[PATCH 0/7] Upgrade cwltool

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2 participants
  • Arun Isaac
  • Ludovic Courtès
Owner
unassigned
Submitted by
Arun Isaac
Severity
normal
A
A
Arun Isaac wrote on 23 Oct 2023 00:27
(address . guix-patches@gnu.org)(name . Arun Isaac)(address . arunisaac@systemreboot.net)
cover.1698013055.git.arunisaac@systemreboot.net
This patchset upgrades cwltool to the latest version.

Arun Isaac (7):
gnu: python-ruamel.yaml.clib: Update to 0.2.7.
gnu: python-ruamel.yaml: Update to 0.17.40.
gnu: python-schema-salad: Update to 8.4.20230927144413.
gnu: Add python-cwlformat.
gnu: Add python-cwl-upgrader.
gnu: Add python-cwl-utils.
gnu: cwltool: Update to 3.1.20230601100705.

gnu/packages/bioinformatics.scm | 232 ++++++++++++++++++++++++--------
gnu/packages/serialization.scm | 9 +-
2 files changed, 178 insertions(+), 63 deletions(-)


base-commit: fb3707762de577074c73d40575fe759095ef83e6
--
2.41.0
A
A
Arun Isaac wrote on 23 Oct 2023 10:09
[PATCH 1/7] gnu: python-ruamel.yaml.clib: Update to 0.2.7.
(address . 66690@debbugs.gnu.org)(name . Arun Isaac)(address . arunisaac@systemreboot.net)
423cca224e93480207d2f6cb86f9c28273cc785d.1698013055.git.arunisaac@systemreboot.net
* gnu/packages/serialization.scm (python-ruamel.yaml.clib): Update to 0.2.7.
---
gnu/packages/serialization.scm | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)

Toggle diff (32 lines)
diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index e836b4f8b3..c1158b10b3 100644
--- a/gnu/packages/serialization.scm
+++ b/gnu/packages/serialization.scm
@@ -15,6 +15,7 @@
;;; Copyright © 2023 Alexey Abramov <levenson@mmer.org>
;;; Copyright © 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
;;; Copyright © 2023 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2023 Arun Isaac <arunisaac@systemreboot.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -705,7 +706,7 @@ (define-public python-ruamel.yaml
(define-public python-ruamel.yaml.clib
(package
(name "python-ruamel.yaml.clib")
- (version "0.2.6")
+ (version "0.2.7")
(source
(origin
;; pypi release code has cythonized code without corresponding source.
@@ -716,7 +717,7 @@ (define-public python-ruamel.yaml.clib
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "05m3y7pjfbaarqbbgw1k6gs6cnnmxnwadjipxvw1aaaqk3s236cs"))
+ "119vvz2f6m5i0443r82j2r4hqqlmryffp25spv2cqky2cwjp5lj0"))
(modules '((guix build utils)))
(snippet
'(begin
--
2.41.0
A
A
Arun Isaac wrote on 23 Oct 2023 10:09
[PATCH 2/7] gnu: python-ruamel.yaml: Update to 0.17.40.
(address . 66690@debbugs.gnu.org)(name . Arun Isaac)(address . arunisaac@systemreboot.net)
3d3b93e37702a963442ec8b63b01811874b43d22.1698013055.git.arunisaac@systemreboot.net
* gnu/packages/serialization.scm (python-ruamel.yaml): Update to 0.17.40.
---
gnu/packages/serialization.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (23 lines)
diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index c1158b10b3..45aaee5a28 100644
--- a/gnu/packages/serialization.scm
+++ b/gnu/packages/serialization.scm
@@ -677,14 +677,14 @@ (define-public python-msgspec
(define-public python-ruamel.yaml
(package
(name "python-ruamel.yaml")
- (version "0.16.13")
+ (version "0.17.40")
(source
(origin
(method url-fetch)
(uri (pypi-uri "ruamel.yaml" version))
(sha256
(base32
- "0hm9yg785f46bkrgqknd6fdvmkby9dpzjnm0b63qf0i748acaj5v"))))
+ "0g9irxrlim93z9ccgjyx4bfhbkdlqin0hzmhnn1d8rb7y23bj930"))))
(build-system python-build-system)
(native-inputs
(list python-pytest))
--
2.41.0
A
A
Arun Isaac wrote on 23 Oct 2023 10:09
[PATCH 3/7] gnu: python-schema-salad: Update to 8.4.20230927144413.
(address . 66690@debbugs.gnu.org)(name . Arun Isaac)(address . arunisaac@systemreboot.net)
a2b6322a76dc75689bf97deeef713c9754391286.1698013055.git.arunisaac@systemreboot.net
* gnu/packages/bioinformatics.scm (python-schema-salad): Update to
8.4.20230927144413.
[propagated-inputs]: Add python-importlib-resources. Replace python-mistune
with python-mistune-next.
[arguments]: Use G-expressions. Set exact version number. Remove arguments
that pytest does not recognize. Skip more tests that require network
access. Skip tests using #:test-flags.
---
gnu/packages/bioinformatics.scm | 48 +++++++++++++++++++++++----------
1 file changed, 34 insertions(+), 14 deletions(-)

