From debbugs-submit-bounces@debbugs.gnu.org Thu May 01 05:30:46 2025 Received: (at submit) by debbugs.gnu.org; 1 May 2025 09:30:46 +0000 Received: from localhost ([127.0.0.1]:48637 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uAQFh-0003mJ-Vs for submit@debbugs.gnu.org; Thu, 01 May 2025 05:30:46 -0400 Received: from lists.gnu.org ([2001:470:142::17]:41286) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1uAQFe-0003lz-9y for submit@debbugs.gnu.org; Thu, 01 May 2025 05:30:43 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1uAQFY-0007pY-6q for guix-patches@gnu.org; Thu, 01 May 2025 05:30:36 -0400 Received: from mout01.posteo.de ([185.67.36.65]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1uAQFV-0006SE-5n for guix-patches@gnu.org; Thu, 01 May 2025 05:30:35 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 32240240027 for ; Thu, 1 May 2025 11:30:29 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1746091829; bh=K55MY5Kw+UbYx5AfhOQeBJ0z4NB1XTCOk/wNfexY0tg=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=PRVSLNi9fu4r32lGQE6R/qNjo8gishizH0nJnsYHw/HDx6EsQnhIDtT2ZY2krwXDh 8I/Qc+wHpB8oWcYuoeV8pqnerOkNhAn/2+Uec9j9Bx+dYoTBFT90BvwyxJWOysFqSE H3tQhYMvFpzmTjTBLl2S3fEBEFvNW6TC+cfhn/i7Oi3qM4iXZQEr0i0TAY7+DgkzM1 tYCIyKvYDb6YeVvDb4p1qLjZttBCLSucuSlROQhvdByLjexSgbeTdx3kw4junLcob/ CxK8F7DOfuCyQRWSuRvk3w7WdCYp9JrwNNl3wBq0MYln/bVNiSbkL2W3cKTt7//2n6 kYUpeJiMiJ9sQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4Zp8103hkHz9rxL; Thu, 1 May 2025 11:30:28 +0200 (CEST) From: David Elsing To: andreas@enge.fr Subject: [PATCH 0/2] Update python-h5py to 3.13 Date: Thu, 1 May 2025 09:30:06 +0000 Message-ID: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=185.67.36.65; envelope-from=david.elsing@posteo.net; helo=mout01.posteo.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, RCVD_IN_VALIDITY_CERTIFIED_BLOCKED=0.001, RCVD_IN_VALIDITY_RPBL_BLOCKED=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: submit Cc: David Elsing , guix-patches@gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.0 (/) 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 From debbugs-submit-bounces@debbugs.gnu.org Thu May 01 05:35:34 2025 Received: (at 78181) by debbugs.gnu.org; 1 May 2025 09:35:34 +0000 Received: from localhost ([127.0.0.1]:48654 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uAQKL-00041m-HY for submit@debbugs.gnu.org; Thu, 01 May 2025 05:35:34 -0400 Received: from mout01.posteo.de ([185.67.36.65]:45907) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1uAQKI-00041R-HO for 78181@debbugs.gnu.org; Thu, 01 May 2025 05:35:31 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 8C460240027 for <78181@debbugs.gnu.org>; Thu, 1 May 2025 11:35:24 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1746092124; bh=yg0AkVzD/l4nHZmP6ejNoXYkn3XA29u+Gf7dND+/bls=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=Ej/KXr9geTuqW5oi5RCMIc522oYn6qFHY72jvaEa7GvmlaFNiE5HIdsUiwOp+O0Bi kZsn1yorqZEysiUApiuC0iRU/n24RbidlmwllIFxSxXAPDELGzLweFuIpMUR0I+aJJ 9ERexLjyoyZLtwapnp6x4LpUdDfuKsQegadn/TT1MxIJeSnKJ2NJkhSFy+S1vBpKJp 5l/tBDCA8IVCH08eBcQN30QS6cAfU1/JGVJNazPkwNTBdwdJiKJF+7CMFtvdtqmgHT c9mXEPGbk2h5K/IYQ4wbjf6nvsKvVKtmLC6Wljlv7jOVePAf7d3aM59ON0HOzd75+O BsVo73S7X2e3g== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4Zp86h1Z88z6tvk; Thu, 1 May 2025 11:35:24 +0200 (CEST) From: David Elsing To: 78181@debbugs.gnu.org Subject: [PATCH 2/2] gnu: python-h5py: Update to 3.13.0. Date: Thu, 1 May 2025 09:35:13 +0000 Message-ID: <28ca4993ad300dc5857aa516d1395c63e1c1df69.1746091586.git.david.elsing@posteo.net> In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 78181 Cc: David Elsing X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * 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 From debbugs-submit-bounces@debbugs.gnu.org Thu May 01 05:35:34 2025 Received: (at 78181) by debbugs.gnu.org; 1 May 2025 09:35:34 +0000 Received: from localhost ([127.0.0.1]:48656 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uAQKM-00041p-2W for submit@debbugs.gnu.org; Thu, 01 May 2025 05:35:34 -0400 Received: from mout01.posteo.de ([185.67.36.65]:46617) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1uAQKI-00041P-F4 for 78181@debbugs.gnu.org; Thu, 01 May 2025 05:35:31 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id DC61F240027 for <78181@debbugs.gnu.org>; Thu, 1 May 2025 11:35:22 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1746092122; bh=TI1pJfj0tzA7WuyuStjsJ27AWyyX9Jq7OmV9IFi5E7M=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version:Content-Type: Content-Transfer-Encoding:From; b=pwKyU8aiNITvhiiuNEuK0V0kFeCdQO5hOWSQkwb6Stho+Bx0ecqPbJ2zcRrd/IjOZ R1JmBX5UQ0XStph6mY8A3xB9RQ4Y16hY/w1n8M2r7geucO5ROO0b7oX7YkTeegpn3a MxfgP95zCXnV8RgJjXs1UG7/5EcCF8R23qX26Ijt4/L+ak3HH5/GZdJHUfkoUUP4Yc 0DCVNZ4GeHZ2mM1Yoenu8LbJh74/zcG4fRnftRB4WgiJlz4UWRQ3W89OLOUluTG/jj PpmLqBUGfhzbwdyvpsIncHbA9UdtE9z1uCCiE2o104rlpZMAyjtup1aGxG7MtRbmoN g7YHQZBUNkksg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4Zp86f2L7qz6v0R; Thu, 1 May 2025 11:35:22 +0200 (CEST) From: David Elsing To: 78181@debbugs.gnu.org Subject: [PATCH 1/2] gnu: Add python-pytest-mpi. Date: Thu, 1 May 2025 09:35:12 +0000 Message-ID: <62e34df96aeae0faa5eea431109c2f77241058bb.1746091586.git.david.elsing@posteo.net> In-Reply-To: References: MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 78181 Cc: David Elsing X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * 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 ;;; Copyright © 2024-2025 Troy Figiel ;;; Copyright © 2024 Navid Afkhami -;;; Copyright © 2024 David Elsing +;;; Copyright © 2024, 2025 David Elsing ;;; Copyright © 2024 Eric Bavier ;;; Copyright © 2024 Markku Korkeala ;;; Copyright © 2025 Evgeny Pisemsky @@ -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 From debbugs-submit-bounces@debbugs.gnu.org Thu May 01 06:36:46 2025 Received: (at 78181-done) by debbugs.gnu.org; 1 May 2025 10:36:46 +0000 Received: from localhost ([127.0.0.1]:48919 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uARHZ-0004pM-Te for submit@debbugs.gnu.org; Thu, 01 May 2025 06:36:46 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:35380) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1uARHX-0004p4-HB for 78181-done@debbugs.gnu.org; Thu, 01 May 2025 06:36:44 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 490BA391; Thu, 1 May 2025 12:36:37 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id L9mGKaV4qdx4; Thu, 1 May 2025 12:36:36 +0200 (CEST) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 54D20319; Thu, 1 May 2025 12:36:36 +0200 (CEST) Date: Thu, 1 May 2025 12:36:34 +0200 From: Andreas Enge To: David Elsing Subject: Re: [PATCH 0/2] Update python-h5py to 3.13 Message-ID: References: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: X-Rspamd-Queue-Id: 490BA391 X-Spamd-Result: default: False [-9.51 / 15.00]; REPLY(-4.00)[]; BAYES_HAM(-3.00)[99.99%]; NEURAL_HAM(-2.91)[-0.971]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; RCVD_COUNT_TWO(0.00)[2]; FROM_EQ_ENVFROM(0.00)[]; MIME_TRACE(0.00)[0:+]; RCPT_COUNT_TWO(0.00)[2]; TO_MATCH_ENVRCPT_ALL(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; RCVD_TLS_ALL(0.00)[]; FROM_HAS_DN(0.00)[]; TO_DN_SOME(0.00)[]; ARC_NA(0.00)[] X-Rspamd-Action: no action X-Spamd-Bar: --------- X-Rspamd-Server: hera X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 78181-done Cc: 78181-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) 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 From unknown Thu Jun 19 14:06:08 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Thu, 29 May 2025 11:24:26 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator