GNU bug report logs - #63176
[PATCH 00/10] Fix some broken python packages.

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Package: guix-patches; Reported by: Felix Gruber <felgru@HIDDEN>; Keywords: patch; dated Sat, 29 Apr 2023 17:07:02 UTC; Maintainer for guix-patches is guix-patches@HIDDEN.

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From: Felix Gruber <felgru@HIDDEN>
To: 63176 <at> debbugs.gnu.org
Subject: [PATCH v3 8/8] gnu: python-astropy: Update to 5.2.2.
Date: Tue,  2 May 2023 21:45:42 +0000
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* gnu/packages/astronomy.scm (python-astropy): Update to 5.2.2.
---
 gnu/packages/astronomy.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 888e5bb1d7..a110c9b636 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1131,13 +1131,13 @@ (define-public celestia-gtk
 (define-public python-astropy
   (package
     (name "python-astropy")
-    (version "5.2.1")
+    (version "5.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy" version))
        (sha256
-        (base32 "08xc6brs7xwiqchhsjq8l10p6qc5p68cfxps7s889spqfyh2gbpn"))
+        (base32 "170ddflli35mvhf6pla7aizfw8a7ckq66g1mi1br99dx2r3y7ag6"))
        (modules '((guix build utils)))
        (snippet
         '(begin
-- 
2.39.2

Information forwarded to guix-patches@HIDDEN:
bug#63176; Package guix-patches. Full text available.

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From: Felix Gruber <felgru@HIDDEN>
To: 63176 <at> debbugs.gnu.org
Subject: [PATCH v3 7/8] gnu: python-pytest-astropy: Fix build.
Date: Tue,  2 May 2023 21:45:41 +0000
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* gnu/packages/python-check.scm (python-pytest-astropy): Fix build
against updated python-pytest-remotedata.
[build-system]: Use pyproject-build-system.
[arguments]: Remove broken version check for pytest-remotedata.
---
 gnu/packages/python-check.scm | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 160d30179b..84d968e061 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -517,17 +517,19 @@ (define-public python-pytest-astropy
        (uri (pypi-uri "pytest-astropy" version))
        (sha256
         (base32 "04g2rh261s3s6ym8mwi4iv2a6anbgwvwzcvkyilfck6yxrncdqw5"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
      `(#:tests? #f ; there are no tests
        #:phases
        (modify-phases %standard-phases
-         ;; There is a bug somewhere that makes pytest-filter-subpackage appear
-         ;; as version 0.0.0 to setup.py.  Remove it from the requirements.
+         ;; There is a bug somewhere that makes pytest-filter-subpackage
+         ;; and pytest-remotedata appear as version 0.0.0 to setup.py.
+         ;; Remove them from the requirements.
          (add-after 'unpack 'remove-requirement
            (lambda _
              (substitute* "setup.cfg"
-               ((".*pytest-filter-subpackage.*") "")))))))
+               ((".*pytest-filter-subpackage.*") "")
+               ((".*pytest-remotedata.*") "")))))))
     (native-inputs
      (list python-attrs python-pytest-mock python-setuptools-scm))
     (propagated-inputs
-- 
2.39.2

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bug#63176; Package guix-patches. Full text available.

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To: 63176 <at> debbugs.gnu.org
Subject: [PATCH v3 6/8] gnu: python-pytest-remotedata: Update to 0.4.0.
Date: Tue,  2 May 2023 21:45:40 +0000
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* gnu/packages/python-check.scm (python-pytest-remotedata): Update to 0.4.0.
[build-system]: Use pyproject-build-system.
[arguments]: Use #:test-flags instead of custom 'check phase.
[propagated-inputs]: Remove python-six.
---
 gnu/packages/python-check.scm | 26 ++++++++++----------------
 1 file changed, 10 insertions(+), 16 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 10731178e3..160d30179b 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -754,30 +754,24 @@ (define-public python-pytest-openfiles
 (define-public python-pytest-remotedata
   (package
     (name "python-pytest-remotedata")
-    (version "0.3.2")
+    (version "0.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-remotedata" version))
        (sha256
-        (base32 "1h6g6shib6z07azf12rnsa053470ggbd7hy3bnbw8nf3nza5h372"))))
-    (build-system python-build-system)
+        (base32 "1j5106j331cfdyfcwzrbs3yby84mq1b0kddfysq12z2dwdcca8dy"))))
+    (build-system pyproject-build-system)
     (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             ;; Make the installed plugin discoverable by Pytest.
-             (add-installed-pythonpath inputs outputs)
-             (invoke "pytest" "-vv" "-k"
-                     (string-append
-                      ;; These tests require internet access. Disable them.
-                      "not test_default_behavior"
-                      " and not test_strict_with_decorator")))))))
+     (list
+      #:test-flags
+      '(list "-k"
+             (string-append
+               ;; These tests require internet access. Disable them.
+               "not test_default_behavior"
+               " and not test_strict_with_decorator"))))
     (native-inputs
      (list python-pytest))
-    (propagated-inputs
-     (list python-six))
     (home-page "https://github.com/astropy/pytest-remotedata")
     (synopsis "Pytest plugin for controlling remote data access")
     (description
-- 
2.39.2

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bug#63176; Package guix-patches. Full text available.

