From patchwork Tue Apr 22 12:04:03 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41925 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 F0A8227BC4A; Tue, 22 Apr 2025 13:05:26 +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=unavailable 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 3278227BC49 for ; Tue, 22 Apr 2025 13:05:25 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u7CNG-0007ix-EQ; Tue, 22 Apr 2025 08:05:14 -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 1u7CN4-0007fj-N2 for guix-patches@gnu.org; Tue, 22 Apr 2025 08:05:04 -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 1u7CN4-0002TF-Ck for guix-patches@gnu.org; Tue, 22 Apr 2025 08:05:02 -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:Date:From:To:In-Reply-To:References:Subject; bh=hteh6ftdy2EMVxHYYr7f6YYSn3Y2lgEIK+6/7tQUwE8=; b=RG6FfbM7i0QT8wCAPoKRvQqKeqXeIKz7Vh9Msq9M64hY24WkstDY6rOGP5MpRHU1NC9GoLbzdKkQnBiW1543JyQIecyOyVsJ50tRgWgplacBLlTwhs3Agm5m/UPcLp6J+31Up0dwJG/3UsOfPmKP6xwukEO9plrTKmNa2YyM1/KEm68mNUwWAR1XdwyABsbqiWR3+JnScLeHp/c5HeTenGvqtXc3M0C2lQJbe8BxtmVujJokhQDPxWlaquA+oEvTxh+XvvkOyIbwAfsm4lkNfZEji/OppAhfo+dpO8CsuDC4yXuGWNYn/Yxv0M8I+Sm9+69ebcsuNr4yHhnZwLlB3Q==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u7CN3-0007I1-Ns for guix-patches@gnu.org; Tue, 22 Apr 2025 08:05:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77986] [PATCH 1/2] gnu: python-zeroc-ice-3.6: Fix build with Python@3.11. 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bh=hteh6ftdy2EMVxHYYr7f6YYSn3Y2lgEIK+6/7tQUwE8=; c=relaxed/relaxed; d=ngraves.fr; h=From; s=ovhmo4487190-selector1; t=1745323455; v=1; b=pjNOfoAnJYhoLtPPKd64L5CXE1VWEhfL2J6X32uQRU+6El50lz2UuWC9oR+fingBLNZoQoVD 6vryE1bGkPt7opkvpU37+F4O3fyWPM+Clb+e0fGs2ntccGuXA83/MiTDcAnfCZYRw9WzkhSS+i8 U0CRmkAeOUHXb5FOOsdsEHQkqbPfxiBlGkkLtzMeGb+n70/j/tC6000vKpjSRhnPNePjbcafHbo TDzstLkRDrNB5Ub+rGZoHglsiKpvpjYHNzsiw9MWFL9Ufp1fQOf0e0bKIJTjLAtHiLlzGtn0UHT n6qGnHQa53cjy9yRscFp084G8AJQuWdZaep78sc/bs5uQ== 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: , Reply-to: Nicolas Graves X-ACL-Warn: , Nicolas Graves via Guix-patches X-Patchwork-Original-From: Nicolas Graves via Guix-patches via From: Nicolas Graves 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-zeroc-ice-3.6) [source]: Add patch. * gnu/packages/patches/python-zeroc-ice-3.6.5-python-3.11-support.patch: Add patch. --- ...-zeroc-ice-3.6.5-python-3.11-support.patch | 33 +++++++++++++++++++ gnu/packages/python-xyz.scm | 5 ++- 2 files changed, 37 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/python-zeroc-ice-3.6.5-python-3.11-support.patch diff --git a/gnu/packages/patches/python-zeroc-ice-3.6.5-python-3.11-support.patch b/gnu/packages/patches/python-zeroc-ice-3.6.5-python-3.11-support.patch new file mode 100644 index 00000000000..17cae7297c0 --- /dev/null +++ b/gnu/packages/patches/python-zeroc-ice-3.6.5-python-3.11-support.patch @@ -0,0 +1,33 @@ +Only in zeroc-ice-3.6.5: setup.py.orig +diff --color -ur zeroc-ice-3.6.5.orig/src/Slice.cpp zeroc-ice-3.6.5/src/Slice.cpp +--- zeroc-ice-3.6.5.orig/src/Slice.cpp 2019-07-31 21:49:38.000000000 +0200 ++++ zeroc-ice-3.6.5/src/Slice.cpp 2023-10-12 10:52:07.029069937 +0200 +@@ -17,12 +17,6 @@ + #include + #include + +-// +-// Python headers needed for PyEval_EvalCode. +-// +-#include +-#include +- + using namespace std; + using namespace IcePy; + using namespace Slice; +diff --color -ur