[med-svn] [Git][med-team/python-biopython][master] 4 commits: Replace skip-xmlio-tests.patch by seqxml-parser.patch.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Wed May 22 14:15:55 BST 2024
Étienne Mollier pushed to branch master at Debian Med / python-biopython
Commits:
305acf9b by Étienne Mollier at 2024-05-22T14:05:35+02:00
Replace skip-xmlio-tests.patch by seqxml-parser.patch.
Instead of skipping the test, upstream introduced a change that fixed
the XML parser for use with the newer version of expat.
Closes: #1064147
- - - - -
d06e8e16 by Étienne Mollier at 2024-05-22T14:08:32+02:00
d/control: declare compliance to standards version 4.7.0.
- - - - -
14d39b1d by Étienne Mollier at 2024-05-22T15:12:36+02:00
d/python3-biopython.lintian-overrides: update file name.
- - - - -
005ea36d by Étienne Mollier at 2024-05-22T15:15:18+02:00
ready to upload to unstable.
- - - - -
6 changed files:
- debian/changelog
- debian/control
- + debian/patches/seqxml-parser.patch
- debian/patches/series
- − debian/patches/skip-xmlio-tests.patch
- debian/python3-biopython.lintian-overrides
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+python-biopython (1.83+dfsg1-3) unstable; urgency=medium
+
+ * Replace skip-xmlio-tests.patch by seqxml-parser.patch.
+ Instead of skipping the test, upstream introduced a change that fixed
+ the XML parser for use with the newer version of expat. (Closes: #1064147)
+ * d/control: declare compliance to standards version 4.7.0.
+ * d/python3-biopython.lintian-overrides: update file name.
+
+ -- Étienne Mollier <emollier at debian.org> Wed, 22 May 2024 15:14:56 +0200
+
python-biopython (1.83+dfsg1-2) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -43,7 +43,7 @@ Build-Depends: debhelper-compat (= 13),
samtools [any-amd64] <!nocheck>,
t-coffee <!nocheck>,
wise <!nocheck>
-Standards-Version: 4.6.2
+Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/python-biopython
Vcs-Git: https://salsa.debian.org/med-team/python-biopython.git
Homepage: https://biopython.org
=====================================
debian/patches/seqxml-parser.patch
=====================================
@@ -0,0 +1,32 @@
+Description: Trying to figure out what is going wrong in the SeqXML parser
+ * using original block size
+ * print data
+ * print data
+ * print data
+ * print data
+ * closing the parser on time does the trick
+
+Author: Michiel de Hoon <mdehoon at tkx249.genome.gsc.riken.jp>
+Origin: upstream, https://github.com/biopython/biopython/pull/4686
+Bug: https://github.com/biopython/biopython/issues/4640
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1064147
+Reviewed-by: Étienne Mollier <emollier at debian.org>
+Last-Update: 2024-05-22
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-biopython.orig/Bio/SeqIO/SeqXmlIO.py
++++ python-biopython/Bio/SeqIO/SeqXmlIO.py
+@@ -440,11 +440,12 @@
+ if not text:
+ break
+ parser.feed(text)
++ # Closing the parser ensures that all XML data fed into it are processed
++ parser.close()
+ # We have reached the end of the XML file;
+ # send out the remaining records
+ yield from records
+ records.clear()
+- parser.close()
+
+
+ class SeqXmlWriter(SequenceWriter):
=====================================
debian/patches/series
=====================================
@@ -6,4 +6,4 @@ reproduciblebuild.patch
croak-on-muscle5.patch
muscle3.patch
#port_tutorial_to_muscle3.patch
-skip-xmlio-tests.patch
+seqxml-parser.patch
=====================================
debian/patches/skip-xmlio-tests.patch deleted
=====================================
@@ -1,88 +0,0 @@
-Description: skip two items in test_SeqIO.
- test_embl7 and test_genbank8 are affected by failures stemming from expat
- migration from 2.5 to 2.6. Python source code is also affected by somewhat
- similar test failures. Looking at Python development tree[1] suggests their
- current approach is to adjust or skip the test suite appropriately to address
- the situation. The present patch will do just that.