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From: Felix Gruber <felgru@HIDDEN>
To: 63176 <at> debbugs.gnu.org
Subject: [PATCH v3 5/8] gnu: python-pytest-httpx: Update to 0.22.0.
Date: Tue,  2 May 2023 21:45:39 +0000
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* gnu/packages/python-check.scm (python-pytest-httpx): Update to 0.22.0.
  [build-system]: Use pyproject-build-system.
  [arguments]: Remove custom 'check phase.
---
 gnu/packages/python-check.scm | 14 +++-----------
 1 file changed, 3 insertions(+), 11 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index f451a5e999..10731178e3 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -2513,7 +2513,7 @@ (define-public python-pytest-parawtf
 (define-public python-pytest-httpx
   (package
     (name "python-pytest-httpx")
-    (version "0.21.0")
+    (version "0.22.0")
     (source
      (origin
        ;; pypi package doesn't include the tests
@@ -2523,16 +2523,8 @@ (define-public python-pytest-httpx
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "12mcy1f5d5cq3rqrqgi2ar0qvzw62ibys17hw6dsdfd0j2syck4r"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (setenv "PYTHONPATH" (getcwd))
-               (invoke "pytest" "-vv")))))))
+        (base32 "1ncpd74hmsz4sadvjg99fnfscxpgh3mc2siini0dhxzwgwdkk5i7"))))
+    (build-system pyproject-build-system)
     (propagated-inputs (list python-httpx))
     (native-inputs (list python-pytest python-pytest-asyncio))
     (home-page "https://colin-b.github.io/pytest_httpx/")
-- 
2.39.2

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bug#63176; Package guix-patches. Full text available.

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From: Felix Gruber <felgru@HIDDEN>
To: 63176 <at> debbugs.gnu.org
Subject: [PATCH v3 4/8] gnu: python-pytest-doctestplus: Update to 0.12.1.
Date: Tue,  2 May 2023 21:45:38 +0000
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* gnu/packages/python-check.scm (python-pytest-doctestplus): Update to 0.12.1.
  [build-system]: Use pyproject-build-system.
  [arguments]: Use #:test-flags instead of custom 'check phase.
---
 gnu/packages/python-check.scm | 33 ++++++++++++++-------------------
 1 file changed, 14 insertions(+), 19 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index c42cd426b1..f451a5e999 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -14,7 +14,7 @@
 ;;; Copyright © 2021, 2022 Guillaume Le Vaillant <glv@HIDDEN>
 ;;; Copyright © 2021 Bonface Munyoki Kilyungi <me@HIDDEN>
 ;;; Copyright © 2022 Malte Frank Gerdes <malte.f.gerdes@HIDDEN>
-;;; Copyright © 2022 Felix Gruber <felgru@HIDDEN>
+;;; Copyright © 2022, 2023 Felix Gruber <felgru@HIDDEN>
 ;;; Copyright © 2022 Tomasz Jeneralczyk <tj@HIDDEN>
 ;;; Copyright © 2022 jgart <jgart@HIDDEN>
 ;;;
@@ -577,30 +577,25 @@ (define-public python-pytest-arraydiff
 (define-public python-pytest-doctestplus
   (package
     (name "python-pytest-doctestplus")
-    (version "0.11.2")
+    (version "0.12.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-doctestplus" version))
        (sha256
-        (base32 "0j1lvlj3ps975q9hmg8i6rpqm0313j3r18bc3l8mz6khb7vav4zk"))))
-    (build-system python-build-system)
+        (base32 "10ciqylgziihxwxryxvxgmkqgws51pqcarn0gbh1d4cxx55rx5vs"))))
+    (build-system pyproject-build-system)
     (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             ;; Make the installed plugin discoverable by Pytest.
-             (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"))))))))
+     (list
+      #:test-flags
+      '(list "-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")
-- 
2.39.2

Information forwarded to guix-patches@HIDDEN:
bug#63176; Package guix-patches. Full text available.

