 @@ (define-public python-bcj-cffi
     (propagated-inputs
      (list python-cffi python-toml python-setuptools-scm))
     (native-inputs
-     (list python-setuptools python-coverage python-pytest
-           python-pytest-cov))
+     (list python-setuptools python-pytest python-pytest-cov))
     (home-page "https://github.com/miurahr/bcj-cffi")
     (synopsis "Branch / Call /Jump CFFI library in Python")
     (description "This package provides an implementation of the Branch / Call /
@@ -466,8 +463,7 @@ (define-public python-pyppmd
                 "03w4x26mar0ha73c3v39psn1i0k6xrzwmaxfsxysic73jz99np07"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage
-           python-hypothesis
+     (list python-hypothesis
            python-pytest
            python-pytest-benchmark
            python-pytest-cov
@@ -500,7 +496,6 @@ (define-public python-ppmd-cffi
     (native-inputs
      (list python-hypothesis
            python-setuptools-scm
-           python-coverage
            python-pytest
            python-pytest-cov))
     (home-page "https://github.com/miurahr/ppmd")
@@ -535,8 +530,7 @@ (define-public python-py7zr
            python-pyzstd
            python-texttable))
     (native-inputs
-     (list python-coverage
-           python-setuptools
+     (list python-setuptools
            python-coveralls
            python-libarchive-c
            python-py-cpuinfo
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index c654f3f13d..6281ca5c8c 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1604,8 +1604,7 @@ (define-public python-ovh
     (build-system pyproject-build-system)
     (arguments (list #:tests? #f))      ; XXX: tests require networking
     (propagated-inputs (list python-requests))
-    (native-inputs (list python-coverage
-                         python-isort
+    (native-inputs (list python-isort
                          python-pytest
                          python-pytest-cov
                          python-setuptools
@@ -3855,8 +3854,7 @@ (define-public python-zope-interface
     (build-system python-build-system)
     (arguments '(#:tests? #f))  ; test suite can't find python-zope-testing
     (native-inputs
-     (list python-coverage python-nose python-zope-event
-           python-zope-testing))
+     (list python-nose python-zope-event python-zope-testing))
     (home-page "https://github.com/zopefoundation/zope.interface")
     (synopsis "Python implementation of the \"design by contract\"
 methodology")
@@ -4152,7 +4150,7 @@ (define-public python-zope-hookable
           "0hc82lfr7bk53nvbxvjkibkarngyrzgfk2i6bg8wshl0ly0pdl19"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-coverage python-zope-testing))
+     (list python-zope-testing))
     (home-page "https://github.com/zopefoundation/zope.hookable")
     (synopsis "Zope hookable")
     (description "This package supports the efficient creation of hookable
@@ -5611,7 +5609,7 @@ (define-public python-url
     (propagated-inputs
      (list python-publicsuffix))
     (native-inputs
-     (list python-coverage python-nose))
+     (list python-nose))
     (arguments
      `(#:tests? #f)) ; FIXME: tests fail with "ImportError: No module named 'tests'"
     (home-page "https://g

This message was truncated. Download the full message here.

Nicolas Graves wrote 2 weeks ago

[PATCH v5 14/48] gnu: python-openid: Remove python-coverage native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-15-ngraves@ngraves.fr

* gnu/packages/python-web.scm (python-openid):

[native-inputs]: Remove python-coverage.

[arguments]<#:phases>: Rewrite check phase.

Change-Id: Id4ea5abc531f5fd84b60ff22407eb608f1e6ac29

---

gnu/packages/python-web.scm | 17 +++++++++--------

1 file changed, 9 insertions(+), 8 deletions(-)

Toggle diff (33 lines)diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 8dd8a58217..4b38c23200 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -3179,17 +3179,18 @@ (define-public python-openid
          "1bxf9a3ny1js422j962zfzl4a9dhj192pvai05whn7j0iy9gdyrk"))))
     (build-system python-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-        (replace 'check
-          (lambda* (#:key tests? #:allow-other-keys)
-            (when tests?
-              (invoke "coverage" "run" "-m"
-                      "unittest" "openid.test.test_suite")))))))
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (if tests?
+                  (invoke "python" "-m" "unittest" "openid.test.test_suite")
+                  (format #t "test suite not run~%")))))))
     (propagated-inputs
      (list python-defusedxml))
     (native-inputs
-     (list python-coverage python-psycopg2 python-django))
+     (list python-psycopg2 python-django))
     (home-page "https://github.com/necaris/python3-openid")
     (synopsis "OpenID support for servers and consumers")
     (description "This library provides OpenID authentication for Python, both
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 16/48] build-system/pyproject: Remove python-pycodestyle native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-17-ngraves@ngraves.fr

* gnu/packages/bioinformatics.scm (python-screed)
* gnu/packages/python-science.scm (python-scipy)
* gnu/packages/python-xyz.scm (python-lsp-jsonrpc, python-diff-cover,
python-fuzzywuzzy, python-jsonargparse, python-lsp-server,
python-orderedmultidict, python-stem)
[native-inputs]: Remove python-pycodestyle.
---
 gnu/packages/bioinformatics.scm |  1 -
 gnu/packages/python-science.scm |  1 -
 gnu/packages/python-xyz.scm     | 14 +++++---------
 3 files changed, 5 insertions(+), 11 deletions(-)

Toggle diff (93 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 12a18cbf80..1cec139812 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11563,7 +11563,6 @@ (define-public python-screed
     (build-system pyproject-build-system)
     (native-inputs
      (list python-importlib-resources
-           python-pycodestyle
            python-pytest
            python-pytest-cov
            python-setuptools
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index c4e577af9c..83e66572e3 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -462,7 +462,6 @@ (define-public python-scipy
            python-doit
            python-hypothesis
            python-pooch
-           python-pycodestyle
            python-pydevtool
            python-pytest
            python-pytest-cov
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index c12b4d74f6..446cba77bb 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -5206,7 +5206,6 @@ (define-public python-jsonargparse
            python-typeshed-client))
     (native-inputs
      (list python-attrs
-           python-pycodestyle
            python-pydantic
            python-pytest
            python-pytest-subtests
@@ -8686,8 +8685,7 @@ (define-public python-lsp-jsonrpc
          "04n95h0cqnsrdyh1gv0abh2i5ynyrq2wfqpppx9djp7mxr9y9226"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-pycodestyle
-           python-pyflakes
+     (list python-pyflakes
            python-pytest
            python-pytest-cov
            python-setuptools
@@ -9051,7 +9049,6 @@ (define-public python-lsp-server
            python-jedi
            python-lsp-jsonrpc
            python-pluggy
-           python-pycodestyle
            python-pydocstyle
            python-ujson
            python-whatthepatch
@@ -11034,7 +11031,7 @@ (define-public python-orderedmultidict
     (propagated-inputs
      (list python-six))
     (native-inputs
-     (list python-flake8 python-pycodestyle python-setuptools python-wheel))
+     (list python-flake8 python-setuptools python-wheel))
     (home-page "https://github.com/gruns/orderedmultidict")
     (synopsis "Python Ordered Multivalue Dictionary - omdict")
     (description "This package contains a library for ordered multivalue
@@ -23902,7 +23899,7 @@ (define-public python-stem
              (invoke "./run_tests.py" "--unit")
              #t)))))
     (native-inputs
-     (list python-mock python-pycodestyle python-pyflakes))
+     (list python-mock python-pyflakes))
     (home-page "https://stem.torproject.org/")
     (synopsis
      "Python controller library that allows applications to interact with Tor")
@@ -26214,8 +26211,7 @@ (define-public python-diff-cover
       ;; Dropp check of flake8 in tests.
       #~(list "-k" "not test_file_does_not_exist")))
     (native-inputs
-     (list python-pycodestyle
-           python-poetry-core
+     (list python-poetry-core
            python-pyflakes
            python-pylint
            python-pytest
@@ -32812,7 +32808,7 @@ (define-public python-fuzzywuzzy
          "1s00zn75y2dkxgnbw8kl8dw4p1mc77cv78fwfa4yb0274s96w0a5"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-hypothesis python-pycodestyle python-pytest))
+     (list python-hypothesis python-pytest))
     (propagated-inputs
      (list python-levenshtein))
     (home-page "https://github.com/seatgeek/fuzzywuzzy")
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 17/48] gnu: python-re-assert: Remove python-covdefaults native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-18-ngraves@ngraves.fr

* gnu/packages/python-check.scm (python-re-assert):

[native-inputs]: Remove python-covdefaults.

Change-Id: Ib30c58b69aef7f255e5893ae6f9a33bdf41ac85d

---

gnu/packages/python-check.scm | 2 +-

1 file changed, 1 insertion(+), 1 deletion(-)

Toggle diff (15 lines)diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 27abc67c58..e57438b2ea 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -1625,7 +1625,7 @@ (define-public python-re-assert
            (lambda _
              (invoke "pytest" "-vv"))))))
     (native-inputs
-     (list python-covdefaults python-pytest))
+     (list python-pytest))
     (propagated-inputs
      (list python-regex))
     (home-page "https://github.com/asottile/re-assert")
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 19/48] build-system/pyproject: Remove python-codecov native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-20-ngraves@ngraves.fr

* gnu/packages/android.scm (python-androguard)
* gnu/packages/astronomy.scm (python-wiimatch, python-tweakwcs)
* gnu/packages/geo.scm (python-geopandas)
* gnu/packages/jupyter.scm (python-papermill)
* gnu/packages/python-xyz.scm (python-can, python-ddlparse)
[native-inputs]: Remove python-codecov.
---
 gnu/packages/android.scm    | 2 +-
 gnu/packages/astronomy.scm  | 9 +++++----
 gnu/packages/geo.scm        | 3 +--
 gnu/packages/jupyter.scm    | 1 -
 gnu/packages/python-xyz.scm | 4 +---
 5 files changed, 8 insertions(+), 11 deletions(-)

Toggle diff (90 lines)diff --git a/gnu/packages/android.scm b/gnu/packages/android.scm
index 58d3815d2a..aa806c475e 100644
--- a/gnu/packages/android.scm
+++ b/gnu/packages/android.scm
@@ -1078,7 +1078,7 @@ (define-public python-androguard
            (lambda _
              (invoke "nosetests" "--with-timer" "--timer-top-n" "50"))))))
     (native-inputs
-     (list python-codecov python-mock python-nose python-nose-timer))
+     (list python-mock python-nose python-nose-timer))
     (propagated-inputs
      (list python-asn1crypto
            python-colorama
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 8c47e7c61c..6b31414940 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -6703,8 +6703,7 @@ (define-public python-tweakwcs
            python-stsci-imagestats
            python-stsci-stimage))
     (native-inputs
-     (list python-codecov
-           python-pytest
+     (list python-pytest
            python-pytest-cov
            python-scipy
            python-setuptools
@@ -6828,8 +6827,10 @@ (define-public python-wiimatch
                 "15kq7z30m9i286ncs9xvpaq3dq1p5fa47jz21prq146qwr7j6dm8"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-numpy python-scipy))
-    (native-inputs (list python-codecov python-pytest python-pytest-cov
-                         python-pytest-doctestplus python-setuptools-scm
+    (native-inputs (list python-pytest
+                         python-pytest-cov
+                         python-pytest-doctestplus
+                         python-setuptools-scm
                          python-wheel))
     (home-page "https://github.com/spacetelescope/wiimatch")
     (synopsis
diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 54f96fef2b..cf8c140040 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -1075,8 +1075,7 @@ (define-public python-geopandas
             python-pyproj
             python-shapely))
     (native-inputs
-      (list python-codecov
-            python-pytest
+      (list python-pytest
             python-pytest-cov
             python-pytest-xdist
             python-setuptools
diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm
index a9f57b2ccc..1ee99c8602 100644
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -1160,7 +1160,6 @@ (define-public python-papermill
                          python-botocore
                          python-bumpversion
                          python-check-manifest
-                         python-codecov
                          python-ipython
                          python-ipywidgets
                          python-moto
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 4993783ab8..cd20064c95 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4294,7 +4294,6 @@ (define-public python-can
            python-setuptools))
     (native-inputs
      (list ;; python-canalystii ; Not packed yet
-           python-codecov
            python-future
            python-hypothesis
            python-mock
@@ -6431,8 +6430,7 @@ (define-public python-ddlparse
         (base32 "1nh8m6rxslwk05daxshxmgk41qfp18yynydba49b13l4m8dnh634"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-codecov
-           python-pytest
+     (list python-pytest
            python-pytest-cov
            python-setuptools
            python-tox
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 18/48] build-system/pyproject: Remove python-covdefaults native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-19-ngraves@ngraves.fr

* gnu/packages/python-web.scm (python-devpi-process)
* gnu/packages/python-xyz.scm (python-pyproject-api, python-platformdirs)
* gnu/packages/version-control.scm (pre-commit)
[native-inputs]: Remove python-covdefaults.
---
 gnu/packages/python-web.scm      | 1 -
 gnu/packages/python-xyz.scm      | 4 +---
 gnu/packages/version-control.scm | 1 -
 3 files changed, 1 insertion(+), 5 deletions(-)

Toggle diff (48 lines)diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index d7aa6f3b02..76e13b3af2 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -260,7 +260,6 @@ (define-public python-devpi-process
                              python-typing-extensions))
     (native-inputs
      (list nss-certs-for-test
-           python-covdefaults
            python-hatchling
            python-hatch-vcs
            python-httpx
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 446cba77bb..4993783ab8 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -23105,8 +23105,7 @@ (define-public python-pyproject-api
                    ;; This fails because wheel shows up in requirements
                    " and not test_setuptools_get_requires_for_build_wheel"))))
     (native-inputs
-     (list python-covdefaults
-           python-hatch-vcs
+     (list python-hatch-vcs
            python-hatchling
            python-pytest
            python-pytest-cov
@@ -37182,7 +37181,6 @@ (define-public python-platformdirs
     (build-system pyproject-build-system)
     (native-inputs
      (list python-appdirs
-           python-covdefaults
            python-hatchling
            python-hatch-vcs
            python-pytest
diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 14acec2e84..8fea330dbb 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -2566,7 +2566,6 @@ (define-public pre-commit
               (invoke "git" "config" "--global" "user.email" "you@example.com"))))))
     (native-inputs
      (list git-minimal/pinned
-           python-covdefaults
            python-distlib
            python-pytest
            python-pytest-env
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 15/48] build-system/pyproject: Remove python-coveralls native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-16-ngraves@ngraves.fr

* gnu/packages/django.scm (python-django-pipeline)[native-inputs]:

Remove python-coveralls.

* gnu/packages/geo.scm (python-cartopy)[native-inputs]: Remove

python-coveralls.

* gnu/packages/graph.scm (python-graphtools,

python-pygsp)[native-inputs]: Remove python-coveralls.

* gnu/packages/python-compression.scm (python-multivolumefile,

python-py7zr)[native-inputs]: Remove python-coveralls.

* gnu/packages/python-science.scm (python-trimesh)[native-inputs]:

Remove python-coveralls.

* gnu/packages/python-web.scm (python-flask-combo-jsonapi,

python-rangehttpserver) [native-inputs]: Remove python-coveralls.

* gnu/packages/python-xyz.scm (python-affine, python-ddlparse,

python-tasklogger, python-minikanren)

[native-inputs]: Remove python-coveralls.

* gnu/packages/syndication.scm (rtv, tuir)[native-inputs]: Remove

python-coveralls.

* gnu/packages/telegram.scm (tgcli)[native-inputs]: Remove

python-coveralls.

---

gnu/packages/django.scm | 3 +--

gnu/packages/graph.scm | 3 +--

gnu/packages/python-compression.scm | 2 --

gnu/packages/python-science.scm | 3 +--

gnu/packages/python-web.scm | 6 ++----

gnu/packages/python-xyz.scm | 8 +++-----

gnu/packages/syndication.scm | 4 +---

gnu/packages/telegram.scm | 3 +--

8 files changed, 10 insertions(+), 22 deletions(-)

Toggle diff (171 lines)diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index 1a66dc8b0b..b7f2e23f9d 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -992,8 +992,7 @@ (define-public python-django-pipeline
      (list python-jsmin
            python-css-html-js-minify))
     (native-inputs
-     (list python-coveralls
-           python-django
+     (list python-django
            python-setuptools
            python-setuptools-scm
            python-tox
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index a11667b678..f45ab42f0b 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -482,7 +482,6 @@ (define-public python-graphtools
     (native-inputs
      (list util-linux ;for lscpu
            python-anndata
-           python-coveralls
            python-nose
            python-nose2
            python-pandas
@@ -569,7 +568,7 @@ (define-public python-pygsp
                 "")))))))
     (propagated-inputs (list python-numpy python-scikit-image python-scipy))
     (native-inputs
-     (list python-coveralls python-pytest))
+     (list python-pytest))
     (home-page "https://github.com/epfl-lts2/pygsp")
     (synopsis "Graph Signal Processing in Python")
     (description "The PyGSP is a Python package to ease signal processing on
diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm
index dfe819733e..b2e62e1d49 100644
--- a/gnu/packages/python-compression.scm
+++ b/gnu/packages/python-compression.scm
@@ -163,7 +163,6 @@ (define-public python-multivolumefile
     (build-system pyproject-build-system)
     (native-inputs
      (list python-setuptools-scm
-           python-coveralls
            python-hypothesis
            python-pyannotate
            python-pytest
@@ -531,7 +530,6 @@ (define-public python-py7zr
            python-texttable))
     (native-inputs
      (list python-setuptools
-           python-coveralls
            python-libarchive-c
            python-py-cpuinfo
            python-pyannotate
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 2e643f1740..c4e577af9c 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -978,8 +978,7 @@ (define-public python-trimesh
           ;; module 'trimesh' has no attribute '__main__'.
           (delete 'sanity-check))))
     (native-inputs
-     (list python-coveralls
-           python-pyinstrument
+     (list python-pyinstrument
            python-pytest))
     (propagated-inputs
      (list ;; python-cascadio       ; not packed yet, optional
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 4b38c23200..d7aa6f3b02 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -8215,8 +8215,7 @@ (define-public python-rangehttpserver
        (sha256
         (base32 "1dx533fsbq1mbz3by7qkm5bh2c253nwvm8214pqbwbfq07kqkwf2"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-coveralls python-pytest
-                         python-setuptools python-wheel))
+    (native-inputs (list python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/danvk/RangeHTTPServer")
     (synopsis "SimpleHTTPServer with support for range requests")
     (description
@@ -9699,8 +9698,7 @@ (define-public python-flask-combo-jsonapi
            python-simplejson
            python-six))
     (native-inputs
-     (list python-coveralls
-           python-pytest
+     (list python-pytest
            python-pytest-runner))
     (home-page "https://github.com/AdCombo/flask-combo-jsonapi")
     (synopsis "Flask extension to quickly create JSON:API 1.0 REST Web APIs")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index fc49715718..c12b4d74f6 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1387,7 +1387,7 @@ (define-public python-affine
                (base32
                 "1shyvajayyzbkp9dihb4mz835jnkp0kqqbyjfqci6v43da6q2kd2"))))
     (build-system pyproject-build-system)
-    (propagated-inputs (list python-coveralls python-pydocstyle
+    (propagated-inputs (list python-pydocstyle
                              python-pytest python-pytest-cov))
     (native-inputs (list python-flit-core))
     (home-page "https://github.com/rasterio/affine")
@@ -6433,7 +6433,6 @@ (define-public python-ddlparse
     (build-system pyproject-build-system)
     (native-inputs
      (list python-codecov
-           python-coveralls
            python-pytest
            python-pytest-cov
            python-setuptools
@@ -17386,7 +17385,7 @@ (define-public python-tasklogger
         (base32 "1901mibcp6aiyjy8afnybrxnb0dkbdxlbvjqbr3gginlw7dr18xh"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-deprecated))
-    (native-inputs (list python-coveralls python-nose2
+    (native-inputs (list python-nose2
                          python-numpy python-setuptools python-wheel))
     (home-page "https://github.com/scottgigante/tasklogger")
     (synopsis "Extension to the core Python logging library")
@@ -36812,8 +36811,7 @@ (define-public python-minikanren
                         (invoke "python" "-m" "pytest" "-v" "tests/" "kanren/"))
                       #t)))))
     (native-inputs
-     (list python-coveralls
-           python-pydocstyle
+     (list python-pydocstyle
            python-pytest
            python-pytest-cov
            python-sympy
diff --git a/gnu/packages/syndication.scm b/gnu/packages/syndication.scm
index ff9e18f064..56677ef91f 100644
--- a/gnu/packages/syndication.scm
+++ b/gnu/packages/syndication.scm
@@ -498,7 +498,6 @@ (define-public rtv
            python-requests python-six))
     (native-inputs
      (list ncurses
-           python-coveralls
            python-mock
            python-pytest
            python-vcrpy))
@@ -540,8 +539,7 @@ (define-public tuir
      (list python-beautifulsoup4 python-decorator python-kitchen
            python-requests python-six))
     (native-inputs
-     (list python-coveralls
-           python-mock
+     (list python-mock
            python-pytest
            python-setuptools
            python-vcrpy
diff --git a/gnu/packages/telegram.scm b/gnu/packages/telegram.scm
index cfcd92fcbc..a4cfc6a9ef 100644
--- a/gnu/packages/telegram.scm
+++ b/gnu/packages/telegram.scm
@@ -839,8 +839,7 @@ (define-public tgcli
                (add-installed-pythonpath inputs outputs)
                (invoke "pytest" "tests")))))))
     (native-inputs
-     `(("coveralls" ,python-coveralls)
-       ("pytest" ,python-pytest)
+     `(("pytest" ,python-pytest)
        ("pytest-click" ,python-pytest-click)
        ("pytest-cov" ,python-pytest-cov)
        ("mkdocs" ,python-mkdocs)
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 22/48] gnu: python-immutables: Remove python-mypy native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-23-ngraves@ngraves.fr

* gnu/packages/python-xyz.scm (python-immutables):
  [origin]: Use git-fetch to use upstream test-data directory.
  [native-inputs]: Remove python-mypy.
  [arguments]<#:phases>: Add phase to remove python-mypy native-input.
---
 gnu/packages/python-xyz.scm | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

Toggle diff (33 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 1cce5e3a54..657ac6e4d0 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -17202,13 +17202,22 @@ (define-public python-immutables
     (version "0.21")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "immutables" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/MagicStack/immutables")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "0jpw9nr2mbzqykigjhqa3a095bx7krwsnmjcxcpj944p8kqglpxm"))))
+        (base32 "1p5g20y7di5xglk6yyhb010vdmz73q9fsxpq0cm2gksp8mj856y1"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list #:phases #~(modify-phases %standard-phases
+                        (add-after 'unpack 'remove-mypy-dependency
+                          (lambda _
+                            (delete-file "tests/test_mypy.py")
+                            (delete-file "tests/conftest.py"))))))
     (native-inputs
-     (list python-mypy python-pytest python-setuptools python-wheel))
+     (list python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/MagicStack/immutables")
     (synopsis "High-performance immutable mapping type for Python")
     (description
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 25/48] build-system/pyproject: Remove python-pytest-cov native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-26-ngraves@ngraves.fr

* gnu/packages/astronomy.scm (python-sncosmo, python-jwst, python-wiimatch,
  python-astroml, python-casa-formats-io, python-cdflib, python-poliastro,
  python-tweakwcs)
* gnu/packages/audio.scm (python-resampy, python-librosa, python-pysox)
* gnu/packages/backup.scm (borgmatic)
* gnu/packages/bioinformatics.scm (python-bed-reader, python-liana-py,
  python-metacells, python-pysnptools, python-pairtools, cwltool,
  python-biom-format, python-pyfaidx, python-cooler, python-screed)
* gnu/packages/build-tools.scm (meson-python)
* gnu/packages/check.scm (python-pytest-nunit, python-pytest-enabler,
  python-pytest-perf, python-pyhamcrest)
* gnu/packages/cpp.scm (cpplint)
* gnu/packages/databases.scm (python-redis)
* gnu/packages/dav.scm (vdirsyncer, radicale)
* gnu/packages/django.scm (python-django-redis, python-django-cleanup,
  python-django-extensions)
* gnu/packages/embedded.scm (mbed-tools)
* gnu/packages/engineering.scm (python-scikit-rf)
* gnu/packages/finance.scm (fava)
* gnu/packages/fontutils.scm (psautohint)
* gnu/packages/geo.scm (python-pyogrio, python-geopandas, python-fiona,
  python-cartopy)
* gnu/packages/gettext.scm (mdpo)
* gnu/packages/gpodder.scm (gpodder)
* gnu/packages/graphviz.scm (python-graphviz, python-uqbar)
* gnu/packages/jupyter.scm (python-nbclassic, python-jupyterlab-server,
  python-hatch-jupyter-builder, python-nbclient, python-papermill,
  python-jupyter-packaging, python-jupyter-server, python-jupyterlite-core,
  python-ipydatawidgets)
* gnu/packages/machine-learning.scm (python-pymanopt, python-botorch,
  python-persim, python-scikit-learn-extra, python-imbalanced-learn,
  python-keras-application, python-keras-preprocessing, python-keras,
  python-tensorly, python-pytorch-geometric, python-captum,
  python-torchmetrics)
* gnu/packages/mastodon.scm (python-mastodon-py)
* gnu/packages/maths.scm (python-libensemble)
* gnu/packages/matrix.scm (python-matrix-nio)
* gnu/packages/messaging.scm (zulip-term)
* gnu/packages/music.scm (beets, stargate)
* gnu/packages/networking.scm (gandi.cli)
* gnu/packages/package-management.scm (conda, python-conda-package-handling)
* gnu/packages/patchutils.scm (pwclient)
* gnu/packages/protobuf.scm (python-pure-protobuf)
* gnu/packages/python-check.scm (python-pandas-vet, python-testfixtures,
  python-vcrpy, python-pytest-filter-subpackage, python-atpublic,
  python-sybil, python-vulture)
* gnu/packages/python-compression.scm (python-zipstream-ng,
  python-multivolumefile, python-pybcj, python-bcj-cffi, python-pyppmd,
  python-ppmd-cffi, python-py7zr)
* gnu/packages/python-crypto.scm (python-cryptography, python-trustme,
  python-certauth)
* gnu/packages/python-science.scm (python-scikit-misc,
  python-mpl-scatter-density, python-modin, python-plotnine,
  python-pynetdicom, python-scipy, python-pandaparallel, python-pyts,
  python-usetplot, python-pingouin, python-opt-einsum, python-salib)
* gnu/packages/python-web.scm (python-devpi-process, python-aiohappyeyeballs,
  python-cheroot, python-jsonpickle, python-flask-babel, python-url-normalize,
  python-elasticsearch, python-hupper, python-simple-websocket,
  python-apiron, python-huggingface-hub, python-portend, python-aiosignal,
  python-aiostream, python-ovh, python-cbor2, python-httplib2, parfive,
  python-jose, python-pyscss, python-mechanicalsoup, python-priority,
  hypercorn, python-aioftp, python-oauthlib, python-tinycss,
  python-cssselect2, python-httpcore, python-wsgiprox, python-venusian,
  python-siosocks, python-zeep, gunicorn, python-warcio)
* gnu/packages/python-xyz.scm (python-archspec, python-colorcet, python-echo,
  python-rich-tables, python-babel, python-pymarshal, python-expandvars,
  autokey, python-lsp-jsonrpc, python-pillow, python-property-manager,
  python-cairocffi, python-jupyter-core, python-ipykernel,
  python-pubmed-parser, python-urwid, python-prettytable, python-xdoctest,
  python-waitress, python-rope, python-wcwidth, python-pyproject-api,
  python-async-lru, python-numcodecs, python-dictpath, python-platformdirs,
  python-multipart, python-apprise, python-janus, python-logbook,
  python-affine, python-mdit-py-plugins, python-pint, python-rasterio,
  python-bidict, python-can, dosage, python-contourpy, python-portalocker,
  python-extension-helpers, python-mizani, python-cligj, python-ddlparse,
  python-robotframework-pythonlibcore, python-lsp-server, python-sparse,
  python-pikepdf, python-imageio, python-manimpango,
  python-importlib-resources, python-jaraco-classes, python-jaraco-collections,
  python-jaraco-context, python-jaraco-functools, python-jaraco-test,
  python-jaraco-text, python-ipyparallel, python-three-merge,
  python-seaborn, python-sentry-sdk, python-sniffio, python-get-version,
  python-path, python-pip-run, python-debugpy, python-notebook,
  python-cookiecutter, python-pyqtgraph, python-pymemcache,
  python-natsort, python-mwclient, python-flasgger, python-tempora,
  python-outcome, python-apscheduler, python-iocapture, python-argh,
  python-flit, python-watchdog, python-cmd2, python-inform,
  python-qtsass, python-scikit-build, python-minikanren, python-tablib,
  python-ansicolors, python-shtab, python-scooby, dynaconf, python-pyan3,
  python-numpydoc, python-loguru)
* gnu/packages/rdf.scm (python-rdflib, python-rdflib-6)
* gnu/packages/simulation.scm (python-fenics-dijitso)
* gnu/packages/sphinx.scm (python-sphinx-design, python-sphinx-gallery)
* gnu/packages/statistics.scm (python-patsy, python-rchitect, python-pymc,
  python-emcee, python-rpy2)
* gnu/packages/task-management.scm (todoman)
* gnu/packages/telegram.scm (tgcli)
* gnu/packages/textutils.scm (python-panflute)
* gnu/packages/time.scm (python-arrow, python-tzlocal)
* gnu/packages/vpn.scm (sshuttle)
* gnu/packages/web.scm (anonip, python-tibanna)
* gnu/packages/wm.scm (qtile)
[native-inputs]: Remove python-pytest-cov.
---
 gnu/packages/astronomy.scm          |   9 +-
 gnu/packages/audio.scm              |   5 +-
 gnu/packages/backup.scm             |   1 -
 gnu/packages/bioinformatics.scm     |  16 +--
 gnu/packages/build-tools.scm        |   1 -
 gnu/packages/check.scm              |   5 +-
 gnu/packages/cpp.scm                |   1 -
 gnu/packages/databases.scm          |   1 -
 gnu/packages/dav.scm                |   2 -
 gnu/packages/django.scm             |   3 -
 gnu/packages/embedded.scm           |   1 -
 gnu/packages/engineering.scm        |   1 -
 gnu/packages/fediverse.scm          |   1 -
 gnu/packages/finance.scm            |   1 -
 gnu/packages/fontutils.scm          |   1 -
 gnu/packages/geo.scm                |   4 +-
 gnu/packages/gettext.scm            |   1 -
 gnu/packages/gpodder.scm            |   1 -
 gnu/packages/graphviz.scm           |   2 -
 gnu/packages/jupyter.scm            |  12 +-
 gnu/packages/machine-learning.scm   |  20 +---
 gnu/packages/maths.scm              |   1 -
 gnu/packages/matrix.scm             |   1 -
 gnu/packages/messaging.scm          |   4 +-
 gnu/packages/music.scm              |   2 -
 gnu/packages/networking.scm         |   2 +-
 gnu/packages/package-management.scm |   2 -
 gnu/packages/patchutils.scm         |   2 +-
 gnu/packages/protobuf.scm           |   2 +-
 gnu/packages/python-check.scm       |  10 +-
 gnu/packages/python-compression.scm |  11 +-
 gnu/packages/python-crypto.scm      |   4 +-
 gnu/packages/python-science.scm     |  21 ++--
 gnu/packages/python-web.scm         |  68 ++++--------
 gnu/packages/python-xyz.scm         | 163 ++++++++++------------------
 gnu/packages/rdf.scm                |   4 +-
 gnu/packages/simulation.scm         |   1 -
 gnu/packages/sphinx.scm             |   2 -
 gnu/packages/statistics.scm         |   7 +-
 gnu/packages/task-management.scm    |   1 -
 gnu/packages/telegram.scm           |   1 -
 gnu/packages/textutils.scm          |   1 -
 gnu/packages/time.scm               |   2 -
 gnu/packages/vpn.scm                |   1 -
 gnu/packages/web.scm                |   3 +-
 gnu/packages/wm.scm                 |   1 -
 46 files changed, 117 insertions(+), 289 deletions(-)

