From patchwork Thu May 1 09:35:12 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 42205 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 703A227BC4B; Thu, 1 May 2025 10:36:17 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id ECA0227BC49 for ; Thu, 1 May 2025 10:36:16 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1uAQKq-0000Uk-OO; Thu, 01 May 2025 05:36:04 -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 1uAQKp-0000UV-Np for guix-patches@gnu.org; Thu, 01 May 2025 05:36:03 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1uAQKo-0006xT-Lo for guix-patches@gnu.org; Thu, 01 May 2025 05:36:03 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=gY/tEn8nqNdjk04hE01GUiPynYxebeQs3k1qkzWBZI4=; b=oxMNGpX4pVVLP+BapVualldIxzMRXT/Sm/muokJPj769j8fWPTGa5w40W+RnuN2J8NX2/7LpL8wKyneiil+QYxXDwfQMVp/IJdY6sZtTeDaaDVIkVRzzLuugzrY0sj8MHeNomutsXKFQSKKAPJT27SiU6AnuUyHnTgtFuc4albedRtdNMqoC86sB//gnzN+gk1Bu8J3JY77Hha5BPrO+gettQukuLA/TePfJQ4wMRkVnNBs08viXsczVU68/uOig2POl+JVjkLbepDSMUvn/CT9DOZKI/pE3FQPT/mTsEqxZKo+c0d4ZDnBOwnyim19OW2/5UpRoocPN5rwfteCsXg==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1uAQKo-000438-Gi for guix-patches@gnu.org; Thu, 01 May 2025 05:36:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#78181] [PATCH 1/2] gnu: Add python-pytest-mpi. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 01 May 2025 09:36:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 78181 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 78181@debbugs.gnu.org Cc: David Elsing Received: via spool by 78181-submit@debbugs.gnu.org id=B78181.174609213415504 (code B ref 78181); Thu, 01 May 2025 09:36:02 +0000 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 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 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * 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") From patchwork Thu May 1 09:35:13 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 42206 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id CB58A27BC4B; Thu, 1 May 2025 10:36:27 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 1C7D027BC49 for ; Thu, 1 May 2025 10:36:27 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1uAQKt-0000VA-Bi; Thu, 01 May 2025 05:36:07 -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 1uAQKp-0000UU-Mf for guix-patches@gnu.org; Thu, 01 May 2025 05:36:03 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1uAQKo-0006xQ-J1 for guix-patches@gnu.org; Thu, 01 May 2025 05:36:02 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=43lzB3LVECMH9nxoUYADhLDPD52ec63L9OzTyLfRUr8=; b=sKxsO8/f+UUo346yrG8BJgQTA0l8P1QSzA8s019HFsxkzjDktiCR6GVAlE7sMpTd3KxKgx/YXB+XEXj776VHDJBAtLZUyUMyK1/NgJST7o8y+lfFVZ6p3oVGTen0c0CsOAskwgWmbLnSssn1bB8a3XmdrYr/ZgClNJBu13raPFV/N8FJJJwfk7dWLoooCrRT1FCtX0+zv1FkTTEhAVQh3EhTluN4BQ3E1TYXJW4s3FzwM2rKbkMd7Pl2Nc/5SvyxlwsQWWjP4vhrTSM0o6p1Tqyr5Ayc2ZaYoHHQkMeP0XPD6OVyp9ewVTsSzHgYF2LQIiW9We2FSEqIYNUANLOMAQ==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1uAQKo-000430-1M for guix-patches@gnu.org; Thu, 01 May 2025 05:36:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#78181] [PATCH 2/2] gnu: python-h5py: Update to 3.13.0. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 01 May 2025 09:36:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 78181 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 78181@debbugs.gnu.org Cc: David Elsing Received: via spool by 78181-submit@debbugs.gnu.org id=B78181.174609213415492 (code B ref 78181); Thu, 01 May 2025 09:36:02 +0000 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 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 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * 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