nixpkgs/pkgs/development/python-modules/pysam/default.nix
Renato Alves 0a41e3f938 pythonPackages.pysam: add libdeflate and enable tests
Some tests still fail due to upstream reasons so we skip those.

Note also that we are not using nix's pytestCheckHook due to
pysam detecting how it's loaded which conflicts with how
pytestCheckHook runs tests. In addition, the selection mode used
by disabledTests causes more tests than the failing ones to be
skipped, which is undesired.
See the discussion in https://github.com/NixOS/nixpkgs/pull/100823
2020-10-19 22:03:08 -07:00

109 lines
3.3 KiB
Nix

{ lib
, buildPythonPackage
, fetchFromGitHub
, bzip2
, bcftools
, curl
, cython
, htslib
, libdeflate
, lzma
, pytest
, samtools
, zlib
}:
buildPythonPackage rec {
pname = "pysam";
version = "0.16.0.1";
# Fetching from GitHub instead of PyPi cause the 0.13 src release on PyPi is
# missing some files which cause test failures.
# Tracked at: https://github.com/pysam-developers/pysam/issues/616
src = fetchFromGitHub {
owner = "pysam-developers";
repo = "pysam";
rev = "v${version}";
sha256 = "168bwwm8c2k22m7paip8q0yajyl7xdxgnik0bgjl7rhqg0majz0f";
};
nativeBuildInputs = [ samtools ];
buildInputs = [
bzip2
curl
cython
libdeflate
lzma
zlib
];
# Use nixpkgs' htslib instead of the bundled one
# See https://pysam.readthedocs.io/en/latest/installation.html#external
# NOTE that htslib should be version compatible with pysam
preBuild = ''
export HTSLIB_MODE=shared
export HTSLIB_LIBRARY_DIR=${htslib}/lib
export HTSLIB_INCLUDE_DIR=${htslib}/include
'';
checkInputs = [
pytest
bcftools
htslib
];
# See https://github.com/NixOS/nixpkgs/pull/100823 for why we aren't using
# disabledTests and pytestFlagsArray through pytestCheckHook
checkPhase = ''
# Needed to avoid /homeless-shelter error
export HOME=$(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
make -C tests/pysam_data
make -C tests/cbcf_data
# Delete pysam folder in current directory to avoid importing it during testing
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::TestIO::testBAM2SAM \
