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python312Packages.pysam: 0.22.1 -> 0.22.1-unstable-2024-10-30 #366911

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@aucub aucub commented Dec 20, 2024

fix test failures

python3.12-pysam> =================================== FAILURES ===================================
python3.12-pysam> _______________________ TestBaseModifications.testChebi ________________________
python3.12-pysam> self = <AlignedSegment_test.TestBaseModifications testMethod=testChebi>
python3.12-pysam>     def testChebi(self):
python3.12-pysam>         """reference bases should always be the same nucleotide
python3.12-pysam>         """
python3.12-pysam>         filename = os.path.join(BAM_DATADIR, "MM-chebi.bam")
python3.12-pysam>         expect = {
python3.12-pysam>             ("C", 0, "m"): [(6, 102), (17, 128), (20, 153), (31, 179), (34, 204)],
python3.12-pysam>             ("N", 0, "n"): [(15, 212)],
python3.12-pysam>             ("C", 0, 76792): [(19, 161), (34, 187)],
python3.12-pysam>         }
python3.12-pysam>         with pysam.AlignmentFile(filename, check_sq=False) as inf:
python3.12-pysam>             r = next(iter(inf))
python3.12-pysam> >           self.assertDictEqual(r.modified_bases, expect)
python3.12-pysam> E           AssertionError: None is not an instance of <class 'dict'> : First argument is not a dictionary
python3.12-pysam> tests/AlignedSegment_test.py:1077: AssertionError
python3.12-pysam> ________________________ TestHeaderWriteRead.test_CRAM _________________________
python3.12-pysam> self = <AlignmentFileHeader_test.TestHeaderWriteRead testMethod=test_CRAM>
python3.12-pysam>     def test_CRAM(self):
python3.12-pysam>         header = copy.copy(self.header)
python3.12-pysam>         if "PG" in header:
python3.12-pysam>             # for CRAM, \t needs to be quoted:
python3.12-pysam>             header['PG'][1]['CL'] = re.sub(r"\t", r"\\\\t", header['PG'][1]['CL'])
python3.12-pysam> >       self.check_read_write("wc", header)
python3.12-pysam> tests/AlignmentFileHeader_test.py:320:
python3.12-pysam> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
python3.12-pysam> tests/AlignmentFileHeader_test.py:290: in check_read_write
python3.12-pysam>     with pysam.AlignmentFile(
python3.12-pysam> pysam/libcalignmentfile.pyx:1755: in pysam.libcalignmentfile.AlignmentFile.__exit__
python3.12-pysam>     ???
python3.12-pysam> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
python3.12-pysam> >   ???
python3.12-pysam> E   FileNotFoundError: [Errno 2] No such file or directory
python3.12-pysam> pysam/libcalignmentfile.pyx:1687: FileNotFoundError
python3.12-pysam> _______________________ TestHeaderLargeContigs.test_CRAM _______________________
python3.12-pysam> self = <AlignmentFileHeader_test.TestHeaderLargeContigs testMethod=test_CRAM>
python3.12-pysam>     def test_CRAM(self):
python3.12-pysam>         header = copy.copy(self.header)
python3.12-pysam>         if "PG" in header:
python3.12-pysam>             # for CRAM, \t needs to be quoted:
python3.12-pysam>             header['PG'][1]['CL'] = re.sub(r"\t", r"\\\\t", header['PG'][1]['CL'])
python3.12-pysam> >       self.check_read_write("wc", header)
python3.12-pysam> tests/AlignmentFileHeader_test.py:320:
python3.12-pysam> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
python3.12-pysam> tests/AlignmentFileHeader_test.py:290: in check_read_write
python3.12-pysam>     with pysam.AlignmentFile(
python3.12-pysam> pysam/libcalignmentfile.pyx:1755: in pysam.libcalignmentfile.AlignmentFile.__exit__
python3.12-pysam>     ???
python3.12-pysam> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
python3.12-pysam> >   ???
python3.12-pysam> E   FileNotFoundError: [Errno 2] No such file or directory
python3.12-pysam> pysam/libcalignmentfile.pyx:1687: FileNotFoundError
python3.12-pysam> =============================== warnings summary ===============================
python3.12-pysam> tests/samtools_test.py::SamtoolsTest::testStatements
python3.12-pysam> tests/samtools_test.py::PysamTest::testStatements
python3.12-pysam>   /build/source/tests/samtools_test.py:133: UserWarning: versions of pysam.samtools and samtools differ: 1.18 != 1.19.2
python3.12-pysam>     warnings.warn(
python3.12-pysam> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
python3.12-pysam> =========================== short test summary info ============================
python3.12-pysam> FAILED tests/AlignedSegment_test.py::TestBaseModifications::testChebi - AssertionError: None is not an instance of <class 'dict'> : First argument ...
python3.12-pysam> FAILED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM - FileNotFoundError: [Errno 2] No such file or directory
python3.12-pysam> FAILED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM - FileNotFoundError: [Errno 2] No such file or directory
python3.12-pysam> ============ 3 failed, 942 passed, 13 skipped, 2 warnings in 20.28s ============
error: builder for '/nix/store/7b6qdi200lqwhsmycd205c29a2pzbvrw-python3.12-pysam-0.22.1.drv' failed with exit code 1;
       last 25 log lines:
       >
       > tests/AlignmentFileHeader_test.py:320:
       > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
       > tests/AlignmentFileHeader_test.py:290: in check_read_write
       >     with pysam.AlignmentFile(
       > pysam/libcalignmentfile.pyx:1755: in pysam.libcalignmentfile.AlignmentFile.__exit__
       >     ???
       > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
       >
       > >   ???
       > E   FileNotFoundError: [Errno 2] No such file or directory
       >
       > pysam/libcalignmentfile.pyx:1687: FileNotFoundError
       > =============================== warnings summary ===============================
       > tests/samtools_test.py::SamtoolsTest::testStatements
       > tests/samtools_test.py::PysamTest::testStatements
       >   /build/source/tests/samtools_test.py:133: UserWarning: versions of pysam.samtools and samtools differ: 1.18 != 1.19.2
       >     warnings.warn(
       >
       > -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
       > =========================== short test summary info ============================
       > FAILED tests/AlignedSegment_test.py::TestBaseModifications::testChebi - AssertionError: None is not an instance of <class 'dict'> : First argument ...
       > FAILED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM - FileNotFoundError: [Errno 2] No such file or directory
       > FAILED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM - FileNotFoundError: [Errno 2] No such file or directory
       > ============ 3 failed, 942 passed, 13 skipped, 2 warnings in 20.28s ============
       For full logs, run 'nix log /nix/store/7b6qdi200lqwhsmycd205c29a2pzbvrw-python3.12-pysam-0.22.1.drv'.