Toggle diff (305 lines)diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index b4c29480ac..7384da6452 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1952,7 +1952,7 @@ (define-public python-astroml
              (setenv "HOME" "/tmp"))))))
     (propagated-inputs (list python-astropy python-matplotlib python-numpy
                              python-scikit-learn python-scipy))
-    (native-inputs (list python-pytest-astropy-header python-pytest-cov
+    (native-inputs (list python-pytest-astropy-header python-pytest
                          python-pytest-doctestplus python-pytest-remotedata
                          python-wheel))
     (home-page "https://astroml.org")
@@ -2022,7 +2022,6 @@ (define-public python-casa-formats-io
               (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-pytest-openfiles
            python-setuptools
            python-wheel))
@@ -2096,7 +2095,6 @@ (define-public python-cdflib
     (native-inputs
      (list python-astropy-minimal
            python-pytest
-           python-pytest-cov
            python-pytest-remotedata
            python-setuptools
            python-setuptools-scm
@@ -3422,7 +3420,6 @@ (define-public python-sncosmo
            python-cython
            python-pytest
            python-pytest-astropy
-           python-pytest-cov
            python-setuptools
            python-wheel))
     (home-page "https://sncosmo.readthedocs.org")
@@ -4220,7 +4217,6 @@ (define-public python-jwst
                              python-wiimatch))
     (native-inputs (list python-colorama
                          python-pytest
-                         python-pytest-cov
                          python-pytest-doctestplus
                          python-pytest-openfiles
                          python-requests-mock
@@ -4632,7 +4628,6 @@ (define-public python-poliastro
      (list python-hypothesis
            python-flit-core
            python-pytest
-           python-pytest-cov
            python-pytest-doctestplus
            python-pytest-mpl
            python-pytest-mypy))
@@ -6703,7 +6698,6 @@ (define-public python-tweakwcs
            python-stsci-stimage))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-scipy
            python-setuptools
            python-setuptools-scm
@@ -6827,7 +6821,6 @@ (define-public python-wiimatch
     (build-system pyproject-build-system)
     (propagated-inputs (list python-numpy python-scipy))
     (native-inputs (list python-pytest
-                         python-pytest-cov
                          python-pytest-doctestplus
                          python-setuptools-scm
                          python-wheel))
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index d392cd2a73..3c4498d38c 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -6644,7 +6644,7 @@ (define-public python-pysox
       (propagated-inputs
        (list python-numpy python-typing-extensions))
       (native-inputs
-       (list sox python-pytest python-pytest-cov python-soundfile))
+       (list sox python-pytest python-soundfile))
       (home-page "https://github.com/rabitt/pysox")
       (synopsis "Python wrapper around SoX")
       (description "@code{python-pysox} is a wrapper around the @command{sox}
@@ -6674,7 +6674,7 @@ (define-public python-resampy
     (propagated-inputs
      (list python-numba python-numpy python-scipy python-six))
     (native-inputs
-     (list python-pytest python-pytest-cov python-setuptools python-wheel))
+     (list python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/bmcfee/resampy")
     (synopsis "Efficient signal resampling")
     (description
@@ -6729,7 +6729,6 @@ (define-public python-librosa
      (list python-matplotlib
            python-packaging
            python-pytest
-           python-pytest-cov
            python-resampy
            python-setuptools
            python-wheel))
diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index 13c5590f55..d3e6f7e16d 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -1375,7 +1375,6 @@ (define-public borgmatic
     (native-inputs
      (list python-flexmock
            python-pytest
-           python-pytest-cov
            python-setuptools
            python-wheel))
     (inputs
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d81791a724..5cb3f86853 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2272,7 +2272,6 @@ (define-public python-bed-reader
               (when tests?
                 (apply invoke "pytest" "-v" #$output test-flags)))))))
     (native-inputs (list python-pytest
-                         python-pytest-cov
                          python-pytest-datadir
                          python-pytest-doctestplus
                          python-recommonmark
@@ -3051,7 +3050,7 @@ (define-public python-liana-py
                              python-tqdm
                              tzdata))
     (native-inputs
-     (list python-poetry-core python-pytest python-pytest-cov))
+     (list python-poetry-core python-pytest))
     (home-page "https://github.com/saezlab/liana-py")
     (synopsis "LIANA is a ligand-receptor analysis framework")
     (description "This is a Ligand-Receptor inference framework.  The
@@ -3172,7 +3171,6 @@ (define-public python-metacells
                          python-mypy-extensions
                          python-pandas-stubs
                          python-pytest
-                         python-pytest-cov
                          python-setuptools
                          python-sphinx
                          python-sphinx-rtd-theme
@@ -3637,7 +3635,6 @@ (define-public python-pysnptools
            python-scipy))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-pytest-datadir
            python-pytest-doctestplus
            python-setuptools
@@ -3923,7 +3920,8 @@ (define-public python-biom-format
            ;;python-scikit-bio ;mutually recursive dependency
            python-scipy))
     (native-inputs
-     (list python-cython python-pytest python-pytest-cov
+     (list python-cython
+           python-pytest
            python-wheel))
     (home-page "https://www.biom-format.org")
     (synopsis "Biological Observation Matrix (BIOM) format utilities")
@@ -3971,7 +3969,6 @@ (define-public python-pairtools
     (native-inputs
      (list python-cython
            python-pytest
-           python-pytest-cov
            python-setuptools
            python-wheel))
     (propagated-inputs
@@ -6664,7 +6661,6 @@ (define-public cwltool
            python-humanfriendly
            python-mock
            python-pytest
-           python-pytest-cov
            python-pytest-mock
            python-pytest-runner
            python-wheel))
@@ -11559,7 +11555,6 @@ (define-public python-screed
     (native-inputs
      (list python-importlib-resources
            python-pytest
-           python-pytest-cov
            python-setuptools
            python-setuptools-scm
            python-setuptools-scm-git-archive
@@ -19880,7 +19875,6 @@ (define-public python-pyfaidx
            python-mock
            python-numpy
            python-pytest
-           python-pytest-cov
            python-wheel))
     (propagated-inputs (list python-setuptools))
     (home-page "http://mattshirley.com")
@@ -19930,9 +19924,7 @@ (define-public python-cooler
            python-scipy
            python-simplejson))
     (native-inputs
-     (list python-hatchling
-           python-pytest
-           python-pytest-cov))
+     (list python-hatchling python-pytest))
     ;; Almost all the projects of the Mirnylab are moved under Open2C umbrella
     (home-page "https://github.com/open2c/cooler")
     (synopsis "Sparse binary format for genomic interaction matrices")
diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm
index 6bf0b2ec67..900ca704e6 100644
--- a/gnu/packages/build-tools.scm
+++ b/gnu/packages/build-tools.scm
@@ -365,7 +365,6 @@ (define-public meson-python
            python-cython-3
            python-gitpython
            python-pytest
-           python-pytest-cov
            python-pytest-mock))
     (home-page "https://github.com/mesonbuild/meson-python")
     (synopsis "Meson-based build backend for Python")
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index e6aa4d6de6..57e62f6af0 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -1874,7 +1874,6 @@ (define-public python-pytest-nunit
     (arguments (list #:tests? #false)) ;no tests included
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-setuptools
            python-wheel
            python-xmlschema))
@@ -2945,7 +2944,6 @@ (define-public python-pytest-enabler
            python-toml))
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
-                         python-pytest-cov
                          python-pytest-flake8
                          python-pytest-mypy
                          python-setuptools
@@ -3118,7 +3116,6 @@ (define-public python-pytest-perf
     (native-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-cov
            python-pytest-enabler
            python-pytest-flake8
            python-pytest-mypy
@@ -3672,7 +3669,7 @@ (define-public python-pyhamcrest
                (base32
                 "05kdzlhs2kvj82pfca13qszszcj6dyrk4b9pbr46x06sq2s4qyls"))))
     (native-inputs                      ;all native inputs are for tests
-     (list python-pytest-cov python-mock python-pytest python-hypothesis))
+     (list python-mock python-pytest python-hypothesis))
     (build-system python-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases
diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index 21aa13b73c..7e35ad09f2 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -1400,7 +1400,6 @@ (define-public cpplint
                            (getenv "TMP_PYTHONPATH")))))))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-pytest-runner
            python-setuptools
            python-testfixtures
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index df2045db9d..d124ba186c 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -4551,7 +4551,6 @@ (define-public python-redis
      (list python-numpy
            python-pytest
            python-pytest-asyncio-0.23
-           python-pytest-cov
            python-pytest-timeout
            python-setuptools
            python-wheel
diff --git a/gnu/packages/dav.scm b/gnu/packages/dav.scm
index 546118055f..7688c9a994 100644
--- a/gnu/packages/dav.scm
+++ b/gnu/packages/dav.scm
@@ -58,7 +58,6 @@ (define-public radicale
     (build-system pyproject-build-system)
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-pytest-flake8
            python-pytest-isort
            python-setuptools
@@ -151,7 +150,6 @@ (define-public vdirsyncer
            python-trustme
            python-pytest
            python-pytest-asyncio
-           python-pytest-cov
            python-pytest-httpserver
            radicale))
     (inputs
diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index c1cf3b1337..287c6fceee 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -269,7 +269,6 @@ (define-public python-django-extensions
      (list python-mock
            python-factory-boy
            python-pytest
-           python-pytest-cov
            python-pytest-django
            python-shortuuid)

This message was truncated. Download the full message here.

Nicolas Graves wrote 2 weeks ago

[PATCH v5 21/48] build-system/pyproject: Remove python-mypy native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-22-ngraves@ngraves.fr

* gnu/packages/astronomy.scm (python-poliastro)[native-inputs]: Remove

python-mypy.

* gnu/packages/databases.scm (python-psycopg2)[native-inputs]: Remove

python-mypy.

* gnu/packages/engineering.scm (uranium, cura)[native-inputs]: Remove

python-mypy.

* gnu/packages/graphviz.scm (python-uqbar)[native-inputs]: Remove

python-mypy.

* gnu/packages/machine-learning.scm (python-imbalanced-learn,

python-captum, python-torchmetrics)[native-inputs]: Remove python-mypy.

* gnu/packages/python-science.scm (python-scipy)[native-inputs]:

Remove python-mypy.

* gnu/packages/python-web.scm (python-huggingface-hub, python-asgiref,

python-starsessions-for-pytorch-lightning)[native-inputs]:

Remove python-mypy.

* gnu/packages/python-xyz.scm (kalamine, python-pydantic-cli,

python-apispec, python-typeguard, python-verspec,

python-catalogue)[native-inputs]: Remove python-mypy.

* gnu/packages/serialization.scm (python-msgspec)[native-inputs]: Remove

python-mypy.

* gnu/packages/virtualization.scm (python-transient)[native-inputs]:

Remove python-mypy.

---

gnu/packages/astronomy.scm | 1 -

gnu/packages/databases.scm | 1 -

gnu/packages/engineering.scm | 2 --

gnu/packages/graphviz.scm | 1 -

gnu/packages/machine-learning.scm | 3 ---

gnu/packages/python-science.scm | 1 -

gnu/packages/python-web.scm | 6 +++---

gnu/packages/python-xyz.scm | 13 +++++--------

gnu/packages/serialization.scm | 1 -

gnu/packages/virtualization.scm | 3 +--

10 files changed, 9 insertions(+), 23 deletions(-)

Toggle diff (214 lines)diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 6b31414940..b4c29480ac 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4630,7 +4630,6 @@ (define-public python-poliastro
               (setenv "HOME" "/tmp"))))))
     (native-inputs
      (list python-hypothesis
-           python-mypy
            python-flit-core
            python-pytest
            python-pytest-cov
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 3b8d1d9d23..085a1d7cd0 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -4305,7 +4305,6 @@ (define-public python-psycopg
                           "-c" "CREATE DATABASE nixbld;"))))))))
     (native-inputs
      (list python-cython-3
-           python-mypy
            python-psycopg-pool
            python-pytest
            python-pytest-asyncio
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index cc84a760e9..fe550d8471 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -4550,7 +4550,6 @@ (define-public uranium
            graphviz
            pkg-config
            python-pytest
-           python-mypy
            python-certifi
            python-twisted))
     (propagated-inputs
@@ -4753,7 +4752,6 @@ (define-public cura
     (build-system qt-build-system)
     (native-inputs
      (list python-certifi
-           python-mypy
            python-pytest
            python-requests))
     (inputs
diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm
index 0d3db31212..6bfe5325ac 100644
--- a/gnu/packages/graphviz.scm
+++ b/gnu/packages/graphviz.scm
@@ -225,7 +225,6 @@ (define-public python-uqbar
     (native-inputs
      (list graphviz
            python-isort
-           python-mypy
            python-pytest
            python-pytest-cov
            python-setuptools
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 2caa64cc08..649648ac4e 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -2149,7 +2149,6 @@ (define-public python-imbalanced-learn
     (propagated-inputs (list python-joblib python-numpy python-scikit-learn
                              python-scipy python-threadpoolctl))
     (native-inputs (list python-keras
-                         python-mypy
                          python-pandas
                          python-pytest
                          python-pytest-cov
@@ -5319,7 +5318,6 @@ (define-public python-captum
                          python-flask-compress
                          python-ipython
                          python-ipywidgets
-                         python-mypy
                          python-parameterized
                          python-pytest
                          python-pytest-cov
@@ -5507,7 +5505,6 @@ (define-public python-torchmetrics
      (list python-cloudpickle
            python-fire
            python-mir-eval
-           python-mypy
            python-pandas
            python-psutil
            python-pytest
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index c6616f3ab6..ad60378944 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -439,7 +439,6 @@ (define-public python-scipy
            '())
        (list python-matplotlib
              python-mpmath
-             python-mypy
              python-numpy
              python-numpydoc
              python-pydata-sphinx-theme
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index c2c6578f2e..5b33ed4568 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -564,7 +564,6 @@ (define-public python-huggingface-hub
            python-fastapi
            python-jedi
            python-jinja2
-           python-mypy
            python-numpy
            python-pillow
            python-pydantic-2
@@ -1216,7 +1215,9 @@ (define-public python-asgiref
                (base32 "146mhkn3zp2bqf7j6r3chdlvfzgs5x1lrnqahsllgjdyl20bshy3"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-mypy python-pytest python-pytest-asyncio python-setuptools
+     (list python-pytest
+           python-pytest-asyncio
+           python-setuptools
            python-wheel))
     (home-page "https://github.com/django/asgiref/")
     (synopsis "ASGI specs, helper code, and adapters")
@@ -10303,7 +10304,6 @@ (define-public python-starsessions
            python-starlette))
     (native-inputs
      (list python-httpx
-           python-mypy
            python-poetry-core
            python-pytest
            python-pytest-asyncio
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e991fe97e8..1cce5e3a54 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7610,7 +7610,7 @@ (define-public kalamine
     ;; TODO: Add python-pytest-ruff to native-inputs once it has been
     ;; packaged.
     (native-inputs
-     (list python-hatchling python-mypy python-pytest))
+     (list python-hatchling python-pytest))
     (home-page "https://github.com/OneDeadKey/kalamine")
     (synopsis "Keyboard layout maker")
     (description
@@ -8850,8 +8850,7 @@ (define-public python-pydantic-cli
     (propagated-inputs
      (list python-pydantic))
     (native-inputs
-     (list python-mypy
-           python-pytest))
+     (list python-pytest))
     (home-page "https://github.com/mpkocher/pydantic-cli")
     (synopsis "Turn Pydantic defined data models into CLI tools")
     (description
@@ -27090,7 +27089,6 @@ (define-public python-apispec
     (build-system pyproject-build-system)
     (native-inputs
      (list python-flit-core
-           python-mypy
            python-openapi-spec-validator
            python-pytest))
     (propagated-inputs
@@ -28511,8 +28509,7 @@ (define-public python-typeguard
         (base32 "06y22d1f5dhpyl71wbhsaibig5hvc2v44pw795yb8lxl02fsh8hd"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-mypy
-           python-pytest
+     (list python-pytest
            python-setuptools
            python-setuptools-scm
            python-typing-extensions
@@ -38256,7 +38253,7 @@ (define-public python-verspec
                (base32
                 "07n06wv85fm4vl1ird2mja0823js3x322wgs9gdnq1djjyk4ql64"))))
     (build-system python-build-system)
-    (native-inputs (list python-mypy python-pretend python-pytest))
+    (native-inputs (list python-pretend python-pytest))
     (arguments
      `(#:phases (modify-phases %standard-phases
                   (replace 'check
@@ -39040,7 +39037,7 @@ (define-public python-catalogue
                 "0srdxiil2xys8q1gpc1nvzhvis3a33d8a7amk2i1rlpbg6p36pak"))))
     (build-system python-build-system)
     (native-inputs (list python-pytest))
-    (inputs (list python python-zipp python-typing-extensions python-mypy))
+    (inputs (list python python-zipp python-typing-extensions))
     (home-page "https://github.com/explosion/catalogue")
     (synopsis "Lightweight function registries for your library")
     (description
diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index c0f7001fa0..8d6abf094b 100644
--- a/gnu/packages/serialization.scm
+++ b/gnu/packages/serialization.scm
@@ -788,7 +788,6 @@ (define-public python-msgspec
     (native-inputs (list python-attrs
                          python-gcovr
                          python-msgpack
-                         python-mypy
                          python-pytest
                          python-setuptools-scm
                          python-versioneer
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index bde357763f..a6872a3f1f 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -2986,8 +2986,7 @@ (define-public python-transient
                         (("==")
                          ">=")))))))
     (native-inputs
-     (list python-mypy
-           python-pyhamcrest
+     (list python-pyhamcrest
            python-setuptools
            python-twine
            python-wheel))
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 20/48] build-system/pyproject: Remove python-tox native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-21-ngraves@ngraves.fr