- .
- [1]: https://github.com/python/cpython/pull/115289/files
- .
- Note that such change is applied due to lack of further options. Please drop
- this change as soon as upstream came up with a definitive approach.
-
-Author: Étienne Mollier <emollier at debian.org>
-Bug: https://github.com/biopython/biopython/issues/4640
-Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1064147
-Last-Update: 2024-03-10
----
-This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- python-biopython.orig/Tests/test_SeqIO.py
-+++ python-biopython/Tests/test_SeqIO.py
-@@ -2786,33 +2786,6 @@
- messages,
- )
-
-- def test_genbank8(self):
-- sequences = ["TCCAGGGGATTCACGCGCAATATGTTTCCCTCGCTCGTCT...TCGATTG"]
-- ids = ["AL138972.1"]
-- names = ["DMBR25B3"]
-- lengths = [154329]
-- alignment = None
-- messages = {
-- "fastq": "No suitable quality scores found in letter_annotations of SeqRecord (id=AL138972.1).",
-- "fastq-illumina": "No suitable quality scores found in letter_annotations of SeqRecord (id=AL138972.1).",
-- "fastq-solexa": "No suitable quality scores found in letter_annotations of SeqRecord (id=AL138972.1).",
-- "phd": "No suitable quality scores found in letter_annotations of SeqRecord (id=AL138972.1).",
-- "qual": "No suitable quality scores found in letter_annotations of SeqRecord (id=AL138972.1).",
-- "sff": "Missing SFF flow information",
-- }
-- self.perform_test(
-- "genbank",
-- False,
-- "GenBank/extra_keywords.gb",
-- 1,
-- ids,
-- names,
-- sequences,
-- lengths,
-- alignment,
-- messages,
-- )
--
- def test_genbank9(self):
- sequences = ["GAATTCAGATAGAATGTAGACAAGAGGGATGGTGAGGAAA...CAAAGGC"]
- ids = ["U18266.1"]
-@@ -3389,33 +3362,6 @@
- molecule_types,
- )
-
-- def test_embl7(self):
-- sequences = ["GATCAGTAGACCCAGCGACAGCAGGGCGGGGCCCAGCAGG...CGAGCAT"]
-- ids = ["AL031232"]
-- names = ["SC10H5"]
-- lengths = [4870]
-- alignment = None
-- messages = {
-- "fastq": "No suitable quality scores found in letter_annotations of SeqRecord (id=AL031232).",
-- "fastq-illumina": "No suitable quality scores found in letter_annotations of SeqRecord (id=AL031232).",
-- "fastq-solexa": "No suitable quality scores found in letter_annotations of SeqRecord (id=AL031232).",
-- "phd": "No suitable quality scores found in letter_annotations of SeqRecord (id=AL031232).",
-- "qual": "No suitable quality scores found in letter_annotations of SeqRecord (id=AL031232).",
-- "sff": "Missing SFF flow information",
-- }
-- self.perform_test(
-- "embl",
-- False,
-- "EMBL/SC10H5.embl",
-- 1,
-- ids,
-- names,
-- sequences,
-- lengths,
-- alignment,
-- messages,
-- )
--
- def test_embl8(self):
- sequences = ["CAATTACTGCAATGCCCTCGTAATTAAGTGAATTTACAAT...CATCACC"]
- ids = ["U87107.1"]
=====================================
debian/python3-biopython.lintian-overrides
=====================================
@@ -1,2 +1,2 @@
# 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/_aligners.cpython-3*.so]
+python3-biopython: spelling-error-in-binary ment meant [usr/lib/python3/dist-packages/Bio/Align/_pairwisealigner.cpython-3*.so]
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/f9f26e80ec4e5466023d8542900cb1e95ca896c5...005ea36db181df719278cd5a3868c0a6f3a83a53
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View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/f9f26e80ec4e5466023d8542900cb1e95ca896c5...005ea36db181df719278cd5a3868c0a6f3a83a53
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