[med-svn] [Git][med-team/python-biopython][master] 3 commits: skip-xmlio-tests.patch: new: skip test failures.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Mar 10 15:34:43 GMT 2024
Étienne Mollier pushed to branch master at Debian Med / python-biopython
Commits:
9902093b by Étienne Mollier at 2024-03-10T14:08:13+01:00
skip-xmlio-tests.patch: new: skip test failures.
This works around #1064147 so it is not a serious failure anymore.
The problem being still latent, said bug is not closed for now.
- - - - -
fa58f2bf by Étienne Mollier at 2024-03-10T16:14:29+01:00
d/t/run-unit-test: deploy newly needed test data.
- - - - -
540686a7 by Étienne Mollier at 2024-03-10T16:16:18+01:00
ready to upload to unstable.
- - - - -
4 changed files:
- debian/changelog
- debian/patches/series
- + debian/patches/skip-xmlio-tests.patch
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,10 +1,17 @@
-python-biopython (1.83+dfsg-1) UNRELEASED; urgency=medium
+python-biopython (1.83+dfsg-1) unstable; urgency=medium
+ [ Andreas Tille ]
* New upstream version
* Exclude emboss from Build-Depends for 32bit architectures since
emboss will be removed for these architectures (see #1062371)
- -- Andreas Tille <tille at debian.org> Sun, 04 Feb 2024 21:27:57 +0100
+ [ Étienne Mollier ]
+ * skip-xmlio-tests.patch: new: skip test failures.
+ This works around #1064147 so it is not a serious failure anymore.
+ The problem being still latent, said bug is not closed for now.
+ * d/t/run-unit-test: deploy newly needed test data.
+
+ -- Étienne Mollier <emollier at debian.org> Sun, 10 Mar 2024 16:15:04 +0100
python-biopython (1.81+dfsg-3) unstable; urgency=medium
=====================================
debian/patches/series
=====================================
@@ -6,3 +6,4 @@ reproduciblebuild.patch
croak-on-muscle5.patch
muscle3.patch
#port_tutorial_to_muscle3.patch
+skip-xmlio-tests.patch
=====================================
debian/patches/skip-xmlio-tests.patch
=====================================
@@ -0,0 +1,88 @@
+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/tests/run-unit-test
=====================================
@@ -12,12 +12,16 @@ cp -a /usr/share/doc/python-biopython-doc/Doc/Tutorial Doc
cp -a /usr/share/doc/python-biopython-doc/Doc/examples Doc
unset GZIP
find . -name "*.gz" -exec gunzip \{\} \;
+SUBSMAT_DIR="Bio/Align/substitution_matrices/data"
+mkdir -pv "$SUBSMAT_DIR/"
+cp -av "/usr/lib/python3/dist-packages/$SUBSMAT_DIR"/* "$SUBSMAT_DIR/"
cd Tests
# we really need this gzipped duplicate of the example.fastq and E3MFGYR02_random_10_reads.sff files to pass the BGZF compression test
gzip --keep Quality/example.fastq
gzip --keep Roche/E3MFGYR02_random_10_reads.sff
gzip --keep Fasta/flowers.pro
+
echo "Remove test test_Tutorial.py which is bound to fail"
find . -name test_Tutorial.py -delete
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/c6faade834ee7cdde15c98c7349157579860e49d...540686a71ce99d7c980ca2083986319f1b08e176
--
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/c6faade834ee7cdde15c98c7349157579860e49d...540686a71ce99d7c980ca2083986319f1b08e176
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20240310/b49e0663/attachment-0001.htm>
More information about the debian-med-commit
mailing list