Toggle diff (79 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a1eac184ad..c6819316ae 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8,7 +8,7 @@
;;; Copyright © 2016, 2020, 2022 Marius Bakke <marius@gnu.org>
;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2017, 2021, 2022 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2017, 2021, 2022, 2023 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
;;; Copyright © 2018-2023 M?d?lin Ionel Patra?cu <madalinionel.patrascu@mdc-berlin.de>
@@ -4327,30 +4327,50 @@ (define-public python-pybigwig
(define-public python-schema-salad
(package
(name "python-schema-salad")
- (version "8.2.20211116214159")
+ (version "8.4.20230927144413")
(source
(origin
(method url-fetch)
(uri (pypi-uri "schema-salad" version))
(sha256
(base32
- "005dh2y45x92zl8sf2sqjmfvcqr4hrz8dfckgkckv87003v7lwqc"))))
+ "0d0mm1cwrdmz2yplfi7vgqjsfaz4z3rdm2gx2103176jdsiwq610"))))
(build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-before 'check 'skip-failing-tests
- (lambda _
- ;; Skip tests that require network access.
- (substitute* "schema_salad/tests/test_cwl11.py"
- (("^def test_(secondaryFiles|outputBinding)" all)
- (string-append "@pytest.mark.skip(reason="
- "\"test requires network access\")\n"
- all))))))))
+ (list
+ #:test-flags
+ ;; Skip tests that require network access.
+ #~(list "-k"
+ (string-append "not test_secondaryFiles"
+ " and not test_outputBinding"
+ " and not test_yaml_tab_error"
+ " and not test_idmap"
+ " and not test_idmap2"
+ " and not test_include"
+ " and not test_load"
+ " and not test_load_cwlschema"
+ " and not test_load_by_yaml_metaschema"
+ " and not test_load_metaschema"
+ " and not test_bad_schemas"))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'set-version
+ (lambda _
+ (substitute* "setup.py"
+ ;; Set exact version number.
+ (("version=\"[[:digit:].]*\"")
+ (string-append "version=\"" #$version "\"")))))
+ (add-after 'unpack 'fix-pytest-arguments
+ (lambda _
+ (substitute* "tox.ini"
+ ;; pytest does not recognize the -n auto arguments. Remove
+ ;; them.
+ (("addopts=-n auto") "")))))))
(propagated-inputs
(list python-cachecontrol
+ python-importlib-resources
python-lockfile
- python-mistune
+ python-mistune-next
python-rdflib
python-rdflib-jsonld
python-requests
--
2.41.0
A
A
Arun Isaac wrote on 23 Oct 2023 10:09
[PATCH 4/7] gnu: Add python-cwlformat.
(address . 66690@debbugs.gnu.org)(name . Arun Isaac)(address . arunisaac@systemreboot.net)
2aa865bdab3d42feca9c17861ea2b4046d02eb2c.1698013055.git.arunisaac@systemreboot.net
* gnu/packages/bioinformatics.scm (python-cwlformat): New variable.
---
gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)

Toggle diff (40 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c6819316ae..3b2fc8de8a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4484,6 +4484,33 @@ (define-public python-scrublet
doublets in single-cell RNA-seq data.")
(license license:expat)))
+(define-public python-cwlformat
+ (package
+ (name "python-cwlformat")
+ (version "2022.02.18")
+ (source
+ ;; The PyPI tarball is missing Readme.md. Readme.md is required for the
+ ;; build.
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/rabix/cwl-format")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0agkz2w86k91rc9m5vx5hsqi5nm6fcmzkng6j99hjapz0r9233ql"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs
+ (list python-importlib-resources
+ python-ruamel.yaml))
+ (home-page "https://github.com/rabix/cwl-format")
+ (synopsis "Prettifier for CWL code")
+ (description "@code{python-cwlformat} is a specification and a reference
+implementation for a very opinionated @acronym{CWL, Common Workflow Language}
+code formatter. It outputs CWL in a standardized YAML format.")
+ (license license:asl2.0)))
+
(define-public cwltool
(package
(name "cwltool")
--
2.41.0
A
A
Arun Isaac wrote on 23 Oct 2023 10:09
[PATCH 5/7] gnu: Add python-cwl-upgrader.
(address . 66690@debbugs.gnu.org)(name . Arun Isaac)(address . arunisaac@systemreboot.net)
62027ed95916324d2e5b545109d97589a7dc869f.1698013055.git.arunisaac@systemreboot.net
* gnu/packages/bioinformatics.scm (python-cwl-upgrader): New variable.
---
gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++
1 file changed, 26 insertions(+)

Toggle diff (39 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3b2fc8de8a..79dbf0f2e6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4511,6 +4511,32 @@ (define-public python-cwlformat
code formatter. It outputs CWL in a standardized YAML format.")
(license license:asl2.0)))
+(define-public python-cwl-upgrader
+ (package
+ (name "python-cwl-upgrader")
+ (version "1.2.9")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "cwl-upgrader" version))
+ (sha256
+ (base32
+ "017nfxrrnrf1bacryyigqgx9pprw6g5m4n2wf69j6pfihl10426a"))))
+ (build-system python-build-system)
+ (native-inputs
+ (list python-mypy-extensions
+ python-pytest-cov
+ python-pytest-runner))
+ (propagated-inputs
+ (list python-ruamel.yaml
+ python-schema-salad))
+ (home-page "https://github.com/common-workflow-language/cwl-upgrader")
+ (synopsis "CWL document upgrader")
+ (description "@code{python-cwl-upgrader} is a standalone upgrader for
+@acronym{CWL, Common Workflow Language} documents from version draft-3, v1.0,
+and v1.1 to v1.2.")
+ (license license:asl2.0)))
+
(define-public cwltool
(package
(name "cwltool")
--
2.41.0
A
A
Arun Isaac wrote on 23 Oct 2023 10:09
[PATCH 6/7] gnu: Add python-cwl-utils.
(address . 66690@debbugs.gnu.org)(name . Arun Isaac)(address . arunisaac@systemreboot.net)
d0e780c4b3a39151471c513f9d22e1ebd5b82dcc.1698013055.git.arunisaac@systemreboot.net
* gnu/packages/bioinformatics.scm (python-cwl-utils): New variable.
---
gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++
1 file changed, 43 insertions(+)