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From: Felix Gruber <felgru@HIDDEN>
To: 63176 <at> debbugs.gnu.org
Subject: [PATCH v3 3/8] gnu: python-dolfin-adjoint: Fix build.
Date: Tue,  2 May 2023 21:45:37 +0000
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* gnu/packages/simulation.scm (python-dolfin-adjoint): Fix build.
  [arguments]: Disable failing test_read_checkpoint in 'check phase.
  Remove broken 'sanity-check phase.
---
 gnu/packages/simulation.scm | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index 059be5a2be..c76654f761 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -1027,10 +1027,17 @@ (define-public python-dolfin-adjoint
              (when tests?
                (add-installed-pythonpath inputs outputs)
                (setenv "HOME" (getcwd))
-               (and (invoke "py.test" "-v" "tests/fenics_adjoint")
+               (and (invoke "py.test" "-v" "tests/fenics_adjoint"
+                            "-k" "not test_read_checkpoint")
                     (invoke "py.test" "-v" "tests/migration")
                     (invoke "py.test" "-v" "tests/pyadjoint")))
-             #t)))))
+             #t))
+         ;; Remove 'sanity-check, because it tries to import
+         ;; firedrake_adjoint after importing fenics_adjoint.
+         ;; Both load a module named 'backend' and firedrake_adjoint
+         ;; fails with an ImportError if it sees that the backend module
+         ;; has already been loaded.
+         (delete 'sanity-check))))
     (home-page "https://www.dolfin-adjoint.org")
     (synopsis "Automatic differentiation library")
     (description "@code{python-dolfin-adjoint} is a solver of
-- 
2.39.2

Information forwarded to guix-patches@HIDDEN:
bug#63176; Package guix-patches. Full text available.

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To: 63176 <at> debbugs.gnu.org
Subject: [PATCH v3 2/8] gnu: python-cftime: Update to 1.6.2.
Date: Tue,  2 May 2023 21:45:36 +0000
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* gnu/packages/python-xyz.scm (python-cftime): Update to 1.6.2.
[build-system]: Use pyproject-build-system.
---
 gnu/packages/python-xyz.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e2d082091f..943686f3ff 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1977,14 +1977,14 @@ (define-public python-sh
 (define-public python-cftime
   (package
     (name "python-cftime")
-    (version "1.5.1.1")
+    (version "1.6.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "cftime" version))
        (sha256
-        (base32 "0l1a22zlhdpgaisibvvm7dhij4vzfm661rnv00y2snpyqxpdgi3d"))))
-    (build-system python-build-system)
+        (base32 "1lp6jrjjgl18csn4bcnphn0l16ag4aynvn7x0kins155p07w0546"))))
+    (build-system pyproject-build-system)
     (propagated-inputs
      (list python-numpy))
     (native-inputs
-- 
2.39.2

Information forwarded to guix-patches@HIDDEN:
bug#63176; Package guix-patches. Full text available.

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From: Felix Gruber <felgru@HIDDEN>
To: 63176 <at> debbugs.gnu.org
Subject: [PATCH v3 1/8] gnu: python-mpi4py: Update to 3.1.4.
Date: Tue,  2 May 2023 21:45:35 +0000
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* gnu/packages/mpi.scm (python-mpi4py): Update to 3.1.4.
[build-system]: Use pyproject-build-system.
---
 gnu/packages/mpi.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/mpi.scm b/gnu/packages/mpi.scm
index 20fc1a16a4..529f197214 100644
--- a/gnu/packages/mpi.scm
+++ b/gnu/packages/mpi.scm
@@ -32,6 +32,7 @@ (define-module (gnu packages mpi)
   #:use-module (guix utils)
   #:use-module (guix deprecation)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system pyproject)
   #:use-module (guix build-system python)
   #:use-module (gnu packages)
   #:use-module (gnu packages base)
@@ -399,14 +400,14 @@ (define-public %openmpi-setup
 (define-public python-mpi4py
   (package
     (name "python-mpi4py")
-    (version "3.0.3")
+    (version "3.1.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "mpi4py" version))
        (sha256
-        (base32 "07ssbhssv27rrjx1c5vd3vsr31vay5d8xcf4zh9yblcyidn72b81"))))
-    (build-system python-build-system)
+        (base32 "101lz7bnm9l17nrkbg6497kxscyh53aah7qd2b820ck2php8z18p"))))
+    (build-system pyproject-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-- 
2.39.2

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bug#63176; Package guix-patches. Full text available.

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To: 63176 <at> debbugs.gnu.org
Subject: [PATCH v3 0/8] Fix some broken python packages.
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This updated patchset removes the patches for adding texlive-alphalph
and updating hypre, both of which already happened on master.
It also fixes the commit message of the patch for python-pytest-astropy.

