[PATCH 0/5] Update Astropy.

DoneSubmitted by Vinicius Monego.
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2 participants
  • Nicolas Goaziou
  • Vinicius Monego
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unassigned
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normal
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Vinicius Monego wrote on 24 Dec 2021 06:46
(address . guix-patches@gnu.org)(name . Vinicius Monego)(address . monego@posteo.net)
20211224054613.1009765-1-monego@posteo.net
Vinicius Monego (5):
gnu: python-pytest-arraydiff: Fix 'sanity-check phase.
gnu: python-pytest-doctestplus: Update to 0.11.2.
gnu: python-pytest-doctestplus: Honor #:tests?.
gnu: erfa: Update to 2.0.0.
gnu: python-astropy: Update to 5.0.

gnu/packages/astronomy.scm | 28 +++++++++++++++-------------
gnu/packages/python-check.scm | 22 ++++++++++++++++------
2 files changed, 31 insertions(+), 19 deletions(-)


base-commit: a296b5fff9f182da7c7b67cc7bdba0957623e650
--
2.30.2
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Vinicius Monego wrote on 24 Dec 2021 06:47
[PATCH 1/5] gnu: python-pytest-arraydiff: Fix 'sanity-check phase.
(address . 52768@debbugs.gnu.org)(name . Vinicius Monego)(address . monego@posteo.net)
20211224054733.1009894-1-monego@posteo.net
* gnu/packages/python-check.scm (python-pytest-arraydiff)[native-inputs]: Add
python-pytest.
---
gnu/packages/python-check.scm | 2 ++
1 file changed, 2 insertions(+)

Toggle diff (15 lines)
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 6bd86d451f..e6cf2a4f85 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -387,6 +387,8 @@ astropy related packages.")
      ;; Tests require python-astropy, which itself requires this package.
      ;; Disable tests to avoid the circular dependency problem.
      '(#:tests? #f))
+    (native-inputs
+     (list python-pytest)) ; for sanity-check
     (propagated-inputs
      (list python-numpy python-six))
     (home-page "https://github.com/astropy/pytest-arraydiff")
-- 
2.30.2
V
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Vinicius Monego wrote on 24 Dec 2021 06:47
[PATCH 2/5] gnu: python-pytest-doctestplus: Update to 0.11.2.
(address . 52768@debbugs.gnu.org)(name . Vinicius Monego)(address . monego@posteo.net)
20211224054733.1009894-2-monego@posteo.net
* gnu/packages/python-check.scm (python-pytest-doctestplus): Update to
0.11.2.
[arguments]<#:phases>: In the custom 'check phase, skip tests that require
remote data.
[native-inputs]: Add python-setuptools-scm.
---
gnu/packages/python-check.scm | 15 +++++++++++----
1 file changed, 11 insertions(+), 4 deletions(-)

Toggle diff (41 lines)
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index e6cf2a4f85..a745e735db 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -402,13 +402,13 @@ are too large to conveniently hard-code them in the tests.")
 (define-public python-pytest-doctestplus
   (package
     (name "python-pytest-doctestplus")
-    (version "0.7.0")
+    (version "0.11.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-doctestplus" version))
        (sha256
-        (base32 "1ai9kvd7xbq2jg2h8gmkb8lqzyrxvdh4zg3vxndg149iwd1hyi7d"))))
+        (base32 "0j1lvlj3ps975q9hmg8i6rpqm0313j3r18bc3l8mz6khb7vav4zk"))))
     (build-system python-build-system)
     (arguments
      '(#:phases
@@ -417,9 +417,16 @@ are too large to conveniently hard-code them in the tests.")
            (lambda* (#:key inputs outputs #:allow-other-keys)
              ;; Make the installed plugin discoverable by Pytest.
              (add-installed-pythonpath inputs outputs)
-             (invoke "pytest" "-vv"))))))
+             (invoke "python" "-m" "pytest" "-k"
+                     (string-append ; skip tests that require remote data
+                      "not test_remote_data_url"
+                      " and not test_remote_data_float_cmp"
+                      " and not test_remote_data_ignore_whitespace"
+                      " and not test_remote_data_ellipsis"
+                      " and not test_remote_data_requires"
+                      " and not test_remote_data_ignore_warnings")))))))
     (native-inputs
-     (list python-pytest))
+     (list python-pytest python-setuptools-scm))
     (home-page "https://github.com/astropy/pytest-doctestplus")
     (synopsis "Pytest plugin with advanced doctest features")
     (description
-- 
2.30.2
V
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Vinicius Monego wrote on 24 Dec 2021 06:47
[PATCH 3/5] gnu: python-pytest-doctestplus: Honor #:tests?.
(address . 52768@debbugs.gnu.org)(name . Vinicius Monego)(address . monego@posteo.net)
20211224054733.1009894-3-monego@posteo.net
* gnu/packages/python-check.scm (python-pytest-doctestplus): Honor #:tests? in
the custom 'check phase.
---
gnu/packages/python-check.scm | 21 +++++++++++----------
1 file changed, 11 insertions(+), 10 deletions(-)