Toggle diff (56 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 79dbf0f2e6..2deec5368e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4537,6 +4537,49 @@ (define-public python-cwl-upgrader
and v1.1 to v1.2.")
(license license:asl2.0)))
+(define-public python-cwl-utils
+ (package
+ (name "python-cwl-utils")
+ (version "0.29")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "cwl-utils" version))
+ (sha256
+ (base32
+ "0rfm49wwnn4bcalkfrhvlmn7bhdf6nnwcr8fvx5gqxqyd4b5izf5"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ #~(list "-k"
+ (string-append "not test_graph_split"
+ " and not test_load_document_with_remote_uri"
+ " and not test_remote_packing"
+ " and not test_remote_packing_github_soft_links"
+ " and not test_value_from_two_concatenated_expressions"))))
+ (inputs
+ (list node))
+ (native-inputs
+ (list python-mypy-extensions
+ python-pytest
+ python-pytest-mock
+ python-pytest-runner))
+ (propagated-inputs
+ (list python-cwl-upgrader
+ python-cwlformat
+ python-packaging
+ python-rdflib
+ python-requests
+ python-ruamel.yaml
+ python-schema-salad))
+ (home-page "https://github.com/common-workflow-language/cwl-utils")
+ (synopsis "Python utilities for CWL")
+ (description "@code{python-cwl-utils} provides python utilities and
+autogenerated classes for loading and parsing CWL v1.0, CWL v1.1, and CWL v1.2
+documents.")
+ (license license:asl2.0)))
+
(define-public cwltool
(package
(name "cwltool")
--
2.41.0
A
A
Arun Isaac wrote on 23 Oct 2023 10:09
[PATCH 7/7] gnu: cwltool: Update to 3.1.20230601100705.
(address . 66690@debbugs.gnu.org)(name . Arun Isaac)(address . arunisaac@systemreboot.net)
eaa84b956d6a4468adfc8d5325ba44b28e4f170e.1698013055.git.arunisaac@systemreboot.net
* gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20230601100705.
[arguments]: Use G-expressions. Set version in setup.py. Do not attempt to
substitute files cwltool/schemas/v1.1/tests/env-tool1.cwl,
cwltool/schemas/v1.1/tests/env-tool2.cwl and
cwltool/schemas/v1.1/tests/imported-hint.cwl that have been removed in this
release.
[inputs]: Add python-cwl-utils.
---
gnu/packages/bioinformatics.scm | 88 ++++++++++++++++-----------------
1 file changed, 43 insertions(+), 45 deletions(-)

Toggle diff (114 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2deec5368e..b4ac896a0d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4583,7 +4583,7 @@ (define-public python-cwl-utils
(define-public cwltool
(package
(name "cwltool")
- (version "3.1.20220119140128")
+ (version "3.1.20231020140205")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -4592,56 +4592,54 @@ (define-public cwltool
(file-name (git-file-name name version))
(sha256
(base32
- "1jmrm0qrqgka79avc1kq63fgh20gx6g07fc8p3iih4k85vhdyl3f"))))
+ "045n594k7zhm5qnf7mippldmm43wj3x0wnizhhpd1n2ak2iiky88"))))
(build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'loosen-version-restrictions
- (lambda _
- (substitute* "setup.py"
- (("== 1.5.1") ">=1.5.1")))) ; prov
- (add-after 'unpack 'dont-use-git
- (lambda _
- (substitute* "gittaggers.py"
- (("self.git_timestamp_tag\\(\\)")
- (string-append "time.strftime('.%Y%m%d%H%M%S', time.gmtime(int("
- (string-drop ,version 4) ")))")))))
- (add-after 'unpack 'modify-tests
- (lambda _
- ;; Tries to connect to the internet.
- (delete-file "tests/test_content_type.py")
- (delete-file "tests/test_udocker.py")
- (delete-file "tests/test_http_input.py")
- (substitute* "tests/test_load_tool.py"
- (("def test_load_graph_fragment_from_packed")
- (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
- "def test_load_graph_fragment_from_packed")))
- (substitute* "tests/test_examples.py"
- (("def test_env_filtering")
- (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
- "def test_env_filtering")))
- ;; Tries to use cwl-runners.
- (substitute* "tests/test_examples.py"
- (("def test_v1_0_arg_empty_prefix_separate_false")
- (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
- "def test_v1_0_arg_empty_prefix_separate_false")))
-
- (substitute* '("cwltool/schemas/v1.1/tests/env-tool1.cwl"
- "cwltool/schemas/v1.1/tests/env-tool2.cwl"
- "cwltool/schemas/v1.1/tests/imported-hint.cwl"
- "tests/subgraph/env-tool2.cwl"
- "tests/subgraph/env-tool2_req.cwl"
- "tests/subgraph/env-wf2_subwf-packed.cwl"
- "tests/subgraph/env-tool2_no_env.cwl")
- (("\"/bin/sh\"") (string-append "\"" (which "sh") "\"")))
- ;; Pytest doesn't know what to do with "-n auto"
- (substitute* "tox.ini"
- (("-n auto") "")))))))
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'loosen-version-restrictions
+ (lambda _
+ (substitute* "setup.py"
+ (("== 1.5.1") "> 1.5.1")))) ; prov
+ (add-after 'unpack 'set-version
+ (lambda _
+ ;; Set exact version.
+ (substitute* "setup.py"
+ (("use_scm_version=True")
+ (string-append "version=\"" #$version "\"")))))
+ (add-after 'unpack 'modify-tests
+ (lambda _
+ ;; Tries to connect to the internet.
+ (delete-file "tests/test_content_type.py")
+ (delete-file "tests/test_udocker.py")
+ (delete-file "tests/test_http_input.py")
+ (substitute* "tests/test_load_tool.py"
+ (("def test_load_graph_fragment_from_packed")
+ (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
+ "def test_load_graph_fragment_from_packed")))
+ (substitute* "tests/test_examples.py"
+ (("def test_env_filtering")
+ (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
+ "def test_env_filtering")))
+ ;; Tries to use cwl-runners.
+ (substitute* "tests/test_examples.py"
+ (("def test_v1_0_arg_empty_prefix_separate_false")
+ (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
+ "def test_v1_0_arg_empty_prefix_separate_false")))
+ (substitute* '("tests/subgraph/env-tool2.cwl"
+ "tests/subgraph/env-tool2_req.cwl"
+ "tests/subgraph/env-wf2_subwf-packed.cwl"
+ "tests/subgraph/env-tool2_no_env.cwl")
+ (("\"/bin/sh\"") (string-append "\"" (which "sh") "\"")))
+ ;; Pytest doesn't know what to do with "-n auto"
+ (substitute* "tox.ini"
+ (("-n auto") "")))))))
(inputs
(list python-argcomplete
python-bagit
python-coloredlogs
+ python-cwl-utils
python-mypy-extensions
python-prov
python-pydot
--
2.41.0
L
L
Ludovic Courtès wrote on 22 Nov 2023 15:37
Re: [bug#66690] [PATCH 0/7] Upgrade cwltool
(name . Arun Isaac)(address . arunisaac@systemreboot.net)(address . 66690@debbugs.gnu.org)
87sf4xluqe.fsf@gnu.org
Hi,