Felix Gruber (8):
  gnu: python-mpi4py: Update to 3.1.4.
  gnu: python-cftime: Update to 1.6.2.
  gnu: python-dolfin-adjoint: Fix build.
  gnu: python-pytest-doctestplus: Update to 0.12.1.
  gnu: python-pytest-httpx: Update to 0.22.0.
  gnu: python-pytest-remotedata: Update to 0.4.0.
  gnu: python-pytest-astropy: Fix build.
  gnu: python-astropy: Update to 5.2.2.

 gnu/packages/astronomy.scm    |  4 +-
 gnu/packages/mpi.scm          |  7 +--
 gnu/packages/python-check.scm | 83 ++++++++++++++---------------------
 gnu/packages/python-xyz.scm   |  6 +--
 gnu/packages/simulation.scm   | 11 ++++-
 5 files changed, 51 insertions(+), 60 deletions(-)

-- 
2.39.2

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To: 63176 <at> debbugs.gnu.org,
	Nicolas Goaziou <mail@HIDDEN>
Subject: [PATCH v2 03/10] gnu: Add texlive-alphalph.
Date: Sun, 30 Apr 2023 21:11:28 +0000
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* gnu/packages/tex.scm (texlive-alphalph): New variable.
---
 gnu/packages/tex.scm | 45 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index a2f1de4e35..a6203300cb 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -27,6 +27,7 @@
 ;;; Copyright © 2023 Thomas Albers Raviola <thomas@HIDDEN>
 ;;; Copyright © 2023 John Kehayias <john.kehayias@HIDDEN>
 ;;; Copyright © 2023 Dominik Delgado Steuter <d@HIDDEN>
+;;; Copyright © 2023 Felix Gruber <felgru@HIDDEN>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -12067,6 +12068,50 @@ (define-public texlive-kastrup
 LaTeX and plain TeX.")
     (license (license:fsf-free "file:/binhex.dtx"))))
 
+(define-public texlive-alphalph
+  (let ((template (simple-texlive-package
+                   "texlive-alphalph"
+                   (list "doc/latex/alphalph/"
+                         "source/latex/alphalph/"
+                         "tex/generic/alphalph/")
+                   (base32
+                    "0ap59hmg0brg2wlh3bl77jxfxrk7hphhdal8cr05mby9bw35gffy"))))
+    (package
+      (inherit template)
+      (outputs '("out" "doc"))
+      (arguments
+       (substitute-keyword-arguments (package-arguments template)
+         ((#:tex-directory _ '())
+          "latex/alphalph")
+         ((#:build-targets _ '())
+          #~(list "alphalph.dtx"))
+         ((#:phases phases)
+          #~(modify-phases #$phases
+              (add-after 'unpack 'chdir
+                (lambda _
+                  (chdir "source/latex/alphalph")))
+              (replace 'copy-files
+                (lambda* (#:key inputs #:allow-other-keys)
+                  (let ((origin (assoc-ref inputs "source"))
+                        (source (string-append #$output
+                                               "/share/texmf-dist/source"))
+                        (doc (string-append #$output:doc
+                                            "/share/texmf-dist/doc")))
+                    (copy-recursively (string-append origin "/source") source)
+                    (copy-recursively (string-append origin "/doc") doc))))))))
+       (propagated-inputs (list texlive-intcalc
+                                texlive-infwarerr))
+       (home-page "https://ctan.org/pkg/alphalph")
+       (synopsis "Convert numbers to letters")
+       (description
+        "This package provides commands @code{\\alphalph} and
+@code{\\AlphAlph}.  They are like @code{\\number} but the expansion
+consists of lowercase and uppercase letters respectively (1 to a, 26 to
+z, 27 to aa, 52 to zz, 53 to ba, 702 to zz, 703 to aaa, etc.).
+Alphalph's commands can be used as a replacement for LaTeX's
+@code{\\@@alph} and @code{\\@@Alph} macros.")
+       (license license:lppl1.3c+))))
+
 (define-public texlive-latex-translations
   (package
     (inherit (simple-texlive-package
-- 
2.39.2

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Hi Nicolas,

thank you for your review.
This was the first time that I've created a texlive package, so your 
comments were quite helpful to better understand how to properly define 
such a package.

I'll shortly submit an updated patch for texlive-alphalph. It would be 
great if you could take another look to see if I got it right this time 
or if there is still something that I should change.

Kind regards,
Felix

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Nicolas Goaziou <mail@HIDDEN> writes:

> Felix Gruber <felgru@HIDDEN> writes:
>
>> * gnu/packages/tex.scm (texlive-alphalph): New variable.
>
> Thanks. I will not comment about other patches in this set, but I will
> do about this one.

Completing myself:

This Texlive package also requires texlive-intcalc and texlive-infwarerr
as propagated inputs.

