Unverified Commit 4fdd43e5 authored by Martin Weinelt's avatar Martin Weinelt Committed by GitHub
Browse files

Merge pull request #232583 from savyajha/pysam-bump 

python310Packages.pysam: 0.20.0 -> 0.21.0
parents 582e084c 880ef65c

pkgs/development/python-modules/pysam/default.nix

+10 −44
Original line number Diff line number Diff line
@@ -8,14 +8,14 @@ 
, htslib

, libdeflate

, xz

, pytest

, pytestCheckHook

, samtools

, zlib

}:



buildPythonPackage rec {

  pname   = "pysam";

  version = "0.20.0";

  version = "0.21.0";



  # Fetching from GitHub instead of PyPi cause the 0.13 src release on PyPi is

  # missing some files which cause test failures.
@@ -24,19 +24,21 @@ buildPythonPackage rec { 
    owner = "pysam-developers";

    repo = "pysam";

    rev = "refs/tags/v${version}";

    hash = "sha256-7yEZJ+iIw4qOxsanlKQlqt1bfi8MvyYjGJWiVDmXBrc=";

    hash = "sha256-C4/AJwcUyLoUEUEnsATLHJb5F8mltP8X2XfktYu0OTo=";

  };



  nativeBuildInputs = [ samtools ];



  buildInputs = [

    bzip2

    curl

    cython

    libdeflate

    xz

    zlib

  ];



  propagatedBuildInputs = [ cython ];



  # Use nixpkgs' htslib instead of the bundled one

  # See https://pysam.readthedocs.io/en/latest/installation.html#external

  # NOTE that htslib should be version compatible with pysam
@@ -47,53 +49,17 @@ buildPythonPackage rec { 
  '';



  nativeCheckInputs = [

    pytest

    pytestCheckHook

    bcftools

    htslib

  ];



  # See https://github.com/NixOS/nixpkgs/pull/100823 for why we aren't using

  # disabledTests and pytestFlagsArray through pytestCheckHook

  checkPhase = ''

    # Needed to avoid /homeless-shelter error

    export HOME=$(mktemp -d)



    # To avoid API incompatibilities, these should ideally show the same version

    echo "> samtools --version"

    samtools --version

    echo "> htsfile --version"

    htsfile --version

    echo "> bcftools --version"

    bcftools --version



    # Create auxiliary test data

  preCheck = ''

    export HOME=$TMPDIR

    make -C tests/pysam_data

    make -C tests/cbcf_data



    # Delete pysam folder in current directory to avoid importing it during testing

    make -C tests/tabix_data

    rm -rf pysam



    # Deselect tests that are known to fail due to upstream issues

    # See https://github.com/pysam-developers/pysam/issues/961

    py.test \

      --deselect tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works \

      --deselect tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected \

      --deselect tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works \

      --deselect tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected \

      --deselect tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile \

      --deselect tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader \

      --deselect tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader \

      --deselect tests/AlignmentFile_test.py::TestIO::testBAM2BAM \

      --deselect tests/AlignmentFile_test.py::TestIO::testBAM2CRAM \

      --deselect tests/AlignmentFile_test.py::TestIO::testBAM2SAM \

      --deselect tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject \

      --deselect tests/AlignmentFile_test.py::TestIO::testOpenFromFilename \

      --deselect tests/AlignmentFile_test.py::TestIO::testSAM2BAM \

      --deselect tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile \

      --deselect tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate \

      --deselect tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing \

      --deselect tests/compile_test.py::BAMTest::testCount \

      tests/

  '';



  pythonImportsCheck = [