Your message dated Thu, 6 Feb 2025 21:07:20 +0100
with message-id <z6uweeskxjflz...@emlwks999.eu>
and subject line python3-pysam: autopkgtest regression with htslib 1.21
has caused the Debian Bug report #1087457,
regarding python3-pysam: autopkgtest regression with htslib 1.21
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1087457: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1087457
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--- Begin Message ---
Package: python3-pysam
Version: 0.22.1+ds-2
Severity: important
Greetings,
Experimental pseudo-excuses reported an autpkgtest regression in
python-pysam following htslib upgrade to version 1.21. The full
log[1] describes the set of test errors better than I would, but
here are a few failures which seemed representative:
160s ________________________ TestHeaderWriteRead.test_CRAM
_________________________
160s
160s self = <AlignmentFileHeader_test.TestHeaderWriteRead
testMethod=test_CRAM>
160s
160s def test_CRAM(self):
160s header = copy.copy(self.header)
160s if "PG" in header:
160s # for CRAM, \t needs to be quoted:
160s header['PG'][1]['CL'] = re.sub(r"\t", r"\\\\t",
header['PG'][1]['CL'])
160s > self.check_read_write("wc", header)
160s
160s tests/AlignmentFileHeader_test.py:320:
160s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _ _ _ _
160s tests/AlignmentFileHeader_test.py:290: in check_read_write
160s with pysam.AlignmentFile(
160s pysam/libcalignmentfile.pyx:1755: in
pysam.libcalignmentfile.AlignmentFile.__exit__
160s self.close()
160s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _ _ _ _
160s
160s > raise IOError(errno, force_str(strerror(errno)))
160s E FileNotFoundError: [Errno 2] No such file or directory
160s
160s pysam/libcalignmentfile.pyx:1687: FileNotFoundError
160s _________________ TestIndexFormatsVCF.test_bcf_with_csi_index
__________________
160s
160s self = <VariantFile_test.TestIndexFormatsVCF
testMethod=test_bcf_with_csi_index>
160s
160s def test_bcf_with_csi_index(self):
160s with get_temp_context("tmp_fn.bcf") as fn:
160s shutil.copyfile(self.bcf_filename, fn)
160s
160s pysam.tabix_index(fn, preset="vcf", force=True,
csi=True)
160s
160s self.assertTrue(os.path.exists(fn + ".csi"))
160s self.assertEqual(read_index_header(fn + ".csi"),
b"CSI\1")
160s self.assertFalse(os.path.exists(fn + ".tbi"))
160s
160s with pysam.VariantFile(fn) as inf:
160s > self.assertEqual(len(list(inf.fetch("20"))), 3)
160s
160s tests/VariantFile_test.py:257:
160s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _ _ _ _
160s pysam/libcbcf.pyx:4466: in pysam.libcbcf.VariantFile.fetch
160s _, tid, start, stop = self.parse_region(contig, start, stop,
region,
160s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _ _ _ _
160s
160s > raise ValueError('invalid contig `%s`' % contig)
160s E ValueError: invalid contig `20`
160s
160s pysam/libchtslib.pyx:683: ValueError
160s ______________________ test_ascii_annotation_can_be_added
______________________
160s
160s vcf_header = <pysam.libcbcf.VariantHeader object at 0x7fbf5b496130>
160s
160s def test_ascii_annotation_can_be_added(vcf_header):
160s vcf_header.formats.add("AN", 1, "String", "An annotation")
160s > record = vcf_header.new_record(
160s contig="1",
160s start=12,
160s stop=13,
160s samples=[
160s {"AN": "anno1"},
160s {"AN": "anno2"}])
160s
160s tests/VariantRecord_test.py:22:
160s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _ _ _ _
160s pysam/libcbcf.pyx:2093: in pysam.libcbcf.VariantHeader.new_record
160s rec.contig = contig
160s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _ _ _ _
160s
160s > raise ValueError('Invalid chromosome/contig')
160s E ValueError: Invalid chromosome/contig
160s
160s pysam/libcbcf.pyx:3096: ValueError
[1]: https://ci.debian.net/packages/p/python-pysam/unstable/amd64/54272356/
I would have had a look upstream to check whether there is a new
version, but it seems this is not the case yet, so this may be a
good candidate of bug to forward upstream.
Note: when I checked whether that was a regression or not, I hit
another issue of failure to load the module pysam with Python
3.13, that was newly introduced as supported interpreter version
lately, but this is fixable with a rebuild of the pysam package.
For information when trying to reproduce the main issue…
Have a nice day, :)
--
.''`. Étienne Mollier <emoll...@debian.org>
: :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
`. `' sent from /dev/pts/4, please excuse my verbosity
`- on air: Cyan - Tomorrow's Here Today
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--- End Message ---
--- Begin Message ---
Version: 0.23.0+ds-0+exp1
The recently released python-pysam 0.23.0 uploaded in
experimental is compatible with htslib 1.21 and does resolve the
issue.
--
.''`. Étienne Mollier <emoll...@debian.org>
: :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
`. `' sent from /dev/pts/1, please excuse my verbosity
`- on air: The Flower Kings - Big Puzzle
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