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Subject: Re: [bug#63176] [PATCH 03/10] gnu: Add texlive-alphalph.
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Hello,

Felix Gruber <felgru@HIDDEN> writes:

> * gnu/packages/tex.scm (texlive-alphalph): New variable.

Thanks. I will not comment about other patches in this set, but I will
do about this one.

> +(define-public texlive-alphalph
> +  (package
> +    (inherit (simple-texlive-package
> +               "texlive-alphalph"
> +               (list "doc/latex/alphalph/"
> +                     "source/latex/alphalph/"
> +                     "tex/generic/alphalph/")
> +               (base32 "0ap59hmg0brg2wlh3bl77jxfxrk7hphhdal8cr05mby9bw35gffy")
> +               #:trivial? #t))

This is not a "trivial" package. It contains a ".dtx" file, that you
need to run in order to generate the runfiles.

As a rule of thumb, if the importer, which I assume you used, doesn't
set #:trivial keyword, you shouldn't either.

> +    (build-system texlive-build-system)
> +    (home-page "https://ctan.org/pkg/alphalph")
> +    (synopsis "Convert numbers to letters")
> +    (description "This package provides commands \\alphalph and
> +\\AlphAlph.  They are like \\number but the expansion consists of
> +lowercase and uppercase letters respectively (1 to a, 26 to z, 27 to
> +aa, 52 to zz, 53 to ba, 702 to zz, 703 to aaa, etc.).  Can be used as a
> +replacement for LaTeX's \\@@alph and \\@@Alph macros.")

I suggest to use @code{...} around LaTeX commands. Also, the last
sentence in not complete.

Regards,
-- 
Nicolas Goaziou

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To: 63176 <at> debbugs.gnu.org
Subject: [PATCH 10/10] gnu: python-astropy: Update to 5.2.2.
Date: Sat, 29 Apr 2023 17:08:40 +0000
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* gnu/packages/astronomy.scm (python-astropy): Update to 5.2.2.
---
 gnu/packages/astronomy.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 888e5bb1d7..a110c9b636 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1131,13 +1131,13 @@ (define-public celestia-gtk
 (define-public python-astropy
   (package
     (name "python-astropy")
-    (version "5.2.1")
+    (version "5.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy" version))
        (sha256
-        (base32 "08xc6brs7xwiqchhsjq8l10p6qc5p68cfxps7s889spqfyh2gbpn"))
+        (base32 "170ddflli35mvhf6pla7aizfw8a7ckq66g1mi1br99dx2r3y7ag6"))
        (modules '((guix build utils)))
        (snippet
         '(begin
-- 
2.39.2

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To: 63176 <at> debbugs.gnu.org
Subject: [PATCH 09/10] gnu: python-pytest-astropy: Update to 0.10.0.
Date: Sat, 29 Apr 2023 17:08:39 +0000
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* gnu/packages/python-check.scm (python-pytest-astropy): Update to 0.10.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove broken version check for pytest-remotedata.
---
 gnu/packages/python-check.scm | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 160d30179b..84d968e061 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -517,17 +517,19 @@ (define-public python-pytest-astropy
        (uri (pypi-uri "pytest-astropy" version))
        (sha256
         (base32 "04g2rh261s3s6ym8mwi4iv2a6anbgwvwzcvkyilfck6yxrncdqw5"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
      `(#:tests? #f ; there are no tests
        #:phases
        (modify-phases %standard-phases
-         ;; There is a bug somewhere that makes pytest-filter-subpackage appear
-         ;; as version 0.0.0 to setup.py.  Remove it from the requirements.
+         ;; There is a bug somewhere that makes pytest-filter-subpackage
+         ;; and pytest-remotedata appear as version 0.0.0 to setup.py.
+         ;; Remove them from the requirements.
          (add-after 'unpack 'remove-requirement
            (lambda _
              (substitute* "setup.cfg"
-               ((".*pytest-filter-subpackage.*") "")))))))
+               ((".*pytest-filter-subpackage.*") "")
+               ((".*pytest-remotedata.*") "")))))))
     (native-inputs
      (list python-attrs python-pytest-mock python-setuptools-scm))
     (propagated-inputs
-- 
2.39.2