* gnu/packages/bioinformatics.scm (python-metacells)
* gnu/packages/django.scm (python-django-pipeline, python-django-extensions)
* gnu/packages/jupyter.scm (python-papermill)
* gnu/packages/logging.scm (tailon)
* gnu/packages/messaging.scm (python-harmony)
* gnu/packages/mp3.scm (python-audioread)
* gnu/packages/networking.scm (gandi.cli)
* gnu/packages/python-check.scm (python-pytest-qt, python-nox)
* gnu/packages/python-science.scm (python-scikit-survival)
* gnu/packages/python-web.scm (python-flask-htpasswd,
  python-simple-websocket, python-omnipath, python-sanic)
* gnu/packages/python-xyz.scm (python-lunr, python-bidict,
  python-jsonargparse, python-ddlparse, python-virtualenv-clone,
  python-honcho, python-shshsh, python-ansicolors)
* gnu/packages/radio.scm (chirp)
* gnu/packages/terminals.scm (python-halo, python-log-symbols,
  python-spinners)
* gnu/packages/textutils.scm (txt2tags)
[native-inputs]: Remove python-tox.
---
 gnu/packages/bioinformatics.scm |  1 -
 gnu/packages/django.scm         |  2 --
 gnu/packages/jupyter.scm        |  1 -
 gnu/packages/logging.scm        |  2 +-
 gnu/packages/messaging.scm      |  2 --
 gnu/packages/mp3.scm            |  3 +--
 gnu/packages/networking.scm     |  2 +-
 gnu/packages/python-check.scm   |  4 +---
 gnu/packages/python-science.scm |  3 +--
 gnu/packages/python-web.scm     |  5 +----
 gnu/packages/python-xyz.scm     | 18 +++++-------------
 gnu/packages/radio.scm          |  3 +--
 gnu/packages/terminals.scm      |  3 ---
 gnu/packages/textutils.scm      |  1 -
 14 files changed, 12 insertions(+), 38 deletions(-)

Toggle diff (304 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1cec139812..bb8ac5c800 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3177,7 +3177,6 @@ (define-public python-metacells
                          python-setuptools
                          python-sphinx
                          python-sphinx-rtd-theme
-                         python-tox
                          python-twine
                          python-wheel))
     (home-page "https://github.com/tanaylab/metacells.git")
diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index b7f2e23f9d..c1cf3b1337 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -268,7 +268,6 @@ (define-public python-django-extensions
     (native-inputs
      (list python-mock
            python-factory-boy
-           python-tox
            python-pytest
            python-pytest-cov
            python-pytest-django
@@ -995,7 +994,6 @@ (define-public python-django-pipeline
      (list python-django
            python-setuptools
            python-setuptools-scm
-           python-tox
            python-wheel))
     (home-page
      "https://github.com/jazzband/django-pipeline")
diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm
index 1ee99c8602..8f900d3f88 100644
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -1171,7 +1171,6 @@ (define-public python-papermill
                          python-recommonmark
                          python-requests
                          python-setuptools
-                         python-tox
                          python-twine
                          python-wheel))
     (home-page "https://github.com/nteract/papermill")
diff --git a/gnu/packages/logging.scm b/gnu/packages/logging.scm
index 9cc28279d7..55a1db4123 100644
--- a/gnu/packages/logging.scm
+++ b/gnu/packages/logging.scm
@@ -159,7 +159,7 @@ (define-public tailon
          "0xkmrivzilsc9wqr8ms67v7399gxnh7pv5687k4rdpdgz4309fwc"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-tox python-wheel))
+     (list python-wheel))
     (inputs
      (list python-pyyaml-5 python-sockjs-tornado python-tornado-http-auth
            python-tornado python-deepmerge))
diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index 1ee8255593..fcb05dbda6 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -3626,8 +3626,6 @@ (define-public python-harmony
                (base32
                 "1bm9xcnzpnpj6rlhbrnl2abwclzl7ivgh1vb5644y9mnhcs489js"))))
     (build-system python-build-system)
-    (native-inputs
-     (list python-tox))
     (inputs
      (list python-librecaptcha python-keyring python-requests))
     (synopsis "Discord account management")
diff --git a/gnu/packages/mp3.scm b/gnu/packages/mp3.scm
index 9dfce6313f..ccf105d7be 100644
--- a/gnu/packages/mp3.scm
+++ b/gnu/packages/mp3.scm
@@ -688,8 +688,7 @@ (define-public python-audioread
      (list gstreamer
            gst-plugins-base
            python-flit-core
-           python-pytest
-           python-tox))
+           python-pytest))
     (home-page "https://github.com/sampsyo/audioread")
     (synopsis "Decode audio files using whichever backend is available")
     (description
diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index 1b97853a59..96561fff3a 100644
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@ -1941,7 +1941,7 @@ (define-public gandi.cli
                #t))))))
     (native-inputs
      (list python-docutils ; for rst2man.py
-           python-pytest python-pytest-cov python-tox))
+           python-pytest python-pytest-cov))
     (propagated-inputs
      (list openssh))           ; used by gandi/cli/modules/iass.py
     (inputs
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index e57438b2ea..c2026f2433 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -2295,7 +2295,6 @@ (define-public python-pytest-qt
      (list python-pre-commit
            python-setuptools
            python-setuptools-scm
-           python-tox
            python-wheel))
     (home-page "https://github.com/pytest-dev/pytest-qt")
     (synopsis "Pytest support for PyQt and PySide applications")
@@ -3012,8 +3011,7 @@ (define-public python-nox
     (native-inputs
      (list python-hatchling
            python-jinja2
-           python-pytest
-           python-tox))
+           python-pytest))
     (home-page "https://nox.thea.codes/")
     (synopsis "Flexible test automation")
     (description
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 83e66572e3..c6616f3ab6 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -893,8 +893,7 @@ (define-public python-scikit-survival
              python-pytest
              python-setuptools
              python-setuptools-scm
-             python-tomli
-             python-tox))
+             python-tomli))
       (home-page "https://github.com/sebp/scikit-survival")
       (synopsis "Survival analysis built on top of scikit-learn")
       (description "Scikit-survival is a Python module for survival analysis
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 76e13b3af2..c2c6578f2e 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -2974,7 +2974,6 @@ (define-public python-omnipath
              python-requests-mock
              python-setuptools
              python-setuptools-scm
-             python-tox
              python-wheel))
       (home-page "https://omnipathdb.org/")
       (synopsis "Python client for the OmniPath web service")
@@ -5826,7 +5825,7 @@ (define-public python-flask-htpasswd
     (build-system pyproject-build-system)
     (arguments (list #:tests? #false)) ;none included
     (propagated-inputs
-     (list python-flask python-passlib python-pyjwt python-tox))
+     (list python-flask python-passlib python-pyjwt))
     (native-inputs (list python-pytest
                          python-setuptools
                          python-wheel))
@@ -8916,7 +8915,6 @@ (define-public python-sanic
            python-setuptools
            python-slotscheck
            python-towncrier
-           python-tox
            python-types-ujson
            python-uvicorn
            python-wheel))
@@ -9040,7 +9038,6 @@ (define-public python-simple-websocket
     (native-inputs (list python-pytest
                          python-pytest-cov
                          python-setuptools
-                         python-tox
                          python-wheel))
     (home-page "https://github.com/miguelgrinberg/simple-websocket")
     (synopsis "Simple WebSocket server and client for Python")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index cd20064c95..e991fe97e8 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1682,8 +1682,7 @@ (define-public python-lunr
      (list python-hatch-fancy-pypi-readme
            python-hatchling
            python-pytest
-           python-pytest-timeout
-           python-tox))
+           python-pytest-timeout))
     (propagated-inputs
      (list python-importlib-metadata python-typing-extensions))
     (home-page
@@ -3344,8 +3343,7 @@ (define-public python-bidict
            python-sortedcollections
            python-sortedcontainers
            python-sphinx
-           python-sphinx-autodoc-typehints
-           python-tox))
+           python-sphinx-autodoc-typehints))
     (arguments
      `(#:phases (modify-phases %standard-phases
                   (add-after 'unpack 'relax-reqs
@@ -5209,7 +5207,6 @@ (define-public python-jsonargparse
            python-pytest
            python-pytest-subtests
            python-responses
-           python-tox
            python-types-requests
            python-setuptools
            python-wheel))
@@ -6433,7 +6430,6 @@ (define-public python-ddlparse
      (list python-pytest
            python-pytest-cov
            python-setuptools
-           python-tox
            python-wheel))
     (propagated-inputs (list python-pyparsing))
     (home-page "https://github.com/shinichi-takii/ddlparse")
@@ -7003,7 +6999,6 @@ (define-public python-virtualenv-clone
                               (delete-file "tox.ini")
                               (invoke "pytest" "-vvv" "tests")))))))
     (native-inputs (list python-pytest
-                         python-tox
                          python-virtualenv
                          python-wheel
                          python-tomli
@@ -12555,7 +12550,7 @@ (define-public python-honcho
         (base32 "1y0r8dw4pqcq7r4n58ixjdg1iy60lp0gxsd7d2jmhals16ij71rj"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-pytest python-mock python-tox which)) ;for tests
+     (list python-pytest python-mock which)) ;for tests
     (propagated-inputs
      (list python-jinja2))
     (arguments
@@ -22772,9 +22767,7 @@ (define-public python-shshsh
          "1wzqyj1a6jj6cyv5ymzy834qm2lyq80yy1kfz0q0zayq9gm1cj7f"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-poetry-core
-           python-pytest
-           python-tox))
+     (list python-poetry-core python-pytest))
     (home-page "https://github.com/zqqqqz2000/shshsh")
     (synopsis "Write Shell commands simply and safely within Python")
     (description "This package provides a way to write Shell commands from
@@ -38043,8 +38036,7 @@ (define-public python-ansicolors
         (base32 "1q3jqglkq4z0f6nkkn8bswcwqg012i2grrc27kabr8286dg4zycr"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-tox
-           python-pytest-cov
+     (list python-pytest-cov
            unzip))
     (home-page "https://github.com/jonathaneunice/colors/")
     (synopsis "ANSI colors for Python")
diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index d2c8bee76b..51d00e68f4 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -3274,8 +3274,7 @@ (define-public chirp
              python-mox3
              python-pytest
              python-pytest-mock
-             python-pyyaml
-             python-tox))
+             python-pyyaml))
       (inputs
        (list python-future
              python-importlib-resources
diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index da9f0e3483..36ad457ca2 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -1178,7 +1178,6 @@ (define-public python-halo
     (native-inputs
      (list python-nose
            python-setuptools
-           python-tox
            python-twine
            python-wheel))
     (home-page "https://github.com/manrajgrover/halo")
@@ -1209,7 +1208,6 @@ (define-public python-log-symbols
     (native-inputs
      (list python-nose
            python-setuptools
-           python-tox
            python-wheel))
     (propagated-inputs (list python-colorama))
     (home-page "https://github.com/manrajgrover/py-log-symbols")
@@ -1241,7 +1239,6 @@ (define-public python-spinners
     (native-inputs
      (list python-nose
            python-setuptools
-           python-tox
            python-wheel))
     (home-page "https://github.com/manrajgrover/py-spinners")
     (synopsis "Python library with graphical spinners for the terminal")
diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index 792ef1f3b3..004f170c25 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -1086,7 +1086,6 @@ (define-public txt2tags
                (base32
                 "0ik7gpr3gymgxnj0p86k8768kyxncbncv93zq67sbak3dbdl8hky"))))
     (build-system python-build-system)
-    (native-inputs (list python-tox))
     (home-page "https://txt2tags.org")
     (synopsis "Convert between markup languages")
     (description
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 23/48] build-system/pyproject: Remove python-isort native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-24-ngraves@ngraves.fr

* gnu/packages/bioinformatics.scm (python-metacells, python-cooler,
  scvelo)
* gnu/packages/databases.scm (aerich)
* gnu/packages/finance.scm (python-trezor)
* gnu/packages/gettext.scm (mdpo)
* gnu/packages/graphviz.scm (python-uqbar)
* gnu/packages/machine-learning.scm (python-pymanopt, python-funsor)
* gnu/packages/mail.scm (python-hyperkitty, postorius)
* gnu/packages/protobuf.scm (python-pure-protobuf)
* gnu/packages/python-web.scm (python-zeep, python-ovh, python-tinycss2)
* gnu/packages/python-xyz.scm (python-archspec)
* gnu/packages/statistics.scm (python-statsmodels)
* gnu/packages/virtualization.scm (python-qemu-qmp)
[native-inputs]: Remove python-isort.
---
 gnu/packages/bioinformatics.scm   | 3 ---
 gnu/packages/databases.scm        | 1 -
 gnu/packages/finance.scm          | 1 -
 gnu/packages/gettext.scm          | 1 -
 gnu/packages/graphviz.scm         | 1 -
 gnu/packages/machine-learning.scm | 4 +---
 gnu/packages/mail.scm             | 2 --
 gnu/packages/protobuf.scm         | 2 +-
 gnu/packages/python-web.scm       | 4 +---
 gnu/packages/python-xyz.scm       | 3 +--
 gnu/packages/statistics.scm       | 1 -
 gnu/packages/virtualization.scm   | 1 -
 12 files changed, 4 insertions(+), 20 deletions(-)

Toggle diff (193 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bb8ac5c800..4294016f44 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3168,7 +3168,6 @@ (define-public python-metacells
                              python-threadpoolctl
                              python-umap-learn))
     (native-inputs (list python-bumpversion
-                         python-isort
                          python-mypy
                          python-mypy-extensions
                          python-pandas-stubs
@@ -19935,7 +19934,6 @@ (define-public python-cooler
            python-simplejson))
     (native-inputs
      (list python-hatchling
-           python-isort
            python-pytest
            python-pytest-cov))
     ;; Almost all the projects of the Mirnylab are moved under Open2C umbrella
@@ -24030,7 +24028,6 @@ (define-public scvelo
     (propagated-inputs
      (list python-anndata
            python-hnswlib
-           python-isort
            python-igraph
            python-loompy
            python-louvain
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 085a1d7cd0..df2045db9d 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -3459,7 +3459,6 @@ (define-public aerich
      (list poetry
            python-bandit
            python-cryptography
-           python-isort
            python-pydantic
            python-pytest
            python-pytest-asyncio
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index f3be674c01..3af525da18 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -1160,7 +1160,6 @@ (define-public python-trezor
            python-typing-extensions))
     (native-inputs ; Only needed for running the tests
      (list protobuf
-           python-isort
            python-pillow
            python-protobuf
            python-pyqt
diff --git a/gnu/packages/gettext.scm b/gnu/packages/gettext.scm
index 29cdbab915..841d3e0c8b 100644
--- a/gnu/packages/gettext.scm
+++ b/gnu/packages/gettext.scm
@@ -228,7 +228,6 @@ (define-public mdpo
      (list python-bump2version
            python-flake8-implicit-str-concat
            python-flake8-print
-           python-isort
            python-pytest
            python-pytest-cov
            python-sphinx
diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm
index 6bfe5325ac..33ddbeba42 100644
--- a/gnu/packages/graphviz.scm
+++ b/gnu/packages/graphviz.scm
@@ -224,7 +224,6 @@ (define-public python-uqbar
 and not test_sphinx_book_text_broken_strict")))
     (native-inputs
      (list graphviz
-           python-isort
            python-pytest
            python-pytest-cov
            python-setuptools
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 649648ac4e..8c1e99ba99 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -229,8 +229,7 @@ (define-public python-funsor
     (propagated-inputs (list python-makefun python-multipledispatch
                              python-numpy python-opt-einsum
                              python-typing-extensions))
-    (native-inputs (list python-isort
-                         python-nbsphinx
+    (native-inputs (list python-nbsphinx
                          python-pandas
                          python-pillow
                          python-pyro-api
@@ -1143,7 +1142,6 @@ (define-public python-pymanopt
     (propagated-inputs (list python-numpy python-scipy))
     (native-inputs (list python-autograd
                          python-flake8-bugbear
-                         python-isort
                          python-matplotlib
                          python-pytest
                          python-pytest-cov
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index cffbca087a..b353e5cf51 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -3813,7 +3813,6 @@ (define-public python-hyperkitty
            python-django-rest-framework
            python-elasticsearch
            python-flufl-lock
-           python-isort
            python-lxml
            python-mailmanclient
            python-mistune
@@ -3864,7 +3863,6 @@ (define-public postorius
            python-django-mailman3))
     (native-inputs
      (list python-beautifulsoup4
-           python-isort
            python-mock
            python-pdm-backend
            python-pytest
diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm
index 203e4909d6..487c03fa94 100644
--- a/gnu/packages/protobuf.scm
+++ b/gnu/packages/protobuf.scm
@@ -502,7 +502,7 @@ (define-public python-pure-protobuf
         (base32 "15dp5pvazd0jx4wzzh79080ah7hkpd3axh40al9vhzs2hf3v90hx"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-pytest python-pytest-cov python-isort))
+     (list python-pytest python-pytest-cov))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 5b33ed4568..2248d62195 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1601,8 +1601,7 @@ (define-public python-ovh
     (build-system pyproject-build-system)
     (arguments (list #:tests? #f))      ; XXX: tests require networking
     (propagated-inputs (list python-requests))
-    (native-inputs (list python-isort
-                         python-pytest
+    (native-inputs (list python-pytest
                          python-pytest-cov
                          python-setuptools
                          python-sphinx
@@ -10131,7 +10130,6 @@ (define-public python-zeep
            python-flake8-blind-except
            python-flake8-debugger
            python-freezegun
-           python-isort
            python-pretend
            python-pytest
            python-pytest-asyncio
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 657ac6e4d0..74cec98420 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -396,8 +396,7 @@ (define-public python-archspec
                              python-scikit-learn
                              python-tables
                              python-typing-extensions))
-    (native-inputs (list python-isort
-                         python-poetry-core
+    (native-inputs (list python-poetry-core
                          python-pytest
                          python-pytest-cov))
     (home-page "https://github.com/archspec/archspec")
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 7a02786ab6..0344074366 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2669,7 +2669,6 @@ (define-public python-statsmodels
     (native-inputs
      (list python-colorama
            python-cython
-           python-isort
            python-joblib
            python-matplotlib
            python-pytest
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index a6872a3f1f..d1e2130980 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -2120,7 +2120,6 @@ (define-public python-qemu-qmp
     (native-inputs
      (list python-avocado-framework
            python-flake8
-           python-isort
            python-setuptools
            python-setuptools-scm
            python-wheel))
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 26/48] gnu: python-django-contact-form: Remove python-pytest-cov native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-27-ngraves@ngraves.fr

* gnu/packages/django.scm (python-django-contact-form):

[native-inputs]: Remove python-pytest-cov.