Arun Isaac <arunisaac@systemreboot.net> skribis:

Toggle quote (11 lines)
> This patchset upgrades cwltool to the latest version.
>
> Arun Isaac (7):
> gnu: python-ruamel.yaml.clib: Update to 0.2.7.
> gnu: python-ruamel.yaml: Update to 0.17.40.
> gnu: python-schema-salad: Update to 8.4.20230927144413.
> gnu: Add python-cwlformat.
> gnu: Add python-cwl-upgrader.
> gnu: Add python-cwl-utils.
> gnu: cwltool: Update to 3.1.20230601100705.

I don’t see it at qa.guix, but if it builds for you, and if the
dependents of the 3 packages being upgraded work fine, please go ahead!

Ludo’.
A
A
Arun Isaac wrote on 23 Nov 2023 01:35
(name . Ludovic Courtès)(address . ludo@gnu.org)(address . 66690@debbugs.gnu.org)
87wmu9e26s.fsf@systemreboot.net
Hi Ludo,

Unfortunately, the upgrade of python-ruamel.yaml breaks conda. We'll
have to upgrade conda too before this patchset can be pushed. And,
that's quite a major upgrade.

Regards,
Arun
L
L
Ludovic Courtès wrote on 11 Dec 2023 23:17
control message for bug #66690
(address . control@debbugs.gnu.org)
87edfs2xl7.fsf@gnu.org
tags 66690 + moreinfo
quit
A
A
Arun Isaac wrote on 15 Feb 21:46 +0100
[PATCH v2 0/8] Upgrade cwltool
(address . 66690@debbugs.gnu.org)(name . Arun Isaac)(address . arunisaac@systemreboot.net)
cover.1708029746.git.arunisaac@systemreboot.net
In this patchset, I have updated cwltool once more to the latest version. And,
I have split out ruamel-yaml into two separate package variants so that conda
no longer breaks. I will push this patchset if it builds successfully on QA
without breaking other packages.

Arun Isaac (8):
gnu: python-ruamel.yaml.clib: Update to 0.2.8.
gnu: python-ruamel-yaml: Update to 0.18.6.
gnu: python-schema-salad: Update to 8.5.20240102191335.
gnu: Add python-cwlformat.
gnu: Add python-cwl-upgrader.
gnu: Add python-cwl-utils.
gnu: Add python-spython.
gnu: cwltool: Update to 3.1.20240112164112.

gnu/packages/bioinformatics.scm | 244 ++++++++++++++++++++--------
gnu/packages/linux.scm | 46 ++++++
gnu/packages/package-management.scm | 3 +-
gnu/packages/serialization.scm | 21 ++-
4 files changed, 240 insertions(+), 74 deletions(-)


base-commit: 5ad54df6b09b08b73453cf1071413693f053a0cc
--
2.41.0
A
A
Arun Isaac wrote on 15 Feb 21:46 +0100
[PATCH v2 1/8] gnu: python-ruamel.yaml.clib: Update to 0.2.8.
(address . 66690@debbugs.gnu.org)(name . Arun Isaac)(address . arunisaac@systemreboot.net)
2509a83da5017c1ed6c16ac7687b6600d6100ab3.1708029746.git.arunisaac@systemreboot.net
* gnu/packages/serialization.scm (python-ruamel.yaml.clib): Update to 0.2.8.

