Étienne Mollier pushed to branch master at Debian Med / python-pysam
Commits: 80e9e2fd by Étienne Mollier at 2022-12-27T11:35:48+01:00 disable-tests-python3.11.patch: add; work around test failure. Thanks: John Marshall and Graham Inggs Closes: #1024425 - - - - - a8954aa9 by Étienne Mollier at 2022-12-27T11:37:21+01:00 d/control: restore dependency on python3-all-dev. - - - - - a76ba743 by Étienne Mollier at 2022-12-27T11:38:43+01:00 d/control: restore autodep8-python autopkgtest. - - - - - d6912281 by Étienne Mollier at 2022-12-27T11:39:50+01:00 update changelog - - - - - 95ddab52 by Étienne Mollier at 2022-12-27T11:40:54+01:00 routine-update: Standards-Version: 4.6.2 - - - - - ecb253ac by Étienne Mollier at 2022-12-27T11:49:02+01:00 routine-update: Ready to upload to unstable - - - - - 4 changed files: - debian/changelog - debian/control - + debian/patches/disable-tests-python3.11.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,13 @@ +python-pysam (0.20.0+ds-2) unstable; urgency=medium + + * disable-tests-python3.11.patch: add; work around test failure. + Thanks to John Marshall and Graham Inggs (Closes: #1024425) + * d/control: restore dependency on python3-all-dev. + * d/control: restore autodep8-python autopkgtest. + * Standards-Version: 4.6.2 (routine-update) + + -- Étienne Mollier <emoll...@debian.org> Tue, 27 Dec 2022 11:41:25 +0100 + python-pysam (0.20.0+ds-1) unstable; urgency=medium * New upstream version ===================================== debian/control ===================================== @@ -4,22 +4,21 @@ Uploaders: Charles Plessy <ple...@debian.org>, Andreas Tille <ti...@debian.org>, Étienne Mollier <emoll...@debian.org> Section: python -# FIXME: restore Testsuite: autopkgtest-pkg-python when #1024425 is resolved. +Testsuite: autopkgtest-pkg-python Priority: optional Build-Depends: debhelper-compat (= 13), dh-exec, dh-python, libhts-dev (>= 1.14~), zlib1g-dev, -# FIXME: restore python3-all-dev when #1024425 is resolved. - python3-dev, + python3-all-dev, python3-setuptools, cython3, tabix <!nocheck>, samtools <!nocheck>, bcftools <!nocheck>, python3-pytest <!nocheck> -Standards-Version: 4.6.1 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/python-pysam Vcs-Git: https://salsa.debian.org/med-team/python-pysam.git Homepage: https://pysam.readthedocs.org/en/latest ===================================== debian/patches/disable-tests-python3.11.patch ===================================== @@ -0,0 +1,28 @@ +Description: skip tests bound to fail past python3.11. + Thanks John Marshall and Graham Inggs for the independent suggestion. +Author: Étienne Mollier <emoll...@debian.org> +Bug: https://github.com/pysam-developers/pysam/issues/1151 +Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1024425 +Last-Update: 2022-12-27 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- python-pysam.orig/tests/AlignmentFilePileup_test.py ++++ python-pysam/tests/AlignmentFilePileup_test.py +@@ -1,5 +1,6 @@ + """Benchmarking module for AlignmentFile functionality""" + import os ++import sys + import pysam + import unittest + from TestUtils import make_data_files, BAM_DATADIR, IS_PYTHON3, force_str, flatten_nested_list +@@ -206,6 +207,10 @@ + def tearDown(self): + self.samfile.close() + ++ @unittest.skipIf((sys.version_info.major == 3 ++ and sys.version_info.minor >= 11) ++ or sys.version_info.major >= 4, ++ "Test known to fail past python3.11.") + def testIteratorOutOfScope(self): + '''test if exception is raised if pileup col is accessed after + iterator is exhausted.''' ===================================== debian/patches/series ===================================== @@ -1,3 +1,4 @@ skip_test_remote.patch clean_less skip-test-on-32-bit.patch +disable-tests-python3.11.patch View it on GitLab: https://salsa.debian.org/med-team/python-pysam/-/compare/33f64515dfa4757a76900275d21e5104b5427b75...ecb253ac5c723737a3f3cf9646b2ef0c8e90a12c -- View it on GitLab: https://salsa.debian.org/med-team/python-pysam/-/compare/33f64515dfa4757a76900275d21e5104b5427b75...ecb253ac5c723737a3f3cf9646b2ef0c8e90a12c You're receiving this email because of your account on salsa.debian.org.
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