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

Previous Next

To add a comment to this bug, you must first unarchive it, by sending
a message to control AT debbugs.gnu.org, with unarchive 63176 in the body.
You can then email your comments to 63176 AT debbugs.gnu.org in the normal way.

Toggle the display of automated, internal messages from the tracker.

Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: guix-patches <at> gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH 00/10] Fix some broken python packages.
Date: Sat, 29 Apr 2023 17:06:11 +0000

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

Message #8 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH 01/10] gnu: python-mpi4py: Update to 3.1.4.
Date: Sat, 29 Apr 2023 17:08:31 +0000

* 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

Message #11 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH 02/10] gnu: python-cftime: Update to 1.6.2.
Date: Sat, 29 Apr 2023 17:08:32 +0000

* 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

Message #14 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH 03/10] gnu: Add texlive-alphalph.
Date: Sat, 29 Apr 2023 17:08:33 +0000

* 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 <at> thomaslabs.org>
 ;;; Copyright © 2023 John Kehayias <john.kehayias <at> protonmail.com>
 ;;; Copyright © 2023 Dominik Delgado Steuter <d <at> delgado.nrw>
+;;; Copyright © 2023 Felix Gruber <felgru <at> posteo.net>
 ;;;
 ;;; 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

Message #17 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH 04/10] gnu: hypre: Fix build.
Date: Sat, 29 Apr 2023 17:08:34 +0000

* 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

Message #20 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH 05/10] gnu: python-dolfin-adjoint: Fix build.
Date: Sat, 29 Apr 2023 17:08:35 +0000

* 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

Message #23 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH 06/10] gnu: python-pytest-doctestplus: Update to 0.12.1.
Date: Sat, 29 Apr 2023 17:08:36 +0000

* 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 <at> posteo.net>
 ;;; Copyright © 2021 Bonface Munyoki Kilyungi <me <at> bonfacemunyoki.com>
 ;;; Copyright © 2022 Malte Frank Gerdes <malte.f.gerdes <at> gmail.com>
-;;; Copyright © 2022 Felix Gruber <felgru <at> posteo.net>
+;;; Copyright © 2022, 2023 Felix Gruber <felgru <at> posteo.net>
 ;;; Copyright © 2022 Tomasz Jeneralczyk <tj <at> schwi.pl>
 ;;; Copyright © 2022 jgart <jgart <at> dismail.de>
 ;;;
@@ -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

Message #26 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH 07/10] gnu: python-pytest-httpx: Update to 0.22.0.
Date: Sat, 29 Apr 2023 17:08:37 +0000

* 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

Message #29 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH 08/10] gnu: python-pytest-remotedata: Update to 0.4.0.
Date: Sat, 29 Apr 2023 17:08:38 +0000

* 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

Message #32 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH 09/10] gnu: python-pytest-astropy: Update to 0.10.0.
Date: Sat, 29 Apr 2023 17:08:39 +0000

* 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

Message #35 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH 10/10] gnu: python-astropy: Update to 5.2.2.
Date: Sat, 29 Apr 2023 17:08:40 +0000

* 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

Message #38 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Goaziou <mail <at> nicolasgoaziou.fr>
To: Felix Gruber <felgru <at> posteo.net>
Cc: 63176 <at> debbugs.gnu.org
Subject: Re: [bug#63176] [PATCH 03/10] gnu: Add texlive-alphalph.
Date: Sat, 29 Apr 2023 21:22:22 +0200

Hello,

Felix Gruber <felgru <at> posteo.net> 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

Message #41 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Goaziou <mail <at> nicolasgoaziou.fr>
To: Felix Gruber <felgru <at> posteo.net>
Cc: 63176 <at> debbugs.gnu.org
Subject: Re: [bug#63176] [PATCH 03/10] gnu: Add texlive-alphalph.
Date: Sat, 29 Apr 2023 21:59:38 +0200

Nicolas Goaziou <mail <at> nicolasgoaziou.fr> writes:

> Felix Gruber <felgru <at> posteo.net> 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.

Message #44 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: Nicolas Goaziou <mail <at> nicolasgoaziou.fr>
Cc: 63176 <at> debbugs.gnu.org
Subject: Re: [bug#63176] [PATCH 03/10] gnu: Add texlive-alphalph.
Date: Sun, 30 Apr 2023 21:07:59 +0000

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

Message #47 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org,
	Nicolas Goaziou <mail <at> nicolasgoaziou.fr>
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH v2 03/10] gnu: Add texlive-alphalph.
Date: Sun, 30 Apr 2023 21:11:28 +0000

* 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 <at> thomaslabs.org>
 ;;; Copyright © 2023 John Kehayias <john.kehayias <at> protonmail.com>
 ;;; Copyright © 2023 Dominik Delgado Steuter <d <at> delgado.nrw>
+;;; Copyright © 2023 Felix Gruber <felgru <at> posteo.net>
 ;;;
 ;;; 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