Toggle diff (35 lines)
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index a745e735db..50e63cb734 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -414,17 +414,18 @@ are too large to conveniently hard-code them in the tests.")
      '(#:phases
        (modify-phases %standard-phases
          (replace 'check
-           (lambda* (#:key inputs outputs #:allow-other-keys)
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
              ;; Make the installed plugin discoverable by Pytest.
-             (add-installed-pythonpath inputs outputs)
-             (invoke "python" "-m" "pytest" "-k"
-                     (string-append ; skip tests that require remote data
-                      "not test_remote_data_url"
-                      " and not test_remote_data_float_cmp"
-                      " and not test_remote_data_ignore_whitespace"
-                      " and not test_remote_data_ellipsis"
-                      " and not test_remote_data_requires"
-                      " and not test_remote_data_ignore_warnings")))))))
+             (when tests?
+               (add-installed-pythonpath inputs outputs)
+               (invoke "python" "-m" "pytest" "-k"
+                       (string-append   ; skip tests that require remote data
+                        "not test_remote_data_url"
+                        " and not test_remote_data_float_cmp"
+                        " and not test_remote_data_ignore_whitespace"
+                        " and not test_remote_data_ellipsis"
+                        " and not test_remote_data_requires"
+                        " and not test_remote_data_ignore_warnings"))))))))
     (native-inputs
      (list python-pytest python-setuptools-scm))
     (home-page "https://github.com/astropy/pytest-doctestplus")
-- 
2.30.2
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Vinicius Monego wrote on 24 Dec 2021 06:47
[PATCH 4/5] gnu: erfa: Update to 2.0.0.
(address . 52768@debbugs.gnu.org)(name . Vinicius Monego)(address . monego@posteo.net)
20211224054733.1009894-4-monego@posteo.net
* gnu/packages/astronomy.scm (erfa): Update to 2.0.0.
(python-pyerfa): Update to 2.0.0.1.
[arguments]<#:phases>: Don't return #t.
[native-inputs]: Use the new style.
[inputs]: Likewise.
---
gnu/packages/astronomy.scm | 17 +++++++----------
1 file changed, 7 insertions(+), 10 deletions(-)