Change-Id: I18172bb4cad80b0e1a5db11fbc8fb937f46a1862
---
gnu/packages/serialization.scm | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)

Toggle diff (32 lines)
diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index ccafb8e802..963028c734 100644
--- a/gnu/packages/serialization.scm
+++ b/gnu/packages/serialization.scm
@@ -17,6 +17,7 @@
;;; Copyright © 2023 Vinicius Monego <monego@posteo.net>
;;; Copyright © 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2023 Zheng Junjie <873216071@qq.com>
+;;; Copyright © 2024 Arun Isaac <arunisaac@systemreboot.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -749,7 +750,7 @@ (define-public python-ruamel.yaml
(define-public python-ruamel.yaml.clib
(package
(name "python-ruamel.yaml.clib")
- (version "0.2.6")
+ (version "0.2.8")
(source
(origin
;; pypi release code has cythonized code without corresponding source.
@@ -760,7 +761,7 @@ (define-public python-ruamel.yaml.clib
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "05m3y7pjfbaarqbbgw1k6gs6cnnmxnwadjipxvw1aaaqk3s236cs"))
+ "0qspqnk72xrjj17b00hjibbzjk3krsrakzf08wxwz7z908cv6278"))
(modules '((guix build utils)))
(snippet
'(begin
--
2.41.0
A
A
Arun Isaac wrote on 15 Feb 21:46 +0100
[PATCH v2 2/8] gnu: python-ruamel-yaml: Update to 0.18.6.
(address . 66690@debbugs.gnu.org)(name . Arun Isaac)(address . arunisaac@systemreboot.net)
14917e292b584625ac25971a4b02cfef83101b9e.1708029746.git.arunisaac@systemreboot.net
* gnu/package/serialization.scm (python-ruamel-yaml): Update to 0.18.6.
(python-ruamel.yaml-0.16): New variable.
* gnu/packages/package-management.scm (conda)[inputs]: Replace
python-ruamel.yaml with python-ruamel.yaml-0.16.

Change-Id: Iff9eeeae043c9547d93a6c780f0c30bd760490d9
---
gnu/packages/package-management.scm | 3 ++-
gnu/packages/serialization.scm | 16 ++++++++++++++--
2 files changed, 16 insertions(+), 3 deletions(-)

Toggle diff (63 lines)
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index c1ad613bee..5d6bc47b8b 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -23,6 +23,7 @@
;;; Copyright © 2022, 2023 Zhu Zihao <all_but_last@163.com>
;;; Copyright © 2023 jgart <jgart@dismail.de>
;;; Copyright © 2023 M?d?lin Ionel Patra?cu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2024 Arun Isaac <arunisaac@systemreboot.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -1251,7 +1252,7 @@ (define-public conda
python-pyyaml
python-requests
python-responses
- python-ruamel.yaml
+ python-ruamel.yaml-0.16
python-tqdm
;; XXX: This is dragged in by libarchive and is needed at runtime.
zstd))
diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index 963028c734..240646748b 100644
--- a/gnu/packages/serialization.scm
+++ b/gnu/packages/serialization.scm
@@ -721,14 +721,14 @@ (define-public python-msgspec
(define-public python-ruamel.yaml
(package
(name "python-ruamel.yaml")
- (version "0.16.13")
+ (version "0.18.6")
(source
(origin
(method url-fetch)
(uri (pypi-uri "ruamel.yaml" version))
(sha256
(base32
- "0hm9yg785f46bkrgqknd6fdvmkby9dpzjnm0b63qf0i748acaj5v"))))
+ "06rimidc9nb3i3r90n3a1zwf0qxw24zqykb3wpxwd1p72yifc9wb"))))
(build-system python-build-system)
(native-inputs
(list python-pytest))
@@ -747,6 +747,18 @@ (define-public python-ruamel.yaml
style and key ordering are kept, so you can diff the source.")
(license license:expat)))
+(define-public python-ruamel.yaml-0.16
+ (package
+ (inherit python-ruamel.yaml)
+ (version "0.16.13")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "ruamel.yaml" version))
+ (sha256
+ (base32
+ "0hm9yg785f46bkrgqknd6fdvmkby9dpzjnm0b63qf0i748acaj5v"))))))
+
(define-public python-ruamel.yaml.clib
(package
(name "python-ruamel.yaml.clib")
--
2.41.0
A
A
Arun Isaac wrote on 15 Feb 21:46 +0100
[PATCH v2 3/8] gnu: python-schema-salad: Update to 8.5.20240102191335.
(address . 66690@debbugs.gnu.org)(name . Arun Isaac)(address . arunisaac@systemreboot.net)
f20397e6cd488968c3d4a6e261ca3ee5db8c4ee1.1708029746.git.arunisaac@systemreboot.net
* gnu/packages/bioinformatics.scm (python-schema-salad): Update to
8.5.20240102191335.
[native-inputs]: Add python-pytest-xdist.
[propagated-inputs]: Add python-importlib-resources and
python-mypy-extensions. Remove python-lockfile, python-rdflib-jsonld and
python-typing-extensions. Replace python-mistune with python-mistune-next.
[arguments]: Use G-expressions. Set exact version number. Skip more tests that
require network access.

Change-Id: I4de4704f58f40fdf9bf4c02e41c2c353beaa3eb2
---
gnu/packages/bioinformatics.scm | 61 ++++++++++++++++++++-------------
1 file changed, 38 insertions(+), 23 deletions(-)

