[Debian-med-packaging] Bug#1149833: python-pybedtools: autopkgtest regression

[Adrian Bunk]

Source: python-pybedtools
Version: 0.12.1-1
Severity: serious

https://tracker.debian.org/pkg/python-pybedtools

Migration status for python-pybedtools (0.10.0-6 to 0.12.1-1): BLOCKED: Rejected/violates migration policy/introduces a regression
Issues preventing migration:
∙ ∙ Autopkgtest for python-pybedtools/0.12.1-1: amd64: Regression ♻ (reference ♻), arm64: Regression ♻ (reference ♻), armhf: Regression ♻ (reference ♻), i386: Regression ♻ (reference ♻), ppc64el: Regression ♻ (reference ♻)


...
117s =================================== FAILURES ===================================
117s ________________________________ test_tabix_csi ________________________________
117s 
117s     def test_tabix_csi():
117s         for idx_type in ("tbi", "csi"):
117s             try:
117s                 a = pybedtools.example_bedtool("a.bed")
117s >               t = a.tabix(force=True, use_csi=True if idx_type == "csi" else False)
117s                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
117s 
117s /usr/lib/python3/dist-packages/pybedtools/test/test_1.py:135: 
117s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
117s /usr/lib/python3/dist-packages/pybedtools/bedtool.py:845: in tabix
117s     fn = self.bgzip(in_place=in_place, force=force, is_sorted=is_sorted)
117s          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
117s /usr/lib/python3/dist-packages/pybedtools/bedtool.py:908: in bgzip
117s     pysam.tabix_compress(fn, outfn, force=force)
117s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
117s 
117s >   ???
117s E   OSError: could not open '/usr/lib/python3/dist-packages/pybedtools/test/data/a.bed.gz' for writing
117s 
117s pysam/libctabix.pyx:843: OSError
117s 
117s During handling of the above exception, another exception occurred:
117s 
117s     def test_tabix_csi():
117s         for idx_type in ("tbi", "csi"):
117s             try:
117s                 a = pybedtools.example_bedtool("a.bed")
117s                 t = a.tabix(force=True, use_csi=True if idx_type == "csi" else False)
117s                 assert t._tabixed()
117s                 results = t.tabix_intervals("chr1:99-200")
117s                 results = str(results)
117s                 print(results)
117s                 assert results == fix(
117s                     """
117s                 chr1	1	100	feature1	0	+
117s                 chr1	100	200	feature2	0	+
117s                 chr1	150	500	feature3	0	-"""
117s                 )
117s     
117s                 assert str(t.tabix_intervals(a[2])) == fix(
117s                     """
117s                 chr1	100	200	feature2	0	+
117s                 chr1	150	500	feature3	0	-"""
117s                 )
117s     
117s             finally:
117s                 # clean up
117s                 fns = [
117s                     pybedtools.example_filename("a.bed.gz"),
117s >                   pybedtools.example_filename("a.bed.gz." + idx_type),
117s                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
117s                 ]
117s 
117s /usr/lib/python3/dist-packages/pybedtools/test/test_1.py:157: 
117s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
117s 
117s fn = '/usr/lib/python3/dist-packages/pybedtools/test/data/a.bed.gz.tbi'
117s 
117s     def example_filename(fn):
117s         """
117s         Return a bed file from the pybedtools examples directory.  Use
117s         func:`list_example_files` to see a list of files that are included.
117s         """
117s         fn = os.path.join(data_dir(), fn)
117s         if not os.path.exists(fn):
117s             msg = "%s does not exist" % fn
117s >           raise FileNotFoundError(msg)
117s E           FileNotFoundError: /usr/lib/python3/dist-packages/pybedtools/test/data/a.bed.gz.tbi does not exist
117s 
117s /usr/lib/python3/dist-packages/pybedtools/filenames.py:26: FileNotFoundError
117s ____________________________ test_tabix_contigs_csi ____________________________
117s 
117s     def test_tabix_contigs_csi():
117s         a = pybedtools.example_bedtool("a.bed")
117s >       a = a.tabix(force=True, use_csi=True)
117s             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
117s 
117s /usr/lib/python3/dist-packages/pybedtools/test/test_1.py:197: 
117s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
117s /usr/lib/python3/dist-packages/pybedtools/bedtool.py:845: in tabix
117s     fn = self.bgzip(in_place=in_place, force=force, is_sorted=is_sorted)
117s          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
117s /usr/lib/python3/dist-packages/pybedtools/bedtool.py:908: in bgzip
117s     pysam.tabix_compress(fn, outfn, force=force)
117s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
117s 
117s >   ???
117s E   OSError: could not open '/usr/lib/python3/dist-packages/pybedtools/test/data/a.bed.gz' for writing
117s 
117s pysam/libctabix.pyx:843: OSError
117s =========================== short test summary info ============================
117s FAILED test/test_1.py::test_tabix_csi - FileNotFoundError: /usr/lib/python3/d...
117s FAILED test/test_1.py::test_tabix_contigs_csi - OSError: could not open '/usr...
117s =========== 2 failed, 507 passed, 2 deselected, 3 xfailed in 10.74s ============
118s E: pybuild pybuild:485: test: plugin pyproject failed with: exit code=1: cd /tmp/autopkgtest.2PZ4Fh/autopkgtest_tmp/build; python3.14 -m pytest -k "not test_chromsizes" --pyargs pybedtools
118s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p 3.14 --parallel= returned exit code 13
118s make: *** [/tmp/zZm58GjnHe/run:4: pybuild-autopkgtest] Error 25
118s pybuild-autopkgtest: error: /tmp/zZm58GjnHe/run pybuild-autopkgtest returned exit code 2
118s autopkgtest [08:54:10]: test pybuild-autopkgtest: -----------------------]
118s autopkgtest [08:54:10]: test pybuild-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
118s pybuild-autopkgtest  FAIL non-zero exit status 25
...