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From: Felix Gruber <felgru@HIDDEN>
To: 63176 <at> debbugs.gnu.org
Subject: [PATCH 08/10] gnu: python-pytest-remotedata: Update to 0.4.0.
Date: Sat, 29 Apr 2023 17:08:38 +0000
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* gnu/packages/python-check.scm (python-pytest-remotedata): Update to 0.4.0.
[build-system]: Use pyproject-build-system.
[arguments]: Use #:test-flags instead of custom 'check phase.
[propagated-inputs]: Remove python-six.
---
 gnu/packages/python-check.scm | 26 ++++++++++----------------
 1 file changed, 10 insertions(+), 16 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 10731178e3..160d30179b 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -754,30 +754,24 @@ (define-public python-pytest-openfiles
 (define-public python-pytest-remotedata
   (package
     (name "python-pytest-remotedata")
-    (version "0.3.2")
+    (version "0.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-remotedata" version))
        (sha256
-        (base32 "1h6g6shib6z07azf12rnsa053470ggbd7hy3bnbw8nf3nza5h372"))))
-    (build-system python-build-system)
+        (base32 "1j5106j331cfdyfcwzrbs3yby84mq1b0kddfysq12z2dwdcca8dy"))))
+    (build-system pyproject-build-system)
     (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             ;; Make the installed plugin discoverable by Pytest.
-             (add-installed-pythonpath inputs outputs)
-             (invoke "pytest" "-vv" "-k"
-                     (string-append
-                      ;; These tests require internet access. Disable them.
-                      "not test_default_behavior"
-                      " and not test_strict_with_decorator")))))))
+     (list
+      #:test-flags
+      '(list "-k"
+             (string-append
+               ;; These tests require internet access. Disable them.
+               "not test_default_behavior"
+               " and not test_strict_with_decorator"))))
     (native-inputs
      (list python-pytest))
-    (propagated-inputs
-     (list python-six))
     (home-page "https://github.com/astropy/pytest-remotedata")
     (synopsis "Pytest plugin for controlling remote data access")
     (description
-- 
2.39.2

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From: Felix Gruber <felgru@HIDDEN>
To: 63176 <at> debbugs.gnu.org
Subject: [PATCH 07/10] gnu: python-pytest-httpx: Update to 0.22.0.
Date: Sat, 29 Apr 2023 17:08:37 +0000
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* gnu/packages/python-check.scm (python-pytest-httpx): Update to 0.22.0.
  [build-system]: Use pyproject-build-system.
  [arguments]: Remove custom 'check phase.
---
 gnu/packages/python-check.scm | 14 +++-----------
 1 file changed, 3 insertions(+), 11 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index f451a5e999..10731178e3 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -2513,7 +2513,7 @@ (define-public python-pytest-parawtf
 (define-public python-pytest-httpx
   (package
     (name "python-pytest-httpx")
-    (version "0.21.0")
+    (version "0.22.0")
     (source
      (origin
        ;; pypi package doesn't include the tests
@@ -2523,16 +2523,8 @@ (define-public python-pytest-httpx
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "12mcy1f5d5cq3rqrqgi2ar0qvzw62ibys17hw6dsdfd0j2syck4r"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (setenv "PYTHONPATH" (getcwd))
-               (invoke "pytest" "-vv")))))))
+        (base32 "1ncpd74hmsz4sadvjg99fnfscxpgh3mc2siini0dhxzwgwdkk5i7"))))
+    (build-system pyproject-build-system)
     (propagated-inputs (list python-httpx))
     (native-inputs (list python-pytest python-pytest-asyncio))
     (home-page "https://colin-b.github.io/pytest_httpx/")
-- 
2.39.2

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From: Felix Gruber <felgru@HIDDEN>
To: 63176 <at> debbugs.gnu.org
Subject: [PATCH 06/10] gnu: python-pytest-doctestplus: Update to 0.12.1.
Date: Sat, 29 Apr 2023 17:08:36 +0000
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* gnu/packages/python-check.scm (python-pytest-doctestplus): Update to 0.12.1.
  [build-system]: Use pyproject-build-system.
  [arguments]: Use #:test-flags instead of custom 'check phase.
---
 gnu/packages/python-check.scm | 33 ++++++++++++++-------------------
 1 file changed, 14 insertions(+), 19 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index c42cd426b1..f451a5e999 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -14,7 +14,7 @@
 ;;; Copyright © 2021, 2022 Guillaume Le Vaillant <glv@HIDDEN>
 ;;; Copyright © 2021 Bonface Munyoki Kilyungi <me@HIDDEN>
 ;;; Copyright © 2022 Malte Frank Gerdes <malte.f.gerdes@HIDDEN>
-;;; Copyright © 2022 Felix Gruber <felgru@HIDDEN>
+;;; Copyright © 2022, 2023 Felix Gruber <felgru@HIDDEN>
 ;;; Copyright © 2022 Tomasz Jeneralczyk <tj@HIDDEN>
 ;;; Copyright © 2022 jgart <jgart@HIDDEN>
 ;;;
@@ -577,30 +577,25 @@ (define-public python-pytest-arraydiff
 (define-public python-pytest-doctestplus
   (package
     (name "python-pytest-doctestplus")
-    (version "0.11.2")
+    (version "0.12.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-doctestplus" version))
        (sha256
-        (base32 "0j1lvlj3ps975q9hmg8i6rpqm0313j3r18bc3l8mz6khb7vav4zk"))))
-    (build-system python-build-system)
+        (base32 "10ciqylgziihxwxryxvxgmkqgws51pqcarn0gbh1d4cxx55rx5vs"))))
+    (build-system pyproject-build-system)
     (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             ;; Make the installed plugin discoverable by Pytest.
-             (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"))))))))
+     (list
+      #:test-flags
+      '(list "-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")
-- 
2.39.2