[build-system]: Upgrade to pyproject-build-system.

[arguments]<#:phases>: Remove coverage tests for check phase.

Change-Id: I4d0fc406401b7e923f7efa084dbe8ea3753e50fc

---

gnu/packages/django.scm | 7 ++-----

1 file changed, 2 insertions(+), 5 deletions(-)

Toggle diff (25 lines)diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index 287c6fceee..79712c4945 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -888,16 +888,13 @@ (define-public python-django-contact-form
               (sha256
                (base32
                 "1my9hkrylckp5vfqg9b0kncrdlxjnwxll56sdciqn4v19i4wbq1y"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
          (replace 'check
            (lambda _
-             (invoke "coverage" "run" "--source" "contact_form"
-                     "runtests.py"))))))
-    (native-inputs
-     (list python-coverage))
+             (invoke "python" "runtests.py"))))))
     (propagated-inputs
      (list python-django))
     (home-page "https://github.com/ubernostrum/django-contact-form")
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 24/48] build-system/pyproject: Remove python-twine native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-25-ngraves@ngraves.fr

* gnu/packages/bioinformatics.scm (python-metacells, python-ngesh,
  python-pyahocorasick)
* gnu/packages/finance.scm (fava)
* gnu/packages/gettext.scm (mdpo)
* gnu/packages/jupyter.scm (python-hatch-jupyter-builder,
  python-papermill)
* gnu/packages/machine-learning.scm (python-linear-operator,
  python-gpytorch)
* gnu/packages/python-check.scm (python-testfixtures)
* gnu/packages/python-web.scm (python-translation-finder,
  python-eventlet, python-transient)
* gnu/packages/python-xyz.scm (python-cftime)
* gnu/packages/terminals.scm (python-halo)
* gnu/packages/virtualization.scm (python-transient)
[native-inputs]: Remove python-twine.
---
 gnu/packages/bioinformatics.scm   | 7 ++-----
 gnu/packages/finance.scm          | 1 -
 gnu/packages/gettext.scm          | 1 -
 gnu/packages/jupyter.scm          | 4 +---
 gnu/packages/machine-learning.scm | 6 ++----
 gnu/packages/python-check.scm     | 2 +-
 gnu/packages/python-web.scm       | 5 ++---
 gnu/packages/python-xyz.scm       | 2 --
 gnu/packages/terminals.scm        | 1 -
 gnu/packages/virtualization.scm   | 1 -
 10 files changed, 8 insertions(+), 22 deletions(-)

Toggle diff (184 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4294016f44..d81791a724 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3176,7 +3176,6 @@ (define-public python-metacells
                          python-setuptools
                          python-sphinx
                          python-sphinx-rtd-theme
-                         python-twine
                          python-wheel))
     (home-page "https://github.com/tanaylab/metacells.git")
     (synopsis "Single-cell RNA Sequencing Analysis")
@@ -3203,8 +3202,7 @@ (define-public python-ngesh
         (base32 "07sj4x95b5hvx57pw24f80sk4ag4hkg1z6wzym3pzi8n5gn85n1z"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-ete3 python-numpy python-six))
-    (native-inputs (list python-pytest python-twine
-                         python-wheel))
+    (native-inputs (list python-pytest python-wheel))
     (home-page "https://github.com/tresoldi/ngesh")
     (synopsis "Library for phylogenetic tree simulation")
     (description
@@ -7775,8 +7773,7 @@ (define-public python-pyahocorasick
        (sha256
         (base32 "1fsnivwcw56q7lwz41c5kbfvxv0v17mmkx43i2a293l49fxj08j8"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-pytest python-twine python-setuptools
-                         python-wheel))
+    (native-inputs (list python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/WojciechMula/pyahocorasick")
     (synopsis "Library for finding multiple key strings in text")
     (description
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index 3af525da18..30ed44aea9 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -2072,7 +2072,6 @@ (define-public fava
            python-pytest
            python-pytest-cov
            python-setuptools
-           python-twine
            python-types-setuptools
            python-types-simplejson
            python-wheel))
diff --git a/gnu/packages/gettext.scm b/gnu/packages/gettext.scm
index 841d3e0c8b..25f4efe1fc 100644
--- a/gnu/packages/gettext.scm
+++ b/gnu/packages/gettext.scm
@@ -233,7 +233,6 @@ (define-public mdpo
            python-sphinx
            python-sphinx-argparse
            python-sphinx-rtd-theme
-           python-twine
            python-yamllint))
     (propagated-inputs
      (list python-polib python-pymd4c))
diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm
index 8f900d3f88..70c13115de 100644
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -546,8 +546,7 @@ (define-public python-hatch-jupyter-builder
     (native-inputs (list python-pytest
                          python-pytest-cov
                          python-pytest-mock
-                         python-tomli
-                         python-twine))
+                         python-tomli))
     (home-page "https://github.com/jupyterlab/hatch-jupyter-builder")
     (synopsis "Hatch plugin to help build Jupyter packages")
     (description
@@ -1171,7 +1170,6 @@ (define-public python-papermill
                          python-recommonmark
                          python-requests
                          python-setuptools
-                         python-twine
                          python-wheel))
     (home-page "https://github.com/nteract/papermill")
     (synopsis "Parameterize and run Jupyter and nteract Notebooks")
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 8c1e99ba99..a7c9e2dc99 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -5888,8 +5888,7 @@ (define-public python-linear-operator
     (native-inputs (list python-flake8-print
                          python-pytest
                          python-setuptools
-                         python-setuptools-scm
-                         python-twine))
+                         python-setuptools-scm))
     (home-page "https://github.com/cornellius-gp/linear_operator/")
     (synopsis "Linear operator implementation")
     (description "LinearOperator is a PyTorch package for abstracting away the
@@ -5918,8 +5917,7 @@ (define-public python-gpytorch
     (native-inputs (list python-flake8-print
                          python-nbval
                          python-pytest
-                         python-setuptools
-                         python-twine))
+                         python-setuptools))
     (home-page "https://gpytorch.ai")
     (synopsis "Implementation of Gaussian Processes in PyTorch")
     (description
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index c2026f2433..35e043b3c8 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -778,7 +778,7 @@ (define-public python-testfixtures
     (native-inputs
      (list python-pytest python-pytest-cov
            ;;("python-pytest-django" ,python-pytest-django)
-           python-twine python-wheel))
+           python-wheel))
     (synopsis "Tests components for Python")
     (description "Testfixtures is a collection of helpers and mock objects that
 are useful when writing automated tests in Python.")
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 2248d62195..1c419c6722 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -426,8 +426,7 @@ (define-public python-eventlet
     (native-inputs
      (list python-hatch-vcs
            python-hatchling
-           python-pytest
-           python-twine))
+           python-pytest))
     (propagated-inputs
      (list python-dnspython
            python-greenlet
@@ -7463,7 +7462,7 @@ (define-public python-translation-finder
      (list python-chardet python-pathlib2 python-ruamel.yaml python-six))
     (native-inputs
      (list python-codecov python-codacy-coverage python-pytest-cov
-           python-pytest-runner python-twine))
+           python-pytest-runner))
     (home-page "https://weblate.org/")
     (synopsis "Translation file finder for Weblate")
     (description "This package provides a function to find translation file in
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 74cec98420..f0a65a968d 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3732,7 +3732,6 @@ (define-public python-cftime
            python-pytest
            python-setuptools
            python-sphinx
-           python-twine
            python-wheel))
     (home-page "https://unidata.github.io/cftime/")
     (synopsis "Library for time handling")
@@ -33509,7 +33508,6 @@ (define-public python-eliot
            python-sphinx
            python-sphinx-rtd-theme
            python-testtools
-           python-twine
            python-twisted
            python-wheel))
     (home-page "https://github.com/itamarst/eliot/")
diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index 36ad457ca2..de47d67e36 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -1178,7 +1178,6 @@ (define-public python-halo
     (native-inputs
      (list python-nose
            python-setuptools
-           python-twine
            python-wheel))
     (home-page "https://github.com/manrajgrover/halo")
     (synopsis "Python library to display graphical spinners in the terminal")
diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm
index d1e2130980..1d9da88eb6 100644
--- a/gnu/packages/virtualization.scm
+++ b/gnu/packages/virtualization.scm
@@ -2987,7 +2987,6 @@ (define-public python-transient
     (native-inputs
      (list python-pyhamcrest
            python-setuptools
-           python-twine
            python-wheel))
     (propagated-inputs
      (list python-beautifultable
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 28/48] build-system/pyproject: Remove python-pytest-isort native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-29-ngraves@ngraves.fr

* gnu/packages/dav.scm (radicale)
* gnu/packages/python-check.scm (python-pytest-isort)
* gnu/packages/python-xyz.scm (python-cairosvg)
[native-inputs]: Remove python-pytest-isort.

python-pytest-isort
---
 gnu/packages/dav.scm          | 1 -
 gnu/packages/python-check.scm | 2 +-
 gnu/packages/python-xyz.scm   | 1 -
 3 files changed, 1 insertion(+), 3 deletions(-)

Toggle diff (39 lines)diff --git a/gnu/packages/dav.scm b/gnu/packages/dav.scm
index 7688c9a994..ff5d8409b0 100644
--- a/gnu/packages/dav.scm
+++ b/gnu/packages/dav.scm
@@ -59,7 +59,6 @@ (define-public radicale
     (native-inputs
      (list python-pytest
            python-pytest-flake8
-           python-pytest-isort
            python-setuptools
            python-waitress
            python-wheel))
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index c5a94582b9..09a56f172e 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -1867,7 +1867,7 @@ (define-public python-pytest-pycodestyle
     (propagated-inputs
      (list python-py python-pycodestyle python-pytest))
     (native-inputs
-     (list python-pytest-isort python-setuptools python-wheel))
+     (list python-setuptools python-wheel))
     (home-page "https://github.com/henry0312/pytest-pycodestyle")
     (synopsis "Pytest plugin to run pycodestyle")
     (description "This package provides a plugin to run @code{pycodestyle}
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 9a6c763eb0..1dec12b664 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -31631,7 +31631,6 @@ (define-public python-cairosvg
            python-pillow python-tinycss2))
     (native-inputs
      (list python-pytest-flake8
-           python-pytest-isort
            python-pytest-runner
            python-setuptools
            python-wheel))
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 27/48] gnu: python-dateutil: Remove python-pytest-cov native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-28-ngraves@ngraves.fr

* gnu/packages/time.scm (python-dateutil):

[native-inputs]: Remove python-pytest-cov.

[arguments]<#:phases>: Add remove-pytest-cov-dep phase.

Change-Id: Id82a147d6e40383ecc2661ac896b65b858c181e0

---

gnu/packages/time.scm | 18 ++++++++++++------

1 file changed, 12 insertions(+), 6 deletions(-)

Toggle diff (33 lines)diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm
index 9ed43d1885..5f07e0860a 100644
--- a/gnu/packages/time.scm
+++ b/gnu/packages/time.scm
@@ -277,14 +277,20 @@ (define-public python-dateutil
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags '(list  ; avoid freezegun dependency
-                     "--ignore=dateutil/test/test_utils.py"
-                     "--ignore=dateutil/test/test_rrule.py"
-                     ;; XXX: Fails to get timezone from /etc/localtime.
-                     "--ignore=dateutil/test/test_tz.py")))
+      #:test-flags '(list "dateutil/test" "docs"
+                          ;; avoid freezegun dependency
+                          "--ignore=dateutil/test/test_utils.py"
+                          "--ignore=dateutil/test/test_rrule.py"
+                          ;; XXX: Fails to get timezone from /etc/localtime.
+                          "--ignore=dateutil/test/test_tz.py")
+      #:phases #~(modify-phases %standard-phases
+                   (add-after 'unpack 'remove-pytest-cov-dep
+                     (lambda _
+                       (substitute* "dateutil/test/conftest.py"
+                         (("item\\.add_marker\\(pytest\\.mark\\.no_cover\\)")
+                          "pass")))))))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
            python-setuptools
            python-setuptools-scm
            python-wheel))
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 47/48] gnu: python-loguru: Remove python-pytest-mypy-plugins.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-48-ngraves@ngraves.fr

* gnu/packages/python-xyz.scm (python-loguru)
[arguments]: Add in {test-flags} to skip the concerned test file.
[native-inputs]: Remove python-pytest-mypy-plugins.
---
 gnu/packages/python-xyz.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

Toggle diff (21 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 58dcb3c896..2537b9a63c 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -35072,11 +35072,12 @@ (define-public python-loguru
       #~(list"--numprocesses" (number->string (parallel-job-count))
              ;; All of these fail with: error: Cannot find implementation or
              ;; library stub for module named "loguru"
-             "--ignore=tests/typesafety/test_logger.yml")))
+             "--ignore=tests/typesafety/test_logger.yml"
+             ;; Removes mypy dependency
+             "--ignore=tests/test_type_hinting.py")))
     (native-inputs
      (list python-freezegun
            python-pytest
-           python-pytest-mypy-plugins
            python-pytest-xdist
            python-setuptools
            python-wheel))
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 48/48] gnu: gunicorn: Migrate 'check phase to pyproject-build-system.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-49-ngraves@ngraves.fr

* gnu/packages/python-web.scm (gunicorn)[arguments]
{phases}: Remove 'check phase and migrate its flags to...
{test-flags}: ...here.
---
 gnu/packages/python-web.scm | 16 +++++-----------
 1 file changed, 5 insertions(+), 11 deletions(-)

Toggle diff (35 lines)diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 846418c4d6..65a102c846 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -7190,23 +7190,17 @@ (define-public gunicorn
     (outputs '("out" "doc"))
     (build-system pyproject-build-system)
     (arguments
-     `(#:phases
+     `(#:test-flags
+       ;; Disable the geventlet tests because eventlet uses dnspython, which
+       ;; does not work in the build container due to lack of /etc/resolv.conf
+       '("--ignore=tests/workers/test_geventlet.py")
+       #:phases
        (modify-phases %standard-phases
          (add-after 'build 'build-doc
            (lambda _
              (invoke "make" "-C" "docs" "PAPER=a4" "html" "info")
              (delete-file "docs/build/texinfo/Makefile")
              (delete-file "docs/build/texinfo/Gunicorn.texi")))
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (if tests?
-                 (begin
-                   (invoke "pytest" "-vv"
-                           ;; Disable the geventlet tests because eventlet uses
-                           ;; dnspython, which does not work in the build
-                           ;; container due to lack of /etc/resolv.conf, etc.
-                           "--ignore=tests/workers/test_geventlet.py"))
-                 (format #t "test suite not run~%"))))
          (add-after 'install 'install-doc
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((doc (string-append (assoc-ref outputs "doc")
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 29/48] build-system/pyproject: Remove python-pytest-flake8 native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-30-ngraves@ngraves.fr

* gnu/packages/bioinformatics.scm (python-muon)
* gnu/packages/check.scm (python-pytest-enabler, python-pytest-perf)
* gnu/packages/dav.scm (radicale)
* gnu/packages/debug.scm (c-vise)
* gnu/packages/matrix.scm (python-matrix-nio)
* gnu/packages/python-web.scm (python-mechanicalsoup)
* gnu/packages/python-xyz.scm (python-pyvips, python-dask-image,
  python-importlib-resources, python-jaraco-classes,
  python-jaraco-context, python-jaraco-functools,
  python-jaraco-packaging, python-jaraco-test, python-path,
  python-pip-run, python-tempora, python-cairosvg)
[native-inputs]: Remove python-pytest-flake8.