Message #50 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH v3 0/8] Fix some broken python packages.
Date: Tue,  2 May 2023 21:45:34 +0000

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

Message #53 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH v3 1/8] gnu: python-mpi4py: Update to 3.1.4.
Date: Tue,  2 May 2023 21:45:35 +0000

* 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

Message #56 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH v3 2/8] gnu: python-cftime: Update to 1.6.2.
Date: Tue,  2 May 2023 21:45:36 +0000

* 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

Message #59 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH v3 3/8] gnu: python-dolfin-adjoint: Fix build.
Date: Tue,  2 May 2023 21:45:37 +0000

* 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

Message #62 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH v3 4/8] gnu: python-pytest-doctestplus: Update to 0.12.1.
Date: Tue,  2 May 2023 21:45:38 +0000

* 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 <at> posteo.net>
 ;;; Copyright © 2021 Bonface Munyoki Kilyungi <me <at> bonfacemunyoki.com>
 ;;; Copyright © 2022 Malte Frank Gerdes <malte.f.gerdes <at> gmail.com>
-;;; Copyright © 2022 Felix Gruber <felgru <at> posteo.net>
+;;; Copyright © 2022, 2023 Felix Gruber <felgru <at> posteo.net>
 ;;; Copyright © 2022 Tomasz Jeneralczyk <tj <at> schwi.pl>
 ;;; Copyright © 2022 jgart <jgart <at> dismail.de>
 ;;;
@@ -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

Message #65 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH v3 5/8] gnu: python-pytest-httpx: Update to 0.22.0.
Date: Tue,  2 May 2023 21:45:39 +0000

* 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

Message #68 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH v3 6/8] gnu: python-pytest-remotedata: Update to 0.4.0.
Date: Tue,  2 May 2023 21:45:40 +0000

* 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

Message #71 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH v3 7/8] gnu: python-pytest-astropy: Fix build.
Date: Tue,  2 May 2023 21:45:41 +0000

* 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

Message #74 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH v3 8/8] gnu: python-astropy: Update to 5.2.2.
Date: Tue,  2 May 2023 21:45:42 +0000

* 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

Message #77 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: reza <reza <at> housseini.me>
To: 63176 <at> debbugs.gnu.org <63176 <at> debbugs.gnu.org>
Subject: [PATCH 00/10] Fix some broken python packages.
Date: Tue, 9 May 2023 07:43:16 +0000

[Message part 1 (text/plain, inline)]

Building the broken paraview [1] with the new version of python-mpi4py 
fixes the build failure.

[1] https://ci.guix.gnu.org/build/1318584/details

[OpenPGP_0xC375C6AF05125C52.asc (application/pgp-keys, attachment)]

[OpenPGP_signature (application/pgp-signature, attachment)]

Message #80 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH v4 0/4]  Fix some broken python packages.
Date: Fri, 12 May 2023 16:23:21 +0000

I've rebased the patchset onto master and removed patches for packages
that have been updated on master in the meantime.

Felix Gruber (4):
  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-httpx: Update to 0.22.0.

 gnu/packages/mpi.scm          |  7 ++++---
 gnu/packages/python-check.scm | 14 +++-----------
 gnu/packages/python-xyz.scm   |  6 +++---
 gnu/packages/simulation.scm   | 11 +++++++++--
 4 files changed, 19 insertions(+), 19 deletions(-)

-- 
2.39.2

Message #83 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH v4 1/4] gnu: python-mpi4py: Update to 3.1.4.
Date: Fri, 12 May 2023 16:24:42 +0000

* 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

Message #86 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH v4 2/4] gnu: python-cftime: Update to 1.6.2.
Date: Fri, 12 May 2023 16:24:43 +0000

* 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 30769e4966..fbcac2c88d 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -2164,14 +2164,14 @@ (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

Message #89 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH v4 3/4] gnu: python-dolfin-adjoint: Fix build.
Date: Fri, 12 May 2023 16:24:44 +0000

* 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

Message #92 received at 63176 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176 <at> debbugs.gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH v4 4/4] gnu: python-pytest-httpx: Update to 0.22.0.
Date: Fri, 12 May 2023 16:24:45 +0000

* 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 f272a252fc..6c5f45d4b5 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -2530,7 +2530,7 @@ (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
@@ -2540,16 +2540,8 @@ (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

Message #97 received at 63176-done <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 63176-done <at> debbugs.gnu.org
Subject: Closing
Date: Tue, 29 Aug 2023 20:16:58 +0000

On 5/12/23 18:23, Felix Gruber wrote:
> Felix Gruber (4):
>    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-httpx: Update to 0.22.0.
> 
>   gnu/packages/mpi.scm          |  7 ++++---
>   gnu/packages/python-check.scm | 14 +++-----------
>   gnu/packages/python-xyz.scm   |  6 +++---
>   gnu/packages/simulation.scm   | 11 +++++++++--
>   4 files changed, 19 insertions(+), 19 deletions(-)

Closing this issue since all patches have been applied to master in the 
meantime.

Previous Next

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.