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To: 63176 <at> debbugs.gnu.org
Subject: [PATCH 05/10] gnu: python-dolfin-adjoint: Fix build.
Date: Sat, 29 Apr 2023 17:08:35 +0000
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* gnu/packages/simulation.scm (python-dolfin-adjoint): Fix build.
  [arguments]: Disable failing test_read_checkpoint in 'check phase.
  Remove broken 'sanity-check phase.
---
 gnu/packages/simulation.scm | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index 059be5a2be..c76654f761 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -1027,10 +1027,17 @@ (define-public python-dolfin-adjoint
              (when tests?
                (add-installed-pythonpath inputs outputs)
                (setenv "HOME" (getcwd))
-               (and (invoke "py.test" "-v" "tests/fenics_adjoint")
+               (and (invoke "py.test" "-v" "tests/fenics_adjoint"
+                            "-k" "not test_read_checkpoint")
                     (invoke "py.test" "-v" "tests/migration")
                     (invoke "py.test" "-v" "tests/pyadjoint")))
-             #t)))))
+             #t))
+         ;; Remove 'sanity-check, because it tries to import
+         ;; firedrake_adjoint after importing fenics_adjoint.
+         ;; Both load a module named 'backend' and firedrake_adjoint
+         ;; fails with an ImportError if it sees that the backend module
+         ;; has already been loaded.
+         (delete 'sanity-check))))
     (home-page "https://www.dolfin-adjoint.org")
     (synopsis "Automatic differentiation library")
     (description "@code{python-dolfin-adjoint} is a solver of
-- 
2.39.2

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From: Felix Gruber <felgru@HIDDEN>
To: 63176 <at> debbugs.gnu.org
Subject: [PATCH 04/10] gnu: hypre: Fix build.
Date: Sat, 29 Apr 2023 17:08:34 +0000
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* gnu/packages/maths.scm (hypre): [native-inputs]: Add missing required
  inputs texlive-alphalph and texlive-enumitem.
---
 gnu/packages/maths.scm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index f69d59273a..eebfdab914 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5756,12 +5756,14 @@ (define-public hypre
            python-breathe
            python-sphinx
            (texlive-updmap.cfg (list texlive-adjustbox
+                                     texlive-alphalph
                                      texlive-amsfonts
                                      texlive-bibtex
                                      texlive-capt-of
                                      texlive-caption
                                      texlive-cm
                                      texlive-courier
+                                     texlive-enumitem
                                      texlive-etoolbox
                                      texlive-fancyhdr
                                      texlive-fancyvrb
-- 
2.39.2

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To: 63176 <at> debbugs.gnu.org
Subject: [PATCH 03/10] gnu: Add texlive-alphalph.
Date: Sat, 29 Apr 2023 17:08:33 +0000
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* gnu/packages/tex.scm (texlive-alphalph): New variable.
---
 gnu/packages/tex.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index a2f1de4e35..b75f4aeaa7 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -27,6 +27,7 @@
 ;;; Copyright © 2023 Thomas Albers Raviola <thomas@HIDDEN>
 ;;; Copyright © 2023 John Kehayias <john.kehayias@HIDDEN>
 ;;; Copyright © 2023 Dominik Delgado Steuter <d@HIDDEN>
+;;; Copyright © 2023 Felix Gruber <felgru@HIDDEN>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -12067,6 +12068,25 @@ (define-public texlive-kastrup
 LaTeX and plain TeX.")
     (license (license:fsf-free "file:/binhex.dtx"))))
 
+(define-public texlive-alphalph
+  (package
+    (inherit (simple-texlive-package
+               "texlive-alphalph"
+               (list "doc/latex/alphalph/"
+                     "source/latex/alphalph/"
+                     "tex/generic/alphalph/")
+               (base32 "0ap59hmg0brg2wlh3bl77jxfxrk7hphhdal8cr05mby9bw35gffy")
+               #:trivial? #t))
+    (build-system texlive-build-system)
+    (home-page "https://ctan.org/pkg/alphalph")
+    (synopsis "Convert numbers to letters")
+    (description "This package provides commands \\alphalph and
+\\AlphAlph.  They are like \\number but the expansion consists of
+lowercase and uppercase letters respectively (1 to a, 26 to z, 27 to
+aa, 52 to zz, 53 to ba, 702 to zz, 703 to aaa, etc.).  Can be used as a
+replacement for LaTeX's \\@@alph and \\@@Alph macros.")
+    (license license:lppl1.3+)))
+
 (define-public texlive-latex-translations
   (package
     (inherit (simple-texlive-package
-- 
2.39.2

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bug#63176; Package guix-patches. Full text available.

