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
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