Toggle diff (82 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 84577ef760..75cfad51a6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5001,37 +5001,52 @@ (define-public python-pyfasta
(define-public python-schema-salad
(package
(name "python-schema-salad")
- (version "8.2.20211116214159")
+ (version "8.5.20240102191335")
(source
- (origin
- (method url-fetch)
- (uri (pypi-uri "schema-salad" version))
- (sha256
- (base32
- "005dh2y45x92zl8sf2sqjmfvcqr4hrz8dfckgkckv87003v7lwqc"))))
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "schema-salad" version))
+ (sha256
+ (base32
+ "035202p696i3jylb8b3nm9qcxsqby15hhqn1dl4nrz73a17p0ckx"))))
(build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-before 'check 'skip-failing-tests
- (lambda _
- ;; Skip tests that require network access.
- (substitute* "schema_salad/tests/test_cwl11.py"
- (("^def test_(secondaryFiles|outputBinding)" all)
- (string-append "@pytest.mark.skip(reason="
- "\"test requires network access\")\n"
- all))))))))
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'set-version
+ (lambda _
+ ;; Set exact version.
+ (substitute* "setup.py"
+ (("use_scm_version=True")
+ (string-append "version=\"" #$version "\"")))))
+ (add-before 'check 'skip-failing-tests
+ (lambda _
+ ;; Skip tests that require network access.
+ (let ((skip-test
+ (lambda (test-pattern)
+ (string-append "@pytest.mark.skip(reason="
+ "\"test requires network access\")\n"
+ test-pattern))))
+ (substitute* "schema_salad/tests/test_cg.py"
+ (("^def test_(load(_by_yaml_metaschema|_metaschema|_cwlschema|)|include|idmap|idmap2)\\(" all)
+ (skip-test all)))
+ (substitute* "schema_salad/tests/test_cwl11.py"
+ (("^def test_(secondaryFiles|outputBinding|yaml_tab_error)\\(" all)
+ (skip-test all)))
+ (substitute* "schema_salad/tests/test_examples.py"
+ (("^def test_bad_schemas\\(" all)
+ (skip-test all)))))))))
(propagated-inputs
(list python-cachecontrol
- python-lockfile
- python-mistune
+ python-importlib-resources
+ python-mistune-next
+ python-mypy-extensions
python-rdflib
- python-rdflib-jsonld
python-requests
- python-ruamel.yaml
- python-typing-extensions))
+ python-ruamel.yaml))
(native-inputs
- (list python-black python-pytest python-pytest-runner))
+ (list python-black python-pytest python-pytest-runner python-pytest-xdist))
(home-page "https://github.com/common-workflow-language/schema_salad")
(synopsis "Schema Annotations for Linked Avro Data (SALAD)")
(description
--
2.41.0
A
A
Arun Isaac wrote on 15 Feb 21:46 +0100
[PATCH v2 4/8] gnu: Add python-cwlformat.
(address . 66690@debbugs.gnu.org)(name . Arun Isaac)(address . arunisaac@systemreboot.net)
baa3a86661953e6b6841244039be1a7f99b929e3.1708029746.git.arunisaac@systemreboot.net
* gnu/packages/bioinformatics.scm (python-cwlformat): New variable.

Change-Id: Ib2d79e350ab100c61c7afe2d5d3eafc72146e493
---
gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)

Toggle diff (40 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 75cfad51a6..48e56945b3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5138,6 +5138,33 @@ (define-public python-scrublet
doublets in single-cell RNA-seq data.")
(license license:expat)))
+(define-public python-cwlformat
+ (package
+ (name "python-cwlformat")
+ (version "2022.02.18")
+ (source
+ ;; The PyPI tarball is missing Readme.md. Readme.md is required for the
+ ;; build.
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/rabix/cwl-format")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0agkz2w86k91rc9m5vx5hsqi5nm6fcmzkng6j99hjapz0r9233ql"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs
+ (list python-importlib-resources
+ python-ruamel.yaml))
+ (home-page "https://github.com/rabix/cwl-format")
+ (synopsis "Prettifier for CWL code")
+ (description "@code{python-cwlformat} is a specification and a reference
+implementation for a very opinionated @acronym{CWL, Common Workflow Language}
+code formatter. It outputs CWL in a standardized YAML format.")
+ (license license:asl2.0)))
+
(define-public cwltool
(package
(name "cwltool")
--
2.41.0
A
A
Arun Isaac wrote on 15 Feb 21:46 +0100
[PATCH v2 5/8] gnu: Add python-cwl-upgrader.
(address . 66690@debbugs.gnu.org)(name . Arun Isaac)(address . arunisaac@systemreboot.net)
3c43ae3420f21566d2ee4cf6fac548db27afc8f8.1708029746.git.arunisaac@systemreboot.net
* gnu/packages/bioinformatics.scm (python-cwl-upgrader): New variable.

Change-Id: I2022239840e9fe9e745689ef8b8bf4279be2ff9e
---
gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++
1 file changed, 24 insertions(+)

Toggle diff (37 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 48e56945b3..438b22800c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5165,6 +5165,30 @@ (define-public python-cwlformat
code formatter. It outputs CWL in a standardized YAML format.")
(license license:asl2.0)))
+(define-public python-cwl-upgrader
+ (package
+ (name "python-cwl-upgrader")
+ (version "1.2.11")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "cwl-upgrader" version))
+ (sha256
+ (base32
+ "12j6z8nvwnzjjyypz59hwj5hmrcri2r6aknw52n9dbj6lbzbdd2p"))))
+ (build-system pyproject-build-system)
+ (native-inputs
+ (list python-pytest))
+ (propagated-inputs
+ (list python-ruamel.yaml
+ python-schema-salad))
+ (home-page "https://github.com/common-workflow-language/cwl-upgrader")
+ (synopsis "CWL document upgrader")
+ (description "@code{python-cwl-upgrader} is a standalone upgrader for
+@acronym{CWL, Common Workflow Language} documents from version draft-3, v1.0,
+and v1.1 to v1.2.")
+ (license license:asl2.0)))
+
(define-public cwltool
(package
(name "cwltool")
--
2.41.0
A
A
Arun Isaac wrote on 15 Feb 21:46 +0100
[PATCH v2 6/8] gnu: Add python-cwl-utils.
(address . 66690@debbugs.gnu.org)(name . Arun Isaac)(address . arunisaac@systemreboot.net)
ade7517f3e3c36a1cafe0b6fbe05df7a08aa96c2.1708029746.git.arunisaac@systemreboot.net
* gnu/packages/bioinformatics.scm (python-cwl-utils): New variable.