zeroc-ice-3.6.5.orig/src/Util.cpp zeroc-ice-3.6.5/src/Util.cpp +--- zeroc-ice-3.6.5.orig/src/Util.cpp 2019-07-31 21:49:38.000000000 +0200 ++++ zeroc-ice-3.6.5/src/Util.cpp 2023-10-12 10:49:15.033366926 +0200 +@@ -214,7 +214,12 @@ + // + // Get name of current function. + // ++ // Use PyEval_GetFrame with Pyhthon >= 3.11 ++#if PY_VERSION_HEX >= 0x030B0000 ++ PyFrameObject *f = PyEval_GetFrame(); ++#else + PyFrameObject *f = PyThreadState_GET()->frame; ++#endif + PyObjectHandle code = PyObject_GetAttrString(reinterpret_cast(f), STRCAST("f_code")); + assert(code.get()); + PyObjectHandle func = PyObject_GetAttrString(code.get(), STRCAST("co_name")); diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index ef66d071677..1fbd1730b01 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -40633,7 +40633,10 @@ (define-public python-zeroc-ice-3.6 (uri (pypi-uri "zeroc-ice" version)) (sha256 (base32 - "0mikjfvq26kh8asnn9v55z41pap4c5ypymqnwwi4xkavc3mzyda2")))))) + "0mikjfvq26kh8asnn9v55z41pap4c5ypymqnwwi4xkavc3mzyda2")) + (patches + (search-patches + "python-zeroc-ice-3.6.5-python-3.11-support.patch")))))) (define-public python-whenever (package From patchwork Tue Apr 22 12:04:04 2025 Content-Type: text/plain; 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[arguments]: Ignore collection of some tests (which should be fixed when updating to numpy@2). [native-inputs]: Add python-portalocker. Update omero-blitz to 5.8.2. --- gnu/packages/python-xyz.scm | 168 +++++++++++++++++++----------------- 1 file changed, 91 insertions(+), 77 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 1fbd1730b01..e60d21207e4 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -5155,84 +5155,98 @@ (define-public python-et-xmlfile (license license:expat))) (define-public python-omero-py - (package - (name "python-omero-py") - (version "5.13.1") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ome/omero-py") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0n94v5dpmh873hjqd9k9ky85iab4xh37ibmi13rqpclv01ibvvxa")))) - (build-system pyproject-build-system) - (arguments - (list - #:test-flags - '(list "-m" "not broken" "-rf" "test" "-s" - ;; TestImport tries to download Java things; TestSessions - ;; and TestBuildQuery require networking. - "-k" "not TestImport and not TestSessions and not TestBuildQuery") - #:modules '((guix build pyproject-build-system) - (guix build utils) - (ice-9 match) - (srfi srfi-1) - (srfi srfi-26)) - #:phases - #~(modify-phases %standard-phases - (add-after 'unpack 'find-artifacts - (lambda* (#:key inputs #:allow-other-keys) - (let ((zip-file - (match inputs - (((labels . files) ...) - (find (cut string-suffix? "omero-blitz-5.5.5-python.zip" <>) - files))))) - (setenv "ZIP_FILE" - (or zip-file (error "failed to find artifact file")))))) - ;; Some tests need this, such as TestTempFileManager - (add-after 'build 'set-HOME - (lambda _ (setenv "HOME" "/tmp"))) - ;; The sanity check mistakes omero_model_TypeAnnotationI.py for a - ;; module to load. - (delete 'sanity-check) - ;; The argument parser is picky and interprets the "-real" part as - ;; the first argument. - (add-after 'wrap 'rename-executable - (lambda _ - (with-directory-excursion (string-append #$output "/bin") - (rename-file ".omero-real" ".omero") - (substitute* "omero" - (("bin/.omero-real") "bin/.omero")))))))) - (propagated-inputs - (list python-appdirs - python-future - python-numpy - python-pillow - python-pyyaml - python-requests - python-tables - python-zeroc-ice-3.6)) - (native-inputs - (list python-mox3 - python-pytest - python-pytest-rerunfailures - python-pytest-xdist - python-setuptools - python-wheel - unzip - (origin - (method url-fetch) - (uri "https://artifacts.openmicroscopy.org/artifactory/\ -ome.releases/org/openmicroscopy/omero-blitz/5.5.5/omero-blitz-5.5.5-python.zip") - (sha256 - (base32 "0wyja1zv19c1r3m31gsp555jzj3cg2v2pl00zlybpw3qd36yffwc"))))) - (home-page "https://github.com/ome/omero-py") - (synopsis "Python bindings to the OMERO.blitz server") - (description "This package provides Python bindings to the OMERO.blitz + (let ((omero-blitz-version "5.8.2")) + (package + (name "python-omero-py") + (version "5.20.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ome/omero-py") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "02zsw1p35n6lkqh410qpgw7c4467dkbg0hxly3gjqrwdh349j47g")))) + (build-system pyproject-build-system) + (arguments + (list + ;; #:tests? #f + #:test-flags + #~(list + "-m" "not broken" "-rf" "test" "-s" + ;; XXX: Failing collection because of Numpy compatibility. + "--ignore=test/unit/tablestest/test_hdfstorage.py" + "--ignore=test/unit/tablestest/test_servants.py" + ;; TestImport tries to download Java things; TestSessions + ;; and TestBuildQuery require networking. + "-k" "not TestImport and not TestSessions and not TestBuildQuery") + #:modules '((guix build pyproject-build-system) + (guix build utils) + (ice-9 match) + (srfi srfi-1) + (srfi srfi-26)) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'find-artifacts + (lambda* (#:key inputs #:allow-other-keys) + (let ((zip-file + (match inputs + (((labels . files) ...) + (find (cut string-suffix? + (string-append "omero-blitz-" + #$omero-blitz-version + "-python.zip") + <>) + files))))) + (setenv "ZIP_FILE" + (or zip-file (error "failed to find artifact file")))))) + ;; Some tests need this, such as TestTempFileManager + (add-after 'build 'set-HOME + (lambda _ (setenv "HOME" "/tmp"))) + ;; The sanity check mistakes omero_model_TypeAnnotationI.py for a + ;; module to load. + (delete 'sanity-check) + ;; The argument parser is picky and interprets the "-real" part as + ;; the first argument. + (add-after 'wrap 'rename-executable + (lambda _ + (with-directory-excursion (string-append #$output "/bin") + (rename-file ".omero-real" ".omero") + (substitute* "omero" + (("bin/.omero-real") "bin/.omero")))))))) + (propagated-inputs + (list python-appdirs + python-future + python-numpy-2 + python-pillow + python-pyyaml + python-requests + python-tables + python-zeroc-ice-3.6)) + (native-inputs + (list python-portalocker + python-pytest + python-pytest-mock + python-pytest-rerunfailures + python-pytest-xdist + python-setuptools + python-wheel + unzip + (origin + (method url-fetch) + (uri (format #f "\ +https://artifacts.openmicroscopy.org/artifactory/ome.releases/org/\ +openmicroscopy/omero-blitz/~a/omero-blitz-~a-python.zip" + omero-blitz-version + omero-blitz-version)) + (sha256 + (base32 "1nb17xmx6n7i5vkcw661iq42yfgc3i0gmhz3x8iwcrhp8pajzm3l"))))) + (home-page "https://github.com/ome/omero-py") + (synopsis "Python bindings to the OMERO.blitz server") + (description "This package provides Python bindings to the OMERO.blitz server.") - (license license:gpl2))) + (license license:gpl2)))) (define-public python-openpyxl (package