* gnu/packages/python-check.scm (python-pytest-csv)
[arguments]{test-flags}: Ignore flake8 related test.
[native-inputs]: Remove python-pytest-flake8.
---
 gnu/packages/bioinformatics.scm |  3 +--
 gnu/packages/check.scm          |  2 --
 gnu/packages/dav.scm            |  1 -
 gnu/packages/debug.scm          |  2 +-
 gnu/packages/matrix.scm         |  1 -
 gnu/packages/python-check.scm   |  5 +++--
 gnu/packages/python-web.scm     |  3 +--
 gnu/packages/python-xyz.scm     | 16 ++--------------
 8 files changed, 8 insertions(+), 25 deletions(-)

Toggle diff (201 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5cb3f86853..2fa52eb5b1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5425,8 +5425,7 @@ (define-public python-muon
                              python-tqdm
                              python-umap-learn))
     (native-inputs (list python-flit-core
-                         python-pytest
-                         python-pytest-flake8))
+                         python-pytest))
     (home-page "https://github.com/scverse/muon")
     (synopsis "Multimodal omics analysis framework")
     (description "muon is a multimodal omics Python framework.")
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 57e62f6af0..ee0f4385e2 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2944,7 +2944,6 @@ (define-public python-pytest-enabler
            python-toml))
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
-                         python-pytest-flake8
                          python-pytest-mypy
                          python-setuptools
                          python-setuptools-scm
@@ -3117,7 +3116,6 @@ (define-public python-pytest-perf
      (list python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools
            python-wheel))
diff --git a/gnu/packages/dav.scm b/gnu/packages/dav.scm
index ff5d8409b0..71d12a0ca1 100644
--- a/gnu/packages/dav.scm
+++ b/gnu/packages/dav.scm
@@ -58,7 +58,6 @@ (define-public radicale
     (build-system pyproject-build-system)
     (native-inputs
      (list python-pytest
-           python-pytest-flake8
            python-setuptools
            python-waitress
            python-wheel))
diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm
index 5580b4eaf4..59d17f2623 100644
--- a/gnu/packages/debug.scm
+++ b/gnu/packages/debug.scm
@@ -255,7 +255,7 @@ (define-public c-vise
        (file-name (git-file-name name version))))
     (build-system cmake-build-system)
     (native-inputs
-     (list flex python-pytest python-pytest-flake8))
+     (list flex python-pytest))
     (inputs
      (list bash-minimal clang llvm unifdef
            python python-pebble python-psutil python-chardet))
diff --git a/gnu/packages/matrix.scm b/gnu/packages/matrix.scm
index 970093d345..e7c1468da4 100644
--- a/gnu/packages/matrix.scm
+++ b/gnu/packages/matrix.scm
@@ -200,7 +200,6 @@ (define-public python-matrix-nio
            python-pytest-aiohttp
            python-pytest-asyncio
            python-pytest-benchmark
-           python-pytest-flake8
            python-setuptools
            python-wheel))
     (propagated-inputs
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 09a56f172e..c7187d1523 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -673,9 +673,10 @@ (define-public python-pytest-csv
         (base32
          "17518f2fn5l98lyk9p8r7215c1whi61imzrh6ahrmcksr8w0zz04"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list #:test-flags '(list "--ignore=tests/test_flake8.py")))
     (native-inputs
-     (list python-pytest-flake8
-           python-pytest-xdist
+     (list python-pytest-xdist
            python-setuptools
            python-tabulate
            python-wheel))
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index f0ccbf3b92..dcfe693178 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -2309,8 +2309,7 @@ (define-public python-mechanicalsoup
     (propagated-inputs
      (list python-beautifulsoup4 python-lxml python-requests python-six))
     (native-inputs
-     (list python-pytest-flake8
-           python-pytest-httpbin
+     (list python-pytest-httpbin
            python-pytest-mock
            python-pytest-runner
            python-requests-mock
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 1dec12b664..86655a9d42 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -12037,7 +12037,6 @@ (define-public python-pyvips
     (native-inputs
      (list python-pyperf
            python-pytest
-           python-pytest-flake8
            python-pytest-runner))
     (inputs
      (list glib vips))
@@ -12792,7 +12791,6 @@ (define-public python-importlib-resources
      (list python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools-57
            python-setuptools-scm))
@@ -12940,7 +12938,6 @@ (define-public python-jaraco-classes
     (native-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools
            python-setuptools-scm
@@ -13031,7 +13028,6 @@ (define-public python-jaraco-context
     (native-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools
            python-setuptools-scm
@@ -13064,7 +13060,6 @@ (define-public python-jaraco-functools
      (list python-jaraco-classes
            python-pytest
            python-pytest-checkdocs
-           python-pytest-flake8
            python-pytest-mypy
            python-setuptools
            python-setuptools-scm
@@ -13094,7 +13089,6 @@ (define-public python-jaraco-packaging
     (propagated-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-flake8
            python-rst.linker
            python-setuptools
            python-setuptools-scm
@@ -17898,7 +17892,6 @@ (define-public python-path
                python-pytest
                python-pytest-checkdocs
                python-pytest-enabler
-               python-pytest-flake8
                python-pytest-mypy)))
     (properties (alist-delete 'hidden?
                               (package-properties
@@ -18002,7 +17995,6 @@ (define-public python-pip-run
                python-pytest
                python-pytest-checkdocs
                python-pytest-enabler
-               python-pytest-flake8
                python-pytest-mypy)))
     (properties (alist-delete 'hidden? (package-properties
                                         python-pip-run-bootstrap)))))
@@ -27862,7 +27854,6 @@ (define-public python-tempora
            python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-flake8
            python-pytest-freezegun
            python-pytest-mypy
            python-setuptools-scm
@@ -30536,7 +30527,7 @@ (define-public python-dask-image
                              python-scipy
                              python-tifffile))
     (native-inputs
-     (list python-pytest-flake8 python-pytest))
+     (list python-pytest))
     (home-page "https://github.com/dask/dask-image")
     (synopsis "Distributed image processing")
     (description "This is a package for image processing with Dask arrays.
@@ -31630,10 +31621,7 @@ (define-public python-cairosvg
      (list python-cairocffi python-cssselect2 python-defusedxml
            python-pillow python-tinycss2))
     (native-inputs
-     (list python-pytest-flake8
-           python-pytest-runner
-           python-setuptools
-           python-wheel))
+     (list python-pytest-runner python-setuptools python-wheel))
     (home-page "https://cairosvg.org/")
     (synopsis "SVG to PDF/PS/PNG converter based on Cairo")
     (description "CairoSVG is a SVG converter based on Cairo.  It can export
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 30/48] build-system/pyproject: Remove python-pytest-mypy inputs.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-31-ngraves@ngraves.fr

* gnu/packages/astronomy.scm (python-poliastro)

[native-inputs]: Remove python-pytest-mypy.

* gnu/packages/check.scm (python-pytest-perf)[native-inputs]: Remove

python-pytest-mypy.

* gnu/packages/python-web.scm (python-portend)[native-inputs]: Remove

python-pytest-mypy.

* gnu/packages/python-xyz.scm (python-importlib-resources,

python-jaraco-classes, python-jaraco-collections,

python-jaraco-context, python-jaraco-functools, python-jaraco-test,

python-path, python-pip-run, python-inflect, python-tempora,

python-portalocker)[native-inputs]: Remove python-pytest-mypy.

---

gnu/packages/astronomy.scm | 3 +--

gnu/packages/check.scm | 1 -

gnu/packages/python-web.scm | 1 -

gnu/packages/python-xyz.scm | 14 ++------------

4 files changed, 3 insertions(+), 16 deletions(-)

Toggle diff (128 lines)diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 7384da6452..2cea636e1b 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4629,8 +4629,7 @@ (define-public python-poliastro
            python-flit-core
            python-pytest
            python-pytest-doctestplus
-           python-pytest-mpl
-           python-pytest-mypy))
+           python-pytest-mpl))
     (propagated-inputs
      (list python-astropy
            python-astroquery
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index ee0f4385e2..40116749a9 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -3116,7 +3116,6 @@ (define-public python-pytest-perf
      (list python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-mypy
            python-setuptools
            python-wheel))
     (propagated-inputs
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index dcfe693178..0b1468fc28 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -699,7 +699,6 @@ (define-public python-portend
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-mypy
                          python-setuptools
                          python-wheel))
     (home-page "https://github.com/jaraco/portend")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 86655a9d42..3146352420 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -5660,7 +5660,6 @@ (define-public python-portalocker
                 "0lawjm736vs86wlnxc3qqh37l11z0yx81xq3dmrw33m86kaq2bh3"))))
     (build-system pyproject-build-system)
     (native-inputs (list python-pytest
-                         python-pytest-mypy
                          python-pytest-timeout
                          python-redis
                          python-setuptools
@@ -12791,7 +12790,6 @@ (define-public python-importlib-resources
      (list python-pytest
            python-pytest-checkdocs
            python-pytest-enabler
-           python-pytest-mypy
            python-setuptools-57
            python-setuptools-scm))
     (propagated-inputs
@@ -12938,7 +12936,6 @@ (define-public python-jaraco-classes
     (native-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-mypy
            python-setuptools
            python-setuptools-scm
            python-wheel))
@@ -12970,7 +12967,6 @@ (define-public python-jaraco-collections
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-mypy
                          python-setuptools
                          python-wheel))
     (home-page "https://github.com/jaraco/jaraco.collections")
@@ -13028,7 +13024,6 @@ (define-public python-jaraco-context
     (native-inputs
      (list python-pytest
            python-pytest-checkdocs
-           python-pytest-mypy
            python-setuptools
            python-setuptools-scm
            python-wheel))
@@ -13060,7 +13055,6 @@ (define-public python-jaraco-functools
      (list python-jaraco-classes
            python-pytest
            python-pytest-checkdocs
-           python-pytest-mypy
            python-setuptools
            python-setuptools-scm
            python-wheel))
@@ -13152,7 +13146,6 @@ (define-public python-jaraco-text
     (native-inputs (list python-pytest
                          python-pytest-checkdocs
                          python-pytest-enabler
-                         python-pytest-mypy
                          python-setuptools
                          python-wheel))
     (home-page "https://github.com/jaraco/jaraco.text")
@@ -17891,8 +17884,7 @@ (define-public python-path
                python-pygments
                python-pytest
                python-pytest-checkdocs
-               python-pytest-enabler
-               python-pytest-mypy)))
+               python-pytest-enabler)))
     (properties (alist-delete 'hidden?
                               (package-properties
                                python-path-bootstrap)))))
@@ -17994,8 +17986,7 @@ (define-public python-pip-run
                python-pygments
                python-pytest
                python-pytest-checkdocs
-               python-pytest-enabler
-               python-pytest-mypy)))
+               python-pytest-enabler)))
     (properties (alist-delete 'hidden? (package-properties
                                         python-pip-run-bootstrap)))))
 
@@ -27855,7 +27846,6 @@ (define-public python-tempora
            python-pytest-checkdocs
            python-pytest-enabler
            python-pytest-freezegun
-           python-pytest-mypy
            python-setuptools-scm
            python-types-freezegun
            python-types-pytz
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 31/48] build-system/pyproject: Stop hiding options.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-32-ngraves@ngraves.fr

* gnu/packages/pdf.scm (python-pydyf, weasyprint)[arguments]
<#:test-flags>: Remove arguments hiding coverage options.

* gnu/packages/python-crypto.scm (python-keyring)
[arguments]<#:test-flags>: Remove arguments hiding coverage options.

* gnu/packages/python-web.scm (python-asgi-lifespan,
python-openapi-schema-validator, python-openapi-spec-validator,
python-openapi-core)[arguments]<#:test-flags>: Remove arguments hiding
coverage options.
(python-openapi-schema-validator, python-openapi-spec-validator)
[arguments]<#:phases>: Remove 'remove-coverage-pytest-options phase.
(python-cssselect2)[arguments]: Remove uneeded field.
(python-quart)[arguments]: Remove uneeded field.
(python-jsonpickle)[arguments]<#:test-flags>: Remove uneeded
test-flags.

* gnu/packages/python-xyz.scm (python-cattrs)
[arguments]<#:phases>: Remove arguments hiding coverage options.
(python-blessed)[arguments]: Remove uneeded field.

python-pytest-cov remove option
---
 gnu/packages/pdf.scm           |  6 +----
 gnu/packages/python-crypto.scm |  1 -
 gnu/packages/python-web.scm    | 42 +++-------------------------------
 gnu/packages/python-xyz.scm    |  8 +------
 4 files changed, 5 insertions(+), 52 deletions(-)

Toggle diff (159 lines)diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm
index ce63306c07..7308b0c661 100644
--- a/gnu/packages/pdf.scm
+++ b/gnu/packages/pdf.scm
@@ -805,9 +805,6 @@ (define-public python-pydyf
        (sha256
         (base32 "18q43g5d9455msipcgd5fvnh8m4a2rz189slzfg80yycjw66rshs"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:test-flags #~'("-c" "/dev/null")))
     (propagated-inputs (list python-pillow))
     (native-inputs
      (list ghostscript
@@ -1669,8 +1666,7 @@ (define-public weasyprint
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags #~(list "-c" "/dev/null"
-                           "-n" (number->string (parallel-job-count)))
+      #:test-flags #~(list "-n" (number->string (parallel-job-count)))
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-library-paths
diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm
index ec4e074a6b..9750302705 100644
--- a/gnu/packages/python-crypto.scm
+++ b/gnu/packages/python-crypto.scm
@@ -268,7 +268,6 @@ (define-public python-keyring
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags '(list "-c" "/dev/null") ;avoid extra test dependencies
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'check 'workaround-test-failure
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 0b1468fc28..c5b904d229 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1267,8 +1267,7 @@ (define-public python-asgi-lifespan
     (arguments
      (list
       #:test-flags
-      '(list "-c" "/dev/null"           ;ignore coverage-related options
-             "-k"
+      '(list "-k"
              (string-append
               ;; XXX: Some tests fail because of "Exceptions from Trio nursery"
               "not (test_lifespan_manager[trio-None-None-StartupFailed]"
@@ -2259,10 +2258,7 @@ (define-public python-jsonpickle
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags
-      ;; Prevent running the flake8 and black pytest plugins, which only tests
-      ;; style and frequently causes harmless failures.
-      '(list "-o" "addopts=''" "tests")
+      #:test-flags '(list "tests")
       #:phases
       '(modify-phases %standard-phases
          (add-before 'check 'pre-check
@@ -3014,10 +3010,6 @@ (define-public python-openapi-schema-validator
       '(list "-k" "not test_array_prefixitems_invalid")
       #:phases
       #~(modify-phases %standard-phases
-          (add-after 'unpack 'remove-coverage-pytest-options
-            (lambda _
-              (substitute* "pyproject.toml"
-                (("^--cov.*") ""))))
           ;; See https://github.com/python-openapi/openapi-schema-validator/issues/204
           (add-after 'unpack 'relax-requirements
             (lambda _
@@ -3061,13 +3053,7 @@ (define-public python-openapi-spec-validator
      (list
       ;; These tests attempt to fetch resources from the Internet
       #:test-flags '(list "--ignore-glob=tests/integration/validation/**"
-                          "-k" "not example")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'remove-coverage-pytest-options
-            (lambda _
-              (substitute* "pyproject.toml"
-                (("^--cov.*") "")))))))
+                          "-k" "not example")))
     (native-inputs
      (list python-poetry-core
            python-pytest))
@@ -3106,9 +3092,6 @@ (define-public python-openapi-core
      (list
       #:test-flags
       '(list "tests/unit"
-             ;; Ignore Pytest configuration in setup.cfg that adds
-             ;; unwanted flake8 and coverage options.
-             "-c" "/dev/null"
              "-k" "not test_chars_valid")))
     (native-inputs (list python-django
                          python-falcon
@@ -7104,17 +7087,6 @@ (define-public python-cssselect2
        (sha256
         (base32 "1j2fcr217rsvkipsg6zjq03rl64rxnvb5hqqpx0dv58fhspvkywk"))))
     (build-system pyproject-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'disable-linters
-           ;; Their check fails; none of our business.
-           (lambda _
-             (substitute* '("setup.py" "pyproject.toml")
-               (("'pytest-flake8',") "")
-               (("'pytest-isort',") "")
-               (("--flake8") "")
-               (("--isort") "")))))))
     (propagated-inputs
      (list python-tinycss2))
     (native-inputs
@@ -9753,14 +9725,6 @@ (define-public python-quart
        (sha256
         (base32 "1h5ifv8g9dc9m07vj4v7dfalam83v38545d845vvgys1gan1pscd"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'remove-coverage-pytest-options
-            (lambda _
-              (substitute* "pyproject.toml"
-                (("--no-cov-on-fail") "")))))))
     (native-inputs
      (list python-poetry-core
            python-pytest
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 3146352420..18b5470573 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -22876,9 +22876,7 @@ (define-public python-cattrs
               (substitute* "pyproject.toml"
                 ;; Fix version string
                 (("dynamic = \\[\"version\"\\]")
-                 (string-append "version = \"" #$version "\""))
-                ;; Just run pytest with no frills
-                (("addopts = \"-l.*") ""))))
+                 (string-append "version = \"" #$version "\"")))))
           ;; XXX Our python-hypothesis package is too old.
           (add-after 'unpack 'compatibility
             (lambda _
@@ -33951,10 +33949,6 @@ (define-public python-blessed
          ;; Don't get hung up on Windows test failures.
          '(delete-file "blessed/win_terminal.py"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list
-      ;; Avoid python-pytest-coverage
-      #:test-flags '(list "-c /dev/null")))
     (propagated-inputs (list python-six python-wcwidth))
     (native-inputs (list python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/jquast/blessed")
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 32/48] gnu: python-linear-operator: Remove python-flake8-print native-input

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-33-ngraves@ngraves.fr

* gnu/packages/machine-learning.scm (python-linear-operator):

[native-inputs]: Remove pytest-flake8-print.

