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python310Packages.pysam: 0.20.0 -> 0.21.0

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Bumped version and changed the test suite to use pytestCheckHook. Also
enabled previously disabled tests.
This commit is contained in:
Savyasachee Jha 2023-05-18 15:15:58 +05:30
parent 1780cbef72
commit 880ef65c44
1 changed files with 10 additions and 44 deletions
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54
pkgs/development/python-modules/pysam/default.nix
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@ -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 = [