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To: 63176 <at> debbugs.gnu.org
Subject: [PATCH 02/10] gnu: python-cftime: Update to 1.6.2.
Date: Sat, 29 Apr 2023 17:08:32 +0000
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* gnu/packages/python-xyz.scm (python-cftime): Update to 1.6.2.
[build-system]: Use pyproject-build-system.
---
 gnu/packages/python-xyz.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e2d082091f..943686f3ff 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1977,14 +1977,14 @@ (define-public python-sh
 (define-public python-cftime
   (package
     (name "python-cftime")
-    (version "1.5.1.1")
+    (version "1.6.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "cftime" version))
        (sha256
-        (base32 "0l1a22zlhdpgaisibvvm7dhij4vzfm661rnv00y2snpyqxpdgi3d"))))
-    (build-system python-build-system)
+        (base32 "1lp6jrjjgl18csn4bcnphn0l16ag4aynvn7x0kins155p07w0546"))))
+    (build-system pyproject-build-system)
     (propagated-inputs
      (list python-numpy))
     (native-inputs
-- 
2.39.2

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bug#63176; Package guix-patches. Full text available.

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From: Felix Gruber <felgru@HIDDEN>
To: 63176 <at> debbugs.gnu.org
Subject: [PATCH 01/10] gnu: python-mpi4py: Update to 3.1.4.
Date: Sat, 29 Apr 2023 17:08:31 +0000
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* gnu/packages/mpi.scm (python-mpi4py): Update to 3.1.4.
[build-system]: Use pyproject-build-system.
---
 gnu/packages/mpi.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/mpi.scm b/gnu/packages/mpi.scm
index 20fc1a16a4..529f197214 100644
--- a/gnu/packages/mpi.scm
+++ b/gnu/packages/mpi.scm
@@ -32,6 +32,7 @@ (define-module (gnu packages mpi)
   #:use-module (guix utils)
   #:use-module (guix deprecation)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system pyproject)
   #:use-module (guix build-system python)
   #:use-module (gnu packages)
   #:use-module (gnu packages base)
@@ -399,14 +400,14 @@ (define-public %openmpi-setup
 (define-public python-mpi4py
   (package
     (name "python-mpi4py")
-    (version "3.0.3")
+    (version "3.1.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "mpi4py" version))
        (sha256
-        (base32 "07ssbhssv27rrjx1c5vd3vsr31vay5d8xcf4zh9yblcyidn72b81"))))
-    (build-system python-build-system)
+        (base32 "101lz7bnm9l17nrkbg6497kxscyh53aah7qd2b820ck2php8z18p"))))
+    (build-system pyproject-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-- 
2.39.2

Information forwarded to guix-patches@HIDDEN:
bug#63176; Package guix-patches. Full text available.

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Subject: [PATCH 00/10] Fix some broken python packages.
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This patchset fixes a few Python packages that fail to build since
core-updates was merged.

Felix Gruber (10):
  gnu: python-mpi4py: Update to 3.1.4.
  gnu: python-cftime: Update to 1.6.2.
  gnu: Add texlive-alphalph.
  gnu: hypre: Fix build.
  gnu: python-dolfin-adjoint: Fix build.
  gnu: python-pytest-doctestplus: Update to 0.12.1.
  gnu: python-pytest-httpx: Update to 0.22.0.
  gnu: python-pytest-remotedata: Update to 0.4.0.
  gnu: python-pytest-astropy: Update to 0.10.0.
  gnu: python-astropy: Update to 5.2.2.

 gnu/packages/astronomy.scm    |  4 +-
 gnu/packages/maths.scm        |  2 +
 gnu/packages/mpi.scm          |  7 +--
 gnu/packages/python-check.scm | 83 ++++++++++++++---------------------
 gnu/packages/python-xyz.scm   |  6 +--
 gnu/packages/simulation.scm   | 11 ++++-
 gnu/packages/tex.scm          | 20 +++++++++
 7 files changed, 73 insertions(+), 60 deletions(-)

-- 
2.39.2

Acknowledgement sent to Felix Gruber <felgru@HIDDEN>:
New bug report received and forwarded. Copy sent to guix-patches@HIDDEN. Full text available.

Report forwarded to guix-patches@HIDDEN:
bug#63176; Package guix-patches. Full text available.

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