[med-svn] [Git][med-team/python-biopython][master] 9 commits: bwa-output.patch: new: fix a test failure.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sat Sep 13 11:41:12 BST 2025
Étienne Mollier pushed to branch master at Debian Med / python-biopython
Commits:
44adacb5 by Étienne Mollier at 2025-09-13T11:04:48+02:00
bwa-output.patch: new: fix a test failure.
Closes: #1114298
- - - - -
8f97bf3e by Étienne Mollier at 2025-09-13T11:08:06+02:00
d/control: build depends on python3-numpy-dev:any.
Lintian flagged that dh_numpy3 needed python3-numpy-dev:any.
- - - - -
35da2c29 by Étienne Mollier at 2025-09-13T11:10:19+02:00
d/watch: update to file format version 5.
- - - - -
0aee5269 by Étienne Mollier at 2025-09-13T11:11:42+02:00
d/patches/*: normalize dep3 headers.
- - - - -
aa6babed by Étienne Mollier at 2025-09-13T11:12:43+02:00
d/python3-biopython.lintian-overrides: delete.
The spelling override that was within is not needed anymore.
- - - - -
8d1d2627 by Étienne Mollier at 2025-09-13T11:17:56+02:00
d/control: fix typoed python3-numpy-dev.
Gbp-Dch: ignore
- - - - -
b02f9afc by Étienne Mollier at 2025-09-13T12:09:57+02:00
d/control: uncondionally deploy some build-dependencies.
Several of the packages that were initially marked as <!nocheck>
turned out to be actually needed outside check context.
Closes: #1103472
- - - - -
a557feaa by Étienne Mollier at 2025-09-13T12:11:23+02:00
d/rules: isolate a code segment irrelevant with nocheck profile.
- - - - -
34afe727 by Étienne Mollier at 2025-09-13T12:40:39+02:00
d/changelog: ready for upload to unstable.
- - - - -
9 changed files:
- debian/changelog
- debian/control
- + debian/patches/bwa-output.patch
- debian/patches/privacy_breach.patch
- debian/patches/remove_mathml-qname.patch
- debian/patches/series
- − debian/python3-biopython.lintian-overrides
- debian/rules
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,19 @@
+python-biopython (1.85+dfsg-5) unstable; urgency=medium
+
+ * bwa-output.patch: new: fix a test failure. (Closes: #1114298)
+ * d/control: build depends on python3-numpy-dev:any.
+ Lintian flagged that dh_numpy3 needed python3-numpy-dev:any.
+ * d/watch: update to file format version 5.
+ * d/patches/*: normalize dep3 headers.
+ * d/python3-biopython.lintian-overrides: delete.
+ The spelling override that was within is not needed anymore.
+ * d/control: uncondionally deploy some build-dependencies.
+ Several of the packages that were initially marked as <!nocheck>
+ turned out to be actually needed outside check context. (Closes: #1103472)
+ * d/rules: isolate a code segment irrelevant with nocheck profile.
+
+ -- Étienne Mollier <emollier at debian.org> Sat, 13 Sep 2025 12:12:17 +0200
+
python-biopython (1.85+dfsg-4) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -10,8 +10,9 @@ Build-Depends: debhelper-compat (= 13),
python3-all-dev:native,
libpython3-all-dev,
python3-numpy,
+ python3-numpy-dev,
flex,
- python3-reportlab (>= 4.0.4-1~) <!nocheck>,
+ python3-reportlab (>= 4.0.4-1~),
hevea,
texlive-latex-base,
texlive-latex-extra,
@@ -32,15 +33,16 @@ Build-Depends: debhelper-compat (= 13),
probcons <!nocheck>,
python3-networkx <!nocheck>,
python3-numpydoc <!nodoc>,
+ python3-msgpack,
python3-mysqldb <!nocheck>,
python3-matplotlib <!nocheck>,
- python3-mmtf <!nocheck>,
+ python3-mmtf,
python3-pil <!nocheck>,
- python3-rdflib <!nocheck>,
+ python3-rdflib,
python3-psycopg2 [any-amd64] <!nocheck>,
python3-pygments <!nocheck>,
python3-igraph <!nocheck>,
- python3-scipy <!nocheck>,
+ python3-scipy,
python3-setuptools,
python3-sphinx <!nodoc>,
python3-sphinx-rtd-theme <!nodoc>,
=====================================
debian/patches/bwa-output.patch
=====================================
@@ -0,0 +1,55 @@
+Description: test_BWA_tool.py: update to bwa 0.7.19 header.
+ This change fixes/worksaround the following test failure, which has
+ begun to appear with the introduction of bwa 0.7.19:
+ .
+ Traceback (most recent call last):
+ File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/Tests/test_BWA_tool.py", line 203, in test_mem
+ self.assertTrue(
+ ~~~~~~~~~~~~~~~^
+ headline.startswith("@SQ"),
+ ^^^^^^^^^^^^^^^^^^^^^^^^^^^
+ f"Error generating sam files:\n{cmdline}\nOutput starts:{headline}",
+ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+ )
+ ^
+ AssertionError: False is not true : Error generating sam files:
+ bwa mem BWA/human_g1k_v37_truncated.fasta BWA/HNSCC1_1_truncated.fastq BWA/HNSCC1_2_truncated.fastq
+ Output starts:@HD VN:1.5 SO:unsorted GO:query
+ .