Toggle diff (58 lines)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index d88a0ef739..2cd3745cfb 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -188,7 +188,7 @@ for reading and writing.")
 (define-public erfa
   (package
     (name "erfa")
-    (version "1.7.3")
+    (version "2.0.0")
     (source
      (origin
        (method git-fetch)
@@ -197,7 +197,7 @@ for reading and writing.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0nh12dr7gk4ki55lz95pkm4fpf7kazirra3zax9pab6v4qql4hlw"))))
+        (base32 "0s9dpj0jdkqcg552f00jhd722czji4pffabmpys5pgi6djckq4f4"))))
     (build-system gnu-build-system)
     (native-inputs
      (list automake autoconf libtool pkg-config))
@@ -1170,13 +1170,13 @@ JPL ephemerides use to predict raw (x,y,z) planetary positions.")
 (define-public python-pyerfa
   (package
     (name "python-pyerfa")
-    (version "1.7.3")
+    (version "2.0.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyerfa" version))
        (sha256
-        (base32 "1jqqrxvrgly4r0br5f6dsy8nab2xmhz915vp6md5f31ysr2sdwvc"))
+        (base32 "0c6y1rm51kj8ahbr1vwbswck3ix77dc3zhc2fkg6w7iczrzn7m1g"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -1189,14 +1189,11 @@ JPL ephemerides use to predict raw (x,y,z) planetary positions.")
        (modify-phases %standard-phases
          (add-before 'build 'use-system-liberfa
            (lambda _
-             (setenv "PYERFA_USE_SYSTEM_LIBERFA" "1")
-             #t)))))
+             (setenv "PYERFA_USE_SYSTEM_LIBERFA" "1"))))))
     (native-inputs
-     `(("pytest-doctestplus" ,python-pytest-doctestplus)
-       ("python-pytest" ,python-pytest)
-       ("python-setuptools-scm" ,python-setuptools-scm)))
+     (list python-pytest-doctestplus python-pytest python-setuptools-scm))
     (inputs
-     `(("liberfa" ,erfa)))
+     (list erfa))
     (propagated-inputs
      (list python-numpy))
     (home-page "https://github.com/liberfa/pyerfa")
-- 
2.30.2
V
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Vinicius Monego wrote on 24 Dec 2021 06:50
[PATCH 5/5] gnu: python-astropy: Update to 5.0.
(address . 52768@debbugs.gnu.org)(name . Vinicius Monego)(address . monego@posteo.net)
20211224055018.1010067-1-monego@posteo.net
* gnu/packages/astronomy.scm (python-astropy): Update to 5.0.
[propagated-inputs]: Add python-packaging, python-pyyaml.
---
gnu/packages/astronomy.scm | 11 ++++++++---
1 file changed, 8 insertions(+), 3 deletions(-)

Toggle diff (36 lines)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 2cd3745cfb..1f9eca9a44 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -612,13 +612,13 @@ accurately in real time at any rate desired.")
 (define-public python-astropy
   (package
     (name "python-astropy")
-    (version "4.3.1")
+    (version "5.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy" version))
        (sha256
-        (base32 "0lfd6n7v7kas4wvacddnwgccax3ks908735dzilg7dsf7ci52f9d"))
+        (base32 "09rr9z2kn5qw34fqpwxgcwsn9m5aw6f0dd0pm232aa8k3qakw83h"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -690,7 +690,12 @@ accurately in real time at any rate desired.")
     (inputs
      (list cfitsio expat))
     (propagated-inputs
-     (list python-configobj python-numpy python-ply python-pyerfa))
+     (list python-configobj
+           python-numpy
+           python-packaging
+           python-ply
+           python-pyerfa
+           python-pyyaml))
     (home-page "https://www.astropy.org/")
     (synopsis "Core package for Astronomy in Python")
     (description
-- 
2.30.2
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Nicolas Goaziou wrote on 26 Dec 2021 21:43
Re: [bug#52768] [PATCH 0/5] Update Astropy.
(name . Vinicius Monego)(address . monego@posteo.net)(address . 52768-done@debbugs.gnu.org)
87ee5zayh5.fsf@nicolasgoaziou.fr
Hello,

Vinicius Monego <monego@posteo.net> writes:

Toggle quote (7 lines)
> Vinicius Monego (5):
> gnu: python-pytest-arraydiff: Fix 'sanity-check phase.
> gnu: python-pytest-doctestplus: Update to 0.11.2.
> gnu: python-pytest-doctestplus: Honor #:tests?.
> gnu: erfa: Update to 2.0.0.
> gnu: python-astropy: Update to 5.0.

Applied. Thank you.

Regards,
--
Nicolas Goaziou
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