GNU bug report logs - #78181
[PATCH 0/2] Update python-h5py to 3.13

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

From: David Elsing <david.elsing <at> posteo.net>
To: andreas <at> enge.fr
Cc: David Elsing <david.elsing <at> posteo.net>, guix-patches <at> gnu.org
Subject: [PATCH 0/2] Update python-h5py to 3.13
Date: Thu,  1 May 2025 09:30:06 +0000

Hello Andreas,

I think the previous QA run was not complete, in particular a test of
python-h5py fails now. This is fixed in a newer version.

Best,
David

David Elsing (2):
  gnu: Add python-pytest-mpi.
  gnu: python-h5py: Update to 3.13.0.

 gnu/packages/python-check.scm | 20 ++++++++++++++++++-
 gnu/packages/python-xyz.scm   | 37 +++++++++++++++++++++++++----------
 2 files changed, 46 insertions(+), 11 deletions(-)

-- 
2.49.0

Message #8 received at 78181 <at> debbugs.gnu.org (full text, mbox):

From: David Elsing <david.elsing <at> posteo.net>
To: 78181 <at> debbugs.gnu.org
Cc: David Elsing <david.elsing <at> posteo.net>
Subject: [PATCH 2/2] gnu: python-h5py: Update to 3.13.0.
Date: Thu,  1 May 2025 09:35:13 +0000

* gnu/packages/python-xyz.scm (python-h5py): Update to 3.13.0.
[build-system]: Switch to pyproject-build-system.
[arguments]: Use gexps. Move a modified 'check phase after the 'install phase.
[native-inputs]: Add python-pytest-mpi, python-setuptools and python-wheel.
---
 gnu/packages/python-xyz.scm | 37 +++++++++++++++++++++++++++----------
 1 file changed, 27 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 9691c48781..baeeed31d3 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3872,24 +3872,41 @@ (define-public python-h5netcdf
 (define-public python-h5py
   (package
     (name "python-h5py")
-    (version "3.8.0")
+    (version "3.13.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "h5py" version))
        (sha256
-        (base32 "0pyr6z4h2xqbp49yx2i1401gl6yqh03h771zslwcy0201hpxiskg"))))
-    (build-system python-build-system)
+        (base32 "1hq5f5mnkv2138xsq7k7qncf6b7zc0cmm2fhhpd2603j31jy8w0q"))))
+    (build-system pyproject-build-system)
     (arguments
-     '(#:phases (modify-phases %standard-phases
-                  (add-after 'unpack 'fix-hdf5-paths
-                    (lambda* (#:key inputs #:allow-other-keys)
-                      (setenv "HDF5_DIR"
-                              (assoc-ref inputs "hdf5")))))))
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-hdf5-paths
+            (lambda _
+              (setenv "HDF5_DIR" #$(this-package-input "hdf5"))))
+          ;; The tests only work after being installed.
+          (delete 'check)
+          (add-after 'install 'check
+            (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+              (when tests?
+                (setenv "H5PY_TEST_CHECK_FILTERS" "1")
+                (with-directory-excursion (site-packages inputs outputs)
+                  (invoke "pytest" "-vv"))))))))
     (propagated-inputs (list python-six python-numpy))
     (inputs (list hdf5))
-    (native-inputs (list pkg-config python-cython python-ipython
-                         python-pkgconfig python-pytest))
+    (native-inputs
+     (list pkg-config
+           python-cython
+           python-ipython
+           python-pkgconfig
+           python-pytest
+           ;; Required to run tests, but the MPI tests are skipped anyway.
+           python-pytest-mpi
+           python-setuptools
+           python-wheel))
     (home-page "https://www.h5py.org/")
     (synopsis "Read and write HDF5 files from Python")
     (description
-- 
2.49.0

Message #11 received at 78181 <at> debbugs.gnu.org (full text, mbox):

From: David Elsing <david.elsing <at> posteo.net>
To: 78181 <at> debbugs.gnu.org
Cc: David Elsing <david.elsing <at> posteo.net>
Subject: [PATCH 1/2] gnu: Add python-pytest-mpi.
Date: Thu,  1 May 2025 09:35:12 +0000

* gnu/packages/python-check.scm (python-pytest-mpi): New variable.
---
 gnu/packages/python-check.scm | 20 +++++++++++++++++++-
 1 file changed, 19 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index eb4d62a294..b23361980f 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -23,7 +23,7 @@
 ;;; Copyright © 2022 jgart <jgart <at> dismail.de>
 ;;; Copyright © 2024-2025 Troy Figiel <troy <at> troyfigiel.com>
 ;;; Copyright © 2024 Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
-;;; Copyright © 2024 David Elsing <david.elsing <at> posteo.net>
+;;; Copyright © 2024, 2025 David Elsing <david.elsing <at> posteo.net>
 ;;; Copyright © 2024 Eric Bavier <bavier <at> posteo.net>
 ;;; Copyright © 2024 Markku Korkeala <markku.korkeala <at> iki.fi>
 ;;; Copyright © 2025 Evgeny Pisemsky <mail <at> pisemsky.site>
@@ -2446,6 +2446,24 @@ (define-public python-pytest-mockito
 @end itemize")
     (license license:expat)))
 
+(define-public python-pytest-mpi
+  (package
+    (name "python-pytest-mpi")
+    (version "0.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pytest-mpi" version))
+       (sha256
+        (base32 "1a954cai5lr327np5f38mg8gw91p4akx8m2z416wvwzq24swvcq9"))))
+    (build-system python-build-system)
+    (propagated-inputs (list python-pytest))
+    (home-page "https://pytest-mpi.readthedocs.io")
+    (synopsis "Pytest plugin for working with MPI")
+    (description "This plugin provides tools for running tests with MPI and
+for testing code using MPI.")
+    (license license:bsd-3)))
+
 (define-public python-pytest-mpl
   (package
     (name "python-pytest-mpl")
-- 
2.49.0

Message #16 received at 78181-done <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: David Elsing <david.elsing <at> posteo.net>
Cc: 78181-done <at> debbugs.gnu.org
Subject: Re: [PATCH 0/2] Update python-h5py to 3.13
Date: Thu, 1 May 2025 12:36:34 +0200

Hello David,

thanks for your reactivity!

I have checked that the updated package builds and pushed;
while I wanted to try a "build -P 1", I did not have enough disk
space to build them all.

Hoping for the best,

Andreas

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