Change-Id: Iba2670b47e479c20a3f4ae1c703ad9fe815e3764

---

gnu/packages/machine-learning.scm | 3 +--

1 file changed, 1 insertion(+), 2 deletions(-)

Toggle diff (16 lines)diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 360325c768..eb818d672f 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -5876,8 +5876,7 @@ (define-public python-linear-operator
                              python-pytorch
                              python-scipy
                              python-typeguard))
-    (native-inputs (list python-flake8-print
-                         python-pytest
+    (native-inputs (list python-pytest
                          python-setuptools
                          python-setuptools-scm))
     (home-page "https://github.com/cornellius-gp/linear_operator/")
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 33/48] gnu: multidict: Remove python-pytest-cov native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-34-ngraves@ngraves.fr

* gnu/packages/python-xyz.scm (multidict)
[native-inputs]: Remove python-pytest-cov.
[arguments]{phases}: Add 'avoid-pytest-cov-preload phase.
---
 gnu/packages/python-xyz.scm | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

Toggle diff (23 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 18b5470573..395d091fd5 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -10988,9 +10988,15 @@ (define-public python-multidict
         (base32
          "0jlgjpclkh5g6vr1danl6alz0cza2jlzdqh3q03d4s8ckfzjxbi2"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list #:phases #~(modify-phases %standard-phases
+                        (add-after 'unpack 'avoid-pytest-cov-preload
+                          (lambda _
+                            (substitute* "pytest.ini"
+                              (("-p pytest_cov") "")))))))
     (propagated-inputs (list python-typing-extensions))
     (native-inputs
-     (list python-pytest python-pytest-cov python-setuptools python-wheel))
+     (list python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/aio-libs/multidict/")
     (synopsis "Multidict implementation")
     (description "Multidict is dict-like collection of key-value pairs
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 34/48] gnu: python-isort: Remove python-black native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-35-ngraves@ngraves.fr

* gnu/packages/python-xyz.scm (python-isort)
[native-inputs]: Remove python-black.
[arguments]: Adapt {test-flags} accordingly.
---
 gnu/packages/python-xyz.scm | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

Toggle diff (39 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 395d091fd5..9daa1cc8e4 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -25918,15 +25918,15 @@ (define-public python-isort
      (list
       #:test-flags
       #~(list "tests/unit/"
-              "-k" (string-join
-                    (list
-                     "not test_gitignore"
-                     ;; See <https://github.com/PyCQA/isort/issues/2234>.
-                     "test_isort_should_warn_on_empty_custom_config_issue_1433"
-                     ;; Fails because of an unexpected linebreak.
-                     "test_black_pyi_file")
-                    " and not ")
-              "--ignore=tests/unit/test_deprecated_finders.py")
+              "-k"
+              (string-join
+               (list
+                "not test_gitignore"
+                ;; See <https://github.com/PyCQA/isort/issues/2234>.
+                "test_isort_should_warn_on_empty_custom_config_issue_1433")
+               " and not ")
+              "--ignore=tests/unit/test_deprecated_finders.py"
+              "--ignore=tests/unit/profiles/test_black.py")
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'install 'install-example-plugins
@@ -25945,7 +25945,6 @@ (define-public python-isort
                        "install"  "--user" "--no-deps" example-whls)))))))
     (native-inputs
      (list python-colorama
-           python-black
            python-hypothesmith
            python-libcst-minimal
            python-natsort
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 35/48] build-system/pyproject: Remove python-mypy native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-36-ngraves@ngraves.fr

---
 gnu/packages/bioinformatics.scm | 2 --
 gnu/packages/check.scm          | 1 -
 gnu/packages/databases.scm      | 3 +--
 gnu/packages/finance.scm        | 1 -
 gnu/packages/matrix.scm         | 1 -
 gnu/packages/openstack.scm      | 1 -
 gnu/packages/python-check.scm   | 8 ++------
 gnu/packages/python-crypto.scm  | 1 -
 gnu/packages/python-science.scm | 3 +--
 gnu/packages/python-web.scm     | 2 --
 gnu/packages/python-xyz.scm     | 7 ++-----
 11 files changed, 6 insertions(+), 24 deletions(-)

Toggle diff (223 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2fa52eb5b1..ce16f31637 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3167,7 +3167,6 @@ (define-public python-metacells
                              python-threadpoolctl
                              python-umap-learn))
     (native-inputs (list python-bumpversion
-                         python-mypy
                          python-mypy-extensions
                          python-pandas-stubs
                          python-pytest
@@ -6392,7 +6391,6 @@ (define-public python-schema-salad
     (native-inputs
      (list python-black
            python-cachecontrol
-           python-mypy
            python-pytest
            python-pytest-runner
            python-setuptools
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 40116749a9..3c9373648f 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2826,7 +2826,6 @@ (define-public python-crosshair
     (native-inputs
      (list python-icontract ;optional
            python-importlib-metadata
-           python-mypy
            python-numpy
            python-pytest
            python-pytest-xdist))
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index d124ba186c..83363cfedd 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -4141,8 +4141,7 @@ (define-public python-aiosqlite
                           (lambda* (#:key tests? #:allow-other-keys)
                             (when tests?
                               (invoke "python" "-m" "aiosqlite.tests")))))))
-    (native-inputs (list python-flit-core
-                         python-mypy))
+    (native-inputs (list python-flit-core))
     (home-page "https://github.com/jreese/aiosqlite")
     (synopsis
      "Asyncio bridge for sqlite3")
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index eb676592b3..ddc9954d8e 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -2068,7 +2068,6 @@ (define-public fava
            python-werkzeug))
     (native-inputs
      (list python-babel
-           python-mypy
            python-pytest
            python-setuptools
            python-types-setuptools
diff --git a/gnu/packages/matrix.scm b/gnu/packages/matrix.scm
index e7c1468da4..e503d17b91 100644
--- a/gnu/packages/matrix.scm
+++ b/gnu/packages/matrix.scm
@@ -193,7 +193,6 @@ (define-public python-matrix-nio
            python-hpack
            python-hyperframe
            python-hypothesis
-           python-mypy
            python-mypy-extensions
            python-poetry-core
            python-pytest
diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index 84696a586f..2b74994cc5 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -552,7 +552,6 @@ (define-public python-oslo.context
     (native-inputs
      (list python-fixtures
            python-hacking
-           python-mypy
            python-oslotest
            python-pbr
            python-stestr))
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index c7187d1523..ac9243b8f4 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -585,8 +585,7 @@ (define-public python-green
               (when tests?
                 (apply invoke "python" "-m" "green" test-flags)))))))
     (native-inputs
-     (list python-mypy
-           python-setuptools
+     (list python-setuptools
            python-testtools
            python-wheel))
     (propagated-inputs
@@ -814,7 +813,6 @@ (define-public python-icontract
     (native-inputs
      (list python-astor
            python-asyncstdlib
-           python-mypy
            python-numpy
            python-setuptools
            python-typeguard
@@ -2620,7 +2618,6 @@ (define-public python-nptyping
     (native-inputs
      (list python-beartype
            python-feedparser
-           python-mypy
            python-pandas
            python-pytest
            python-setuptools
@@ -3113,8 +3110,7 @@ (define-public python-sybil
         (sha256
          (base32 "0r491k91fi2nb0kdd6di8cb2kxcvsk1xzw3sgwsxhhg4qynsp3bi"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-mypy
-                         python-myst-parser
+    (native-inputs (list python-myst-parser
                          python-pytest
                          python-pyyaml
                          python-seedir
diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm
index 9750302705..ca4539c551 100644
--- a/gnu/packages/python-crypto.scm
+++ b/gnu/packages/python-crypto.scm
@@ -584,7 +584,6 @@ (define-public python-cryptography
            python-cffi
            python-click
            python-cryptography-vectors
-           python-mypy
            python-pretend
            python-pytest
            python-pytest-benchmark
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 55d522b21c..80aa14e166 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -4054,8 +4054,7 @@ (define-public python-pynetdicom
                          python-pytest-xdist
                          python-sphinx
                          python-sphinx-rtd-theme))
-    (propagated-inputs (list python-mypy
-                             python-numpydoc
+    (propagated-inputs (list python-numpydoc
                              python-pydicom
                              python-pyfakefs
                              python-sqlalchemy))
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index c5b904d229..0d343e79e3 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -8850,7 +8850,6 @@ (define-public python-sanic
            python-chardet
            python-cryptography
            python-docutils
-           python-mypy
            python-pygments
            python-pytest
            python-pytest-benchmark
@@ -9873,7 +9872,6 @@ (define-public python-scrapy
            python-zope-interface))
     (native-inputs
      (list nss-certs-for-test
-           python-mypy
            python-pexpect
            python-pytest
            python-pytest-xdist
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 9daa1cc8e4..ad6f9c61f2 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -9496,7 +9496,6 @@ (define-public python-numpy
            meson-python
            pkg-config
            python-hypothesis
-           python-mypy
            python-pytest
            python-pytest-xdist
            python-setuptools
@@ -9575,7 +9574,6 @@ (define-public python-numpy-2
            ninja
            pkg-config
            python-hypothesis
-           python-mypy
            python-pytest
            python-pytest-xdist
            python-setuptools
@@ -9817,7 +9815,6 @@ (define-public python-multiscale-spatial-image
            python-nbmake
            python-pooch
            python-pytest
-           python-pytest-mypy
            python-urllib3
            python-zarr))
     (home-page "https://github.com/spatial-image/multiscale-spatial-image")
@@ -13401,7 +13398,6 @@ (define-public python-traitlets
     (native-inputs
      (list python-argcomplete
            python-hatchling
-           python-mypy
            python-pytest
            python-pytest-mock
            python-pytest-mypy-testing))
@@ -15043,7 +15039,6 @@ (define-public python-seaborn
            python-ipykernel
            python-nbconvert
            python-numpydoc
-           python-mypy
            python-pytest
            python-pytest-xdist
            python-pyyaml))
@@ -28461,6 +28456,8 @@ (define-public python-typeguard
        (sha256
         (base32 "06y22d1f5dhpyl71wbhsaibig5hvc2v44pw795yb8lxl02fsh8hd"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list #:test-flags ''("--ignore=tests/mypy")))
     (native-inputs
      (list python-pytest
            python-setuptools
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 36/48] build-system/pyproject: Add option #:use-pytest-plugin?

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-37-ngraves@ngraves.fr

In the very rare cases where our plugin actually breaks a test, adding

a flag is more convenient than replacing the phase.

* guix/build-system/pyproject.scm (pyproject-build): Add option

use-pytest-plugin?

* guix/build/pyproject-build-system.scm (check): Add and use option

use-pytest-plugin?

* gnu/packages/check.scm (python-coverage,

python-pytest-mypy)[arguments]{use-pytest-plugin}: Set to #f to fix

tests.

* gnu/packages/python-check.scm (python-pytest-flake8)[arguments]:

Likewise.

---

gnu/packages/check.scm | 6 +++++-

gnu/packages/python-check.scm | 1 +

guix/build-system/pyproject.scm | 2 ++

guix/build/pyproject-build-system.scm | 9 ++++++---

4 files changed, 14 insertions(+), 4 deletions(-)

Toggle diff (85 lines)diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 3c9373648f..5bb5edd369 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2500,6 +2500,8 @@ (define-public python-coverage
          "--deselect=tests/test_filereporter.py::FileReporterTest::test_zipfile"
          ;; XXX: Checking coverage for too much files, not only the target one.
          "--deselect=tests/test_oddball.py::DoctestTest::test_doctest")
+      ;; This is one of the rare cases where our plugin causes a test to fail.
+      #:use-pytest-plugin? #f
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-pyproject
@@ -2997,7 +2999,9 @@ (define-public python-pytest-mypy
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags #~(list "--numprocesses" "auto")))
+      #:use-pytest-plugin? #f
+      #:test-flags #~(list "--numprocesses"
+                           (number->string (parallel-job-count)))))
     (native-inputs
      (list python-pexpect
            python-pytest-xdist
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index ac9243b8f4..bbf3e47655 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -1704,6 +1704,7 @@ (define-public python-pytest-flake8
         (base32
          "1rhz7mxcg7x9dbabfcjai3zxikfgw7az07m4ddf92bg35ib3byw8"))))
     (build-system pyproject-build-system)
+    (arguments (list #:use-pytest-plugin? #f))
     (native-inputs
      (list python-pytest
            python-setuptools
diff --git a/guix/build-system/pyproject.scm b/guix/build-system/pyproject.scm
index bdf8f440ac..1cd38ce349 100644
--- a/guix/build-system/pyproject.scm
+++ b/guix/build-system/pyproject.scm
@@ -93,6 +93,7 @@ (define private-keywords
 (define* (pyproject-build name inputs
                           #:key source
                           (tests? #t)
+                          (use-pytest-plugin? #t)
                           (configure-flags ''(@))
                           (backend-path #f)
                           (build-backend #f)
@@ -125,6 +126,7 @@ (define build
                  #:test-backend #$test-backend
                  #:test-flags #$test-flags
                  #:tests? #$tests?
+                 #:use-pytest-plugin? #$use-pytest-plugin?
                  #:phases #$(if (pair? phases)
                                 (sexp->gexp phases)
                                 phases)
diff --git a/guix/build/pyproject-build-system.scm b/guix/build/pyproject-build-system.scm
index 2df9f2f479..a96ec05ad6 100644
--- a/guix/build/pyproject-build-system.scm
+++ b/guix/build/pyproject-build-system.scm
@@ -231,7 +231,8 @@ (define-syntax-rule (with-guix-pytest-plugin inputs exp ...)
   "Evaluate EXP in a context where the Guix pytest plugin is added."
   (call-with-guix-pytest-plugin inputs (lambda () exp ...)))
 
-(define* (check #:key inputs tests? test-backend test-flags #:allow-other-keys)
+(define* (check #:key inputs tests? test-backend test-flags use-pytest-plugin?
+                #:allow-other-keys)
   "Run the test suite of a given Python package."
   (if tests?
       ;; Unfortunately with PEP 517 there is no common method to specify test
@@ -254,8 +255,10 @@ (define* (check #:key inputs tests? test-backend test-flags #:allow-other-keys)
         (format #t "Using ~a~%" use-test-backend)
         (match use-test-backend
           ('pytest
-           (with-guix-pytest-plugin inputs
-             (apply invoke pytest "-vv" test-flags)))
+           (if use-pytest-plugin?
+               (with-guix-pytest-plugin inputs
+                 (apply invoke pytest "-vv" test-flags))
+               (apply invoke pytest "-vv" test-flags)))
           ('nose
            (apply invoke nosetests "-v" test-flags))
           ('nose2
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 37/48] gnu: python-pixell: Update to 0.28.1.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-38-ngraves@ngraves.fr

See https://github.com/simonsobs/pixell/issues/291for the reasons
behind the patch.