+ This test failure occurs in a portion that has been obsoleted upstream,
+ therefore no forwarding was possible in that regard.
+Author: Étienne Mollier <emollier at debian.org>
+Bug: https://github.com/biopython/biopython/pull/5063
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1114298
+Last-Update: 2025-09-13
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-biopython.orig/Tests/test_BWA_tool.py
++++ python-biopython/Tests/test_BWA_tool.py
+@@ -161,7 +161,7 @@
+ with open(self.samfile1) as handle:
+ headline = handle.readline()
+ self.assertTrue(
+- headline.startswith("@SQ"),
++ headline.startswith("@SQ") or headline.startswith("@HD"),
+ f"Error generating sam files:\n{cmdline}\nOutput starts:{headline}",
+ )
+
+@@ -184,7 +184,7 @@
+ with open(self.samfile) as handle:
+ headline = handle.readline()
+ self.assertTrue(
+- headline.startswith("@SQ"),
++ headline.startswith("@SQ") or headline.startswith("@HD"),
+ f"Error generating sam files:\n{cmdline}\nOutput starts:{headline}",
+ )
+
+@@ -201,7 +201,7 @@
+ with open(self.samfile) as handle:
+ headline = handle.readline()
+ self.assertTrue(
+- headline.startswith("@SQ"),
++ headline.startswith("@SQ") or headline.startswith("@HD"),
+ f"Error generating sam files:\n{cmdline}\nOutput starts:{headline}",
+ )
+
=====================================
debian/patches/privacy_breach.patch
=====================================
@@ -2,7 +2,7 @@ From: Andreas Tille <tille at debian.org>
Date: Sat, 14 Sep 2024 09:48:28 +0200
Subject: Do not use privacy-breach-logo
-Last-Update: Tue, 12 May 2015 11:08:43 +0200
+Last-Update: 2015-05-12
Forwarded: not-needed
---
Tests/Blast/html_msgid_29_blastx_001.html | 5 ++---
=====================================
debian/patches/remove_mathml-qname.patch
=====================================
@@ -2,8 +2,8 @@ From: Andreas Tille <tille at debian.org>
Date: Sat, 14 Sep 2024 09:48:28 +0200
Subject: Remove non DFSG free DTD
-Last-Update: Wed, 30 Apr 2014 14:47:53 +0200
-Bugs-Debian: http://bugs.debian.org/746484
+Last-Update: 2014-04-30
+Bug-Debian: http://bugs.debian.org/746484
Forwarded: https://bugs.debian.org/746484#15
---
Bio/Entrez/DTDs/modules.ent | 7 -------
=====================================
debian/patches/series
=====================================
@@ -6,3 +6,4 @@ muscle3.patch
#port_tutorial_to_muscle3.patch
skip-scipy-in-codonalign.patch
fix-type-cast-i386.patch
+bwa-output.patch
=====================================
debian/python3-biopython.lintian-overrides deleted
=====================================
@@ -1,2 +0,0 @@
-# The affected word doesn't show up when scanning the source code.
-python3-biopython: spelling-error-in-binary ment meant [usr/lib/python3/dist-packages/Bio/Align/_pairwisealigner.cpython-3*.so]
=====================================
debian/rules
=====================================
@@ -160,12 +160,15 @@ override_dh_installdocs-indep:
ifeq (,$(filter nodoc,$(DEB_BUILD_OPTIONS)))
dh_installdocs -i
find debian -name __pycache__ -type d | xargs rm -rf
+
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
# dh_installdocs seems to refuse copying zero length files (for
# instance Tests/Blast/tab_2226_tblastn_002.txt) but these are
# needed for the tests as well
# The following line breaks the build with nocheck, but
# we can't remove it yet because doing so seems to break autopkgtests
cp -a debian/tmp_tests/* $(DOCDIR)
+endif
# Tackle privacy breaches caused by MathML.
sed -i 's at https://cdn.jsdelivr.net/npm/mathjax\@3/es5/tex-mml-chtml.js at file:///usr/share/nodejs/mathjax-full/es5/tex-mml-chtml.js@' \
=====================================
debian/watch
=====================================
@@ -1,11 +1,11 @@
-version=4
+Version: 5
-opts="\
-filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%,\
-uversionmangle=s/b/~b/;s/(\d)(\d+)/$1.$2/,\
-repacksuffix=+dfsg,\
-dversionmangle=s/\+dfsg.*//,\
-repack,\
-compression=xz" \
- https://github.com/biopython/biopython/tags \
- (?:.*?/)?biopython[v-]?(\d[\d.]*)\.tar\.gz debian uupdate
+Source: https://github.com/biopython/biopython/tags
+Matching-Pattern: (?:.*?/)?biopython[v-]?(\d[\d.]*)\.tar\.gz
+Compression: xz
+Dversionmangle: s/\+dfsg.*//
+Filenamemangle: s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%
+Repack: yes
+Repacksuffix: +dfsg
+Update-Script: uupdate
+Uversionmangle: s/b/~b/;s/(\d)(\d+)/$1.$2/
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/849284ef285a6b71dbb655aea1af069e40f497b8...34afe727f25446c22093143f4c4636f754e46969
--
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/849284ef285a6b71dbb655aea1af069e40f497b8...34afe727f25446c22093143f4c4636f754e46969
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