[med-svn] [Git][med-team/python-pysam][master] 6 commits: disable-tests-python3.11.patch: add; work around test failure.

[Étienne Mollier (@emollier)]

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 <emollier at 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 <plessy at debian.org>,
            Andreas Tille <tille at debian.org>,
            Étienne Mollier <emollier at 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 <emollier at 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
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