Things done

  • Built on platform(s)
    • x86_64-linux
    • aarch64-linux
    • x86_64-darwin
    • aarch64-darwin
  • For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)
    • sandbox = relaxed
    • sandbox = true
  • Tested, as applicable:
  • Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
  • Tested basic functionality of all binary files (usually in ./result/bin/)
  • 25.05 Release Notes (or backporting 24.11 and 25.05 Release notes)
    • (Package updates) Added a release notes entry if the change is major or breaking
    • (Module updates) Added a release notes entry if the change is significant
    • (Module addition) Added a release notes entry if adding a new NixOS module
  • Fits CONTRIBUTING.md.

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@ofborg ofborg bot requested a review from unode December 21, 2024 07:21
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This pull request has been mentioned on NixOS Discourse. There might be relevant details there:

https://discourse.nixos.org/t/prs-ready-for-review/3032/4991

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aucub commented Jan 4, 2025

nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 366911

x86_64-linux

❌ 4 packages failed to build:
  • deeptools
  • deeptools.dist
  • python312Packages.cnvkit
  • python312Packages.cnvkit.dist
✅ 17 packages built:
  • hap-py
  • python312Packages.htseq
  • python312Packages.htseq.dist
  • python312Packages.pysam
  • python312Packages.pysam.dist
  • python312Packages.pywfa
  • python312Packages.pywfa.dist
  • python313Packages.htseq
  • python313Packages.htseq.dist
  • python313Packages.pysam
  • python313Packages.pysam.dist
  • python313Packages.pywfa
  • python313Packages.pywfa.dist
  • tebreak
  • tebreak.dist
  • tiddit
  • tiddit.dist

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This pull request has been mentioned on NixOS Discourse. There might be relevant details there:

https://discourse.nixos.org/t/prs-ready-for-review/3032/5042

@aucub aucub mentioned this pull request Jan 5, 2025
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