* gnu/packages/astronomy.scm (python-pixell): Update to 0.28.1.
[source]: Switch to git-fetch. Add patch.
[propagated-inputs]: Remove python-cython, python-coveralls.
* gnu/packages/patches/python-pixell-avoid-dependency-propagation.patch
New file.
* gnu/local.mk: Add patch.
---
 gnu/local.mk                                    |  1 +
 gnu/packages/astronomy.scm                      | 15 +++++++++------
 ...on-pixell-avoid-dependency-propagation.patch | 17 +++++++++++++++++
 3 files changed, 27 insertions(+), 6 deletions(-)
 create mode 100644 gnu/packages/patches/python-pixell-avoid-dependency-propagation.patch

Toggle diff (73 lines)diff --git a/gnu/local.mk b/gnu/local.mk
index cd6c5d5483..dd187f571b 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -2006,6 +2006,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-matplotlib-fix-legend-loc-best-test.patch	\
   %D%/packages/patches/python-random2-getrandbits-test.patch		\
   %D%/packages/patches/python-pillow-use-zlib-1.3.patch	\
+  %D%/packages/patches/python-pixell-avoid-dependency-propagation.patch	\
   %D%/packages/patches/python-pydocstyle-add-support-for-pep701.patch	\
   %D%/packages/patches/python-pyreadstat-link-libiconv.patch	\
   %D%/packages/patches/python-sip-include-dirs.patch	\
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 2cea636e1b..4804e74a81 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3045,13 +3045,18 @@ (define-public python-mapsims
 (define-public python-pixell
   (package
     (name "python-pixell")
-    (version "0.28.0")
+    (version "0.28.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "pixell" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/simonsobs/pixell")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "11xd0ld329vr3spg5nzszn0bxzahnvkrh2akkd7qff33ndf75hkk"))))
+        (base32 "0p3pndy04n0hd352gjgwpqafp9sm1iq6c45pj745z1cswaf2lmc8"))
+       (patches (search-patches
+                 "python-pixell-avoid-dependency-propagation.patch"))))
     (build-system pyproject-build-system)
     (native-inputs
      (list gfortran
@@ -3062,8 +3067,6 @@ (define-public python-pixell
            python-pytest))
     (propagated-inputs
      (list python-astropy
-           python-coveralls
-           python-cython ; check why it needs in installation
            python-dateutil
            python-ducc0
            python-h5py
diff --git a/gnu/packages/patches/python-pixell-avoid-dependency-propagation.patch b/gnu/packages/patches/python-pixell-avoid-dependency-propagation.patch
new file mode 100644
index 0000000000..52c27bad6f
--- /dev/null
+++ b/gnu/packages/patches/python-pixell-avoid-dependency-propagation.patch
@@ -0,0 +1,17 @@
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -22,14 +22,10 @@
+     'h5py>=2.7',
+     'scipy>=1.0',
+     'python_dateutil>=2.7',
+-    'cython',
+     'healpy>=1.13',
+     'matplotlib>=2.0',
+     'pyyaml>=5.0',
+     'Pillow>=5.3.0, != 10.4.0',
+-    'pytest-cov>=2.6',
+-    'coveralls>=1.5',
+-    'pytest>=4.6',
+     'ducc0>=0.36.0',
+     'numba>=0.54.0'
+ ]
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 40/48] gnu: python-matrix-nio: Remove python-mypy-extension native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-41-ngraves@ngraves.fr

* gnu/packages/matrix.scm (python-matrix-nio)[native-inputs]: Remove
python-mypy-extension.
---
 gnu/packages/matrix.scm | 1 -
 1 file changed, 1 deletion(-)

Toggle diff (14 lines)diff --git a/gnu/packages/matrix.scm b/gnu/packages/matrix.scm
index e503d17b91..1a090c05a7 100644
--- a/gnu/packages/matrix.scm
+++ b/gnu/packages/matrix.scm
@@ -193,7 +193,6 @@ (define-public python-matrix-nio
            python-hpack
            python-hyperframe
            python-hypothesis
-           python-mypy-extensions
            python-poetry-core
            python-pytest
            python-pytest-aiohttp
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 39/48] build-system/pyproject: Remove python-mypy-extensions native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-40-ngraves@ngraves.fr

---

gnu/packages/bioinformatics.scm | 1 -

gnu/packages/web.scm | 3 +--

2 files changed, 1 insertion(+), 3 deletions(-)

Toggle diff (28 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ce16f31637..4d4ec7015b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3167,7 +3167,6 @@ (define-public python-metacells
                              python-threadpoolctl
                              python-umap-learn))
     (native-inputs (list python-bumpversion
-                         python-mypy-extensions
                          python-pandas-stubs
                          python-pytest
                          python-setuptools
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 386dbfa036..15fc5047d9 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -9656,8 +9656,7 @@ (define-public archivebox
            python-crontab
            python-dateparser
            python-django-extensions
-           python-django-3.1.14
-           python-mypy-extensions))
+           python-django-3.1.14))
     (native-inputs
      (list python-wheel))
     (synopsis "Self-hosted Web archiving")
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 38/48] build-system/pyproject: Remove python-check-manifest native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-39-ngraves@ngraves.fr

* guix/import/pypi.scm (pypi-ignored-inputs): Add "check-manifest".

* gnu/packages/jupyter.scm (python-papermill)
* gnu/packages/python-xyz.scm (python-pillow, python-mercantile)
* gnu/packages/time.scm (python-tzlocal)
[native-inputs]: Remove python-check-manifest.
---
 gnu/packages/jupyter.scm    | 1 -
 gnu/packages/python-xyz.scm | 6 ++----
 gnu/packages/time.scm       | 3 +--
 guix/import/pypi.scm        | 2 +-
 4 files changed, 4 insertions(+), 8 deletions(-)

Toggle diff (65 lines)diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm
index 8ce856f128..62f028077f 100644
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -1151,7 +1151,6 @@ (define-public python-papermill
                          python-boto3
                          python-botocore
                          python-bumpversion
-                         python-check-manifest
                          python-ipython
                          python-ipywidgets
                          python-moto
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index ad6f9c61f2..84b1e01cb5 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -11383,9 +11383,7 @@ (define-public python-pillow
                (add-installed-pythonpath inputs outputs)
                (invoke "python" "selftest.py" "--installed")
                (invoke "python" "-m" "pytest" "-vv")))))))
-    (native-inputs (list python-check-manifest
-                         python-coverage
-                         python-defusedxml
+    (native-inputs (list python-defusedxml
                          python-markdown2
                          python-olefile
                          python-packaging
@@ -31466,7 +31464,7 @@ (define-public python-mercantile
     (build-system python-build-system)
     (propagated-inputs (list python-click))
     (native-inputs
-     (list python-check-manifest python-hypothesis python-pytest))
+     (list python-hypothesis python-pytest))
     (home-page "https://github.com/mapbox/mercantile")
     (synopsis "Web mercator XYZ tile utilities")
     (description "The mercantile module provides @code{ul(xtile, ytile, zoom)}
diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm
index 5f07e0860a..310b1ce5cb 100644
--- a/gnu/packages/time.scm
+++ b/gnu/packages/time.scm
@@ -454,8 +454,7 @@ (define-public python-tzlocal
     (propagated-inputs
      (list python-tzdata))
     (native-inputs
-     (list python-check-manifest
-           python-pytest
+     (list python-pytest
            python-pytest-mock))
     (home-page "https://github.com/regebro/tzlocal")
     (synopsis "Local timezone information for Python")
diff --git a/guix/import/pypi.scm b/guix/import/pypi.scm
index a49ab1e429..2e3ea6403d 100644
--- a/guix/import/pypi.scm
+++ b/guix/import/pypi.scm
@@ -87,7 +87,7 @@ (define pypi-ignored-inputs
         "tox" ; test wrapper for other environments
         "codecov" "coverage"  ; coverage
         "black" "isort" "pycodestyle" "pep8"  ; style
-        "pyflakes" "flake8" "pylint" "mypy"  ; style+lint
+        "check-manifest" "pyflakes" "flake8" "pylint" "mypy"  ; style+lint
         "coveralls" "twine"  ; upload integration tools
         "pytest-isort" "pytest-flake8" "pytest-cov" "pytest-black"
         "pytest-pep8" "pytest-mypy" "pytest-pep8" "pre-commit"))  ; variants
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 42/48] build-system/pyproject: Remove python-pre-commit native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-43-ngraves@ngraves.fr

---

gnu/packages/python-check.scm | 3 +--

gnu/packages/python-xyz.scm | 2 --

2 files changed, 1 insertion(+), 4 deletions(-)

Toggle diff (36 lines)diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index bbf3e47655..b37f925b69 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -2291,8 +2291,7 @@ (define-public python-pytest-qt
     (propagated-inputs
      (list python-pluggy python-pyqt python-pytest))
     (native-inputs
-     (list python-pre-commit
-           python-setuptools
+     (list python-setuptools
            python-setuptools-scm
            python-wheel))
     (home-page "https://github.com/pytest-dev/pytest-qt")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 5a3f523899..a9f04d2886 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -11436,7 +11436,6 @@ (define-public python-pillow-heif
                          python-defusedxml
                          python-numpy
                          python-packaging
-                         python-pre-commit
                          python-pympler
                          python-setuptools
                          python-pytest
@@ -13510,7 +13509,6 @@ (define-public python-jupyter-core
     (propagated-inputs (list python-platformdirs python-traitlets))
     (native-inputs (list python-hatchling
                          python-pip
-                         python-pre-commit
                          python-pytest
                          python-pytest-timeout))
     ;; This package provides the `jupyter` binary and thus also exports the
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 41/48] build-system/pyproject: Remove python-pip native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-42-ngraves@ngraves.fr

---
 gnu/packages/bioinformatics.scm |  2 +-
 gnu/packages/databases.scm      |  1 -
 gnu/packages/python-science.scm |  1 -
 gnu/packages/python-web.scm     |  4 +---
 gnu/packages/python-xyz.scm     | 15 ++++-----------
 gnu/packages/shells.scm         |  1 -
 gnu/packages/web.scm            |  1 -
 7 files changed, 6 insertions(+), 19 deletions(-)

Toggle diff (153 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4d4ec7015b..dd33eee8d8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7719,7 +7719,7 @@ (define-public python-illumina-utils
     (build-system pyproject-build-system)
     (arguments (list #:tests? #false))  ;there are none
     (propagated-inputs (list python-matplotlib python-numpy python-levenshtein))
-    (native-inputs (list python-setuptools python-wheel python-pip))
+    (native-inputs (list python-setuptools python-wheel))
     (home-page "https://github.com/meren/illumina-utils")
     (synopsis "Library and scripts to work with Illumina paired-end data")
     (description
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 83363cfedd..ca50dd1bfc 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -5795,7 +5795,6 @@ (define-public datasette
      (list nss-certs-for-test
            python-beautifulsoup4
            python-cogapp
-           python-pip
            python-pytest
            python-pytest-asyncio
            python-pytest-runner
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 80aa14e166..6b7672a816 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -551,7 +551,6 @@ (define-public python-scikit-build-core
                          python-hatch-vcs
                          python-hatchling
                          python-numpy
-                         python-pip
                          python-pypa-build
                          python-pytest
                          python-pytest-subprocess
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 0d343e79e3..6484c5290d 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -2029,7 +2029,6 @@ (define-public httpie
            python-defusedxml
            python-importlib-metadata
            python-multidict
-           python-pip
            python-pygments
            python-requests
            python-requests-toolbelt
@@ -4475,8 +4474,7 @@ (define-public python-requests
            python-idna
            python-urllib3))
     (native-inputs
-     (list python-pip
-           python-pytest
+     (list python-pytest
            python-pytest-mock
            python-setuptools
            python-wheel))
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 84b1e01cb5..5a3f523899 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -5752,8 +5752,7 @@ (define-public python-extension-helpers
            python-setuptools-scm
            python-tomli
            python-setuptools
-           python-wheel
-           python-pip))
+           python-wheel))
     (home-page "https://extension-helpers.readthedocs.io")
     (synopsis "Astropy ecosystem utilities for building and installing packages")
     (description
@@ -19504,8 +19503,7 @@ (define-public python-argparse-manpage
          "1nq4sq1zk1xzdsqq61hd27jhj978ys136aba1zjg02x1g0c0cg11"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-pip python-pytest python-setuptools python-tomli
-           python-wheel))
+     (list python-pytest python-setuptools python-tomli python-wheel))
     (home-page "https://github.com/praiskup/argparse-manpage")
     (synopsis "Build manual page from Python's ArgumentParser object")
     (description
@@ -23002,7 +23000,6 @@ (define-public poetry
            python-keyring
            python-packaging
            python-pexpect
-           python-pip
            python-pkginfo
            python-platformdirs
            python-poetry-core
@@ -23325,8 +23322,7 @@ (define-public python-lazy-object-proxy
         (base32 "0sdc92bbzy6slcl432j04mr131cy8n0many26ppm4fpl8mnpn93q"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-pip
-           python-setuptools
+     (list python-setuptools
            python-setuptools-scm
            python-wheel))
     (home-page "https://github.com/ionelmc/python-lazy-object-proxy")
@@ -25941,7 +25937,6 @@ (define-public python-isort
            python-hypothesmith
            python-libcst-minimal
            python-natsort
-           python-pip
            python-poetry-core
            python-pylama
            python-pypa-build
@@ -26671,8 +26666,7 @@ (define-public python-rfc3986-validator
         (base32 "0mfh82r37ma5n54n8ibnqvmwr3j3f2ixqfjfmv1rwfqvjbkvsi1x"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-pip
-           python-pytest
+     (list python-pytest
            python-pytest-runner
            python-rfc3987
            python-setuptools
@@ -34359,7 +34353,6 @@ (define-public python-pypandoc
      (list (texlive-updmap.cfg
             (list texlive-xpatch texlive-lm
                   texlive-xcolor))
-           python-pip
            python-poetry-core
            python-setuptools))
     (inputs (list pandoc python-pandocfilters))
diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm
index 6f830d54aa..7763c2729b 100644
--- a/gnu/packages/shells.scm
+++ b/gnu/packages/shells.scm
@@ -620,7 +620,6 @@ (define-public xonsh
                    (setenv "HOME" "/tmp"))))))
     (native-inputs
      (list git-minimal
-           python-pip
            python-pyte
            python-pytest
            python-pytest-mock
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 15fc5047d9..a38fc46bdb 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -5262,7 +5262,6 @@ (define-public python-lambda-4dn
      (list python-boto3
            python-botocore
            python-docutils
-           python-pip
            python-six
            python-virtualenv))
     (home-page "https://github.com/4dn-dcic/python-lambda")
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 43/48] gnu: python-django-ldap: Remove uneeded native-inputs.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-44-ngraves@ngraves.fr

* gnu/packages/django.scm (python-django-ldap)[native-inputs]: Remove
python-pypa-build, python-pip.
---
 gnu/packages/django.scm | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

Toggle diff (18 lines)diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index 79712c4945..aacc1f7109 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -1550,10 +1550,7 @@ (define-public python-django-auth-ldap
                      (invoke "pip" "--no-cache-dir" "--no-input"
                              "install" "--no-deps" "--prefix" #$output whl)))))))
     (native-inputs
-     (list openldap python-wheel python-setuptools-scm python-toml
-
-           ;; These can be removed after <https://bugs.gnu.org/46848>.
-           python-pypa-build python-pip))
+     (list openldap python-wheel python-setuptools-scm python-toml))
     (propagated-inputs
      (list python-django python-ldap))
     (home-page "https://github.com/django-auth-ldap/django-auth-ldap")
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 44/48] gnu: python-docstring-to-markdown: Remove uneeded native-inputs.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-45-ngraves@ngraves.fr

* gnu/packages/python-xyz.scm (python-docstring-to-markdown)
[native-inputs]: Remove python-pytest-cov, python-pytest-flake8.
[arguments]: Remove field.
---
 gnu/packages/python-xyz.scm | 10 ----------
 1 file changed, 10 deletions(-)

Toggle diff (25 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index a9f04d2886..58dcb3c896 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1837,18 +1837,8 @@ (define-public python-docstring-to-markdown
        (sha256
         (base32 "0gdpabnyl1kyy0cjrnph6xl4fyhgim50a1amsaqq3hahki6i2ip1"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'reduce-test-coverage-since-failing
-            (lambda _
-              (substitute* "setup.cfg"
-                (("(^.*cov.*$|^.*flake8.*$)") "")))))))
     (native-inputs
      (list python-pytest
-           python-pytest-cov
-           python-pytest-flake8
            python-setuptools
            python-wheel))
     (home-page "https://github.com/python-lsp/docstring-to-markdown")
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 45/48] gnu: python-translation-finder: Remove python coverage native-inputs.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-46-ngraves@ngraves.fr

* gnu/packages/python-web.scm (python-translation-finder)
[native-inputs]: Remove python-codecov, python-codacy-coverage,
python-pytest-cov.
---
 gnu/packages/python-web.scm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

Toggle diff (16 lines)diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 6484c5290d..846418c4d6 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -7410,8 +7410,7 @@ (define-public python-translation-finder
     (propagated-inputs
      (list python-chardet python-pathlib2 python-ruamel.yaml python-six))
     (native-inputs
-     (list python-codecov python-codacy-coverage python-pytest-cov
-           python-pytest-runner))
+     (list python-codacy-coverage python-pytest-runner))
     (home-page "https://weblate.org/")
     (synopsis "Translation file finder for Weblate")
     (description "This package provides a function to find translation file in
-- 
2.48.1

Nicolas Graves wrote 2 weeks ago

[PATCH v5 46/48] gnu: python-pymanopt: Remove python-flake8-bugbear native-input.

Recipients:(address . 70858@debbugs.gnu.org)(name . Nicolas Graves)(address . ngraves@ngraves.fr)

Message-ID:20250227143028.12499-47-ngraves@ngraves.fr

* gnu/packages/machine-learning.scm (python-pymanopt)[native-input]:
Remove python-flake8-bugbear.
---
 gnu/packages/machine-learning.scm | 1 -
 1 file changed, 1 deletion(-)

Toggle diff (14 lines)diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index eb818d672f..37f84017da 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1140,7 +1140,6 @@ (define-public python-pymanopt
                ((",!=1.12\\.\\*") "")))))))
     (propagated-inputs (list python-numpy python-scipy))
     (native-inputs (list python-autograd
-                         python-flake8-bugbear
                          python-matplotlib
                          python-pytest
                          python-setuptools
-- 
2.48.1

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