Change-Id: I9347c80c0e866b89a7d432091fbcf1bc009209a5
---
gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++
1 file changed, 43 insertions(+)

Toggle diff (56 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 438b22800c..35c4d7d993 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5189,6 +5189,49 @@ (define-public python-cwl-upgrader
and v1.1 to v1.2.")
(license license:asl2.0)))
+(define-public python-cwl-utils
+ (package
+ (name "python-cwl-utils")
+ (version "0.32")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "cwl-utils" version))
+ (sha256
+ (base32
+ "06wkw8d8cqm3hnz8xwnysz874gwaym36c358cr7frw5iglhvsj98"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ #~(list "-k"
+ (string-append "not test_graph_split"
+ " and not test_load_document_with_remote_uri"
+ " and not test_remote_packing"
+ " and not test_remote_packing_github_soft_links"
+ " and not test_value_from_two_concatenated_expressions"))))
+ (inputs
+ (list node))
+ (native-inputs
+ (list python-mypy-extensions
+ python-pytest
+ python-pytest-mock
+ python-pytest-runner))
+ (propagated-inputs
+ (list python-cwl-upgrader
+ python-cwlformat
+ python-packaging
+ python-rdflib
+ python-requests
+ python-ruamel.yaml
+ python-schema-salad))
+ (home-page "https://github.com/common-workflow-language/cwl-utils")
+ (synopsis "Python utilities for CWL")
+ (description "@code{python-cwl-utils} provides python utilities and
+autogenerated classes for loading and parsing CWL v1.0, CWL v1.1, and CWL v1.2
+documents.")
+ (license license:asl2.0)))
+
(define-public cwltool
(package
(name "cwltool")
--
2.41.0
A
A
Arun Isaac wrote on 15 Feb 21:46 +0100
[PATCH v2 7/8] gnu: Add python-spython.
(address . 66690@debbugs.gnu.org)(name . Arun Isaac)(address . arunisaac@systemreboot.net)
a7407a22c850d3bb4591f6de6e062a91a6e92cc2.1708029746.git.arunisaac@systemreboot.net
* gnu/packages/linux.scm (python-spython): New variable.

Change-Id: I758f879608bc4b0c0411918b4ee0fa9cc3abc639
---
gnu/packages/linux.scm | 46 ++++++++++++++++++++++++++++++++++++++++++
1 file changed, 46 insertions(+)

Toggle diff (66 lines)
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index d798c44a8f..99bc517a96 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -80,6 +80,7 @@
;;; Copyright © 2023 Jaeme Sifat <jaeme@runbox.com>
;;; Copyright © 2024 Gabriel Wicki <gabriel@erlikon.ch>
;;; Copyright © 2024 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2024 Arun Isaac <arunisaac@systemreboot.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -5265,6 +5266,51 @@ (define-public singularity
isolation or root privileges.")
(license license:bsd-3)))
+(define-public python-spython
+ (package
+ (name "python-spython")
+ (version "0.3.13")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "spython" version))
+ (sha256
+ (base32 "0kly851k6mj7xzcybciav5d0pq5q04pzg7c5a1g712bqbxkha4ck"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; Configure absolute path to singularity.
+ (add-after 'unpack 'configure
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((singularity (search-input-file inputs "bin/singularity")))
+ (substitute* "spython/utils/terminal.py"
+ (("software=\"singularity\"")
+ (string-append "software=\"" singularity "\"")))
+ (substitute* (list "spython/utils/terminal.py"
+ "spython/main/help.py"
+ "spython/main/base/command.py")
+ (("\\[\"singularity\"")
+ (string-append "[\"" singularity "\"")))
+ (substitute* "spython/main/execute.py"
+ (("shutil.which\\(\"singularity\"\\)")
+ (string-append "shutil.which(\"" singularity "\")"))))))
+ ;; Skip tests that require network access.
+ (add-before 'check 'skip-tests
+ (lambda _
+ (delete-file "spython/tests/test_client.py"))))))
+ (inputs
+ (list singularity))
+ (native-inputs
+ (list python-pytest
+ python-pytest-runner))
+ (home-page "https://github.com/singularityhub/singularity-cli")
+ (synopsis "Singularity Python client")
+ (description "@code{python-spython} is a Python library to interact with
+Singularity containers.")
+ (license license:mpl2.0)))
+
(define-public libnvme
(package
(name "libnvme")
--
2.41.0
A
A
Arun Isaac wrote on 15 Feb 21:46 +0100
[PATCH v2 8/8] gnu: cwltool: Update to 3.1.20240112164112.
(address . 66690@debbugs.gnu.org)(name . Arun Isaac)(address . arunisaac@systemreboot.net)
e37d08319f0b7608fc2ac47e9281cba0918fe77e.1708029746.git.arunisaac@systemreboot.net
* gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20240112164112.
[arguments]: Use G-expressions. Set version in setup.py. Do not attempt to
substitute files cwltool/schemas/v1.1/tests/env-tool1.cwl,
cwltool/schemas/v1.1/tests/env-tool2.cwl and
cwltool/schemas/v1.1/tests/imported-hint.cwl that have been removed in this
release. Do not remove "-n auto" from pytest flags.
[inputs]: Add python-cwl-utils and python-spython.
[native-inputs]: Add python-pytest-xdist.

Change-Id: If1be7cdf39b767c5ef2a1dbddfdc95f59ea98cb6

Change-Id: I2ba81e8569abcf43cd0fad33daab1e4f8689e77f
---
gnu/packages/bioinformatics.scm | 89 ++++++++++++++++-----------------
1 file changed, 43 insertions(+), 46 deletions(-)

Toggle diff (129 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 35c4d7d993..cc1a966b41 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5235,7 +5235,7 @@ (define-public python-cwl-utils
(define-public cwltool
(package
(name "cwltool")
- (version "3.1.20220119140128")
+ (version "3.1.20240112164112")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -5244,56 +5244,51 @@ (define-public cwltool
(file-name (git-file-name name version))
(sha256
(base32
- "1jmrm0qrqgka79avc1kq63fgh20gx6g07fc8p3iih4k85vhdyl3f"))))
+ "1fpc5kqgpbn48g5vlvy64p297x2wm3gfz8casgpk15ap593wwh33"))))
(build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'loosen-version-restrictions
- (lambda _
- (substitute* "setup.py"
- (("== 1.5.1") ">=1.5.1")))) ; prov
- (add-after 'unpack 'dont-use-git
- (lambda _
- (substitute* "gittaggers.py"
- (("self.git_timestamp_tag\\(\\)")
- (string-append "time.strftime('.%Y%m%d%H%M%S', time.gmtime(int("
- (string-drop ,version 4) ")))")))))
- (add-after 'unpack 'modify-tests
- (lambda _
- ;; Tries to connect to the internet.
- (delete-file "tests/test_content_type.py")
- (delete-file "tests/test_udocker.py")
- (delete-file "tests/test_http_input.py")
- (substitute* "tests/test_load_tool.py"
- (("def test_load_graph_fragment_from_packed")
- (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
- "def test_load_graph_fragment_from_packed")))
- (substitute* "tests/test_examples.py"
- (("def test_env_filtering")
- (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
- "def test_env_filtering")))
- ;; Tries to use cwl-runners.
- (substitute* "tests/test_examples.py"
- (("def test_v1_0_arg_empty_prefix_separate_false")
- (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
- "def test_v1_0_arg_empty_prefix_separate_false")))
-
- (substitute* '("cwltool/schemas/v1.1/tests/env-tool1.cwl"
- "cwltool/schemas/v1.1/tests/env-tool2.cwl"
- "cwltool/schemas/v1.1/tests/imported-hint.cwl"
- "tests/subgraph/env-tool2.cwl"
- "tests/subgraph/env-tool2_req.cwl"
- "tests/subgraph/env-wf2_subwf-packed.cwl"
- "tests/subgraph/env-tool2_no_env.cwl")
- (("\"/bin/sh\"") (string-append "\"" (which "sh") "\"")))
- ;; Pytest doesn't know what to do with "-n auto"
- (substitute* "tox.ini"
- (("-n auto") "")))))))
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'loosen-version-restrictions
+ (lambda _
+ (substitute* "setup.py"
+ (("== 1.5.1") "> 1.5.1")))) ; prov
+ (add-after 'unpack 'set-version
+ (lambda _
+ ;; Set exact version.
+ (substitute* "setup.py"
+ (("use_scm_version=True")
+ (string-append "version=\"" #$version "\"")))))
+ (add-after 'unpack 'modify-tests
+ (lambda _
+ ;; Tries to connect to the internet.
+ (delete-file "tests/test_content_type.py")
+ (delete-file "tests/test_udocker.py")
+ (delete-file "tests/test_http_input.py")
+ (substitute* "tests/test_load_tool.py"
+ (("def test_load_graph_fragment_from_packed")
+ (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
+ "def test_load_graph_fragment_from_packed")))
+ (substitute* "tests/test_examples.py"
+ (("def test_env_filtering")
+ (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
+ "def test_env_filtering")))
+ ;; Tries to use cwl-runners.
+ (substitute* "tests/test_examples.py"
+ (("def test_v1_0_arg_empty_prefix_separate_false")
+ (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
+ "def test_v1_0_arg_empty_prefix_separate_false")))
+ (substitute* '("tests/subgraph/env-tool2.cwl"
+ "tests/subgraph/env-tool2_req.cwl"
+ "tests/subgraph/env-wf2_subwf-packed.cwl"
+ "tests/subgraph/env-tool2_no_env.cwl")
+ (("\"/bin/sh\"") (string-append "\"" (which "sh") "\""))))))))
(inputs
(list python-argcomplete
python-bagit
python-coloredlogs
+ python-cwl-utils
python-mypy-extensions
python-prov
python-pydot
@@ -5303,6 +5298,7 @@ (define-public cwltool
python-ruamel.yaml
python-schema-salad
python-shellescape
+ python-spython
python-typing-extensions
;; Not listed as needed but still necessary:
node))
@@ -5313,7 +5309,8 @@ (define-public cwltool
python-pytest
python-pytest-cov
python-pytest-mock
- python-pytest-runner))
+ python-pytest-runner
+ python-pytest-xdist))
(home-page
"https://github.com/common-workflow-language/common-workflow-language")
(synopsis "Common Workflow Language reference implementation")
--
2.41.0
L
L
Ludovic Courtès wrote on 18 Feb 23:39 +0100
Re: [bug#66690] [PATCH v2 0/8] Upgrade cwltool
(name . Arun Isaac)(address . arunisaac@systemreboot.net)(address . 66690@debbugs.gnu.org)
87y1bhjt2u.fsf@gnu.org
Hi Arun!

Arun Isaac <arunisaac@systemreboot.net> skribis:

Toggle quote (5 lines)
> In this patchset, I have updated cwltool once more to the latest version. And,
> I have split out ruamel-yaml into two separate package variants so that conda
> no longer breaks. I will push this patchset if it builds successfully on QA
> without breaking other packages.

I skimmed over the patches and they LGTM.

Thanks,
Ludo’.
A
A
Arun Isaac wrote on 22 Feb 14:16 +0100
(name . Ludovic Courtès)(address . ludo@gnu.org)(address . 66690-done@debbugs.gnu.org)
8734tkljvo.fsf@systemreboot.net
Thanks, Ludo. I pushed this patchset after moving a couple of more
packages to the older python-ruamel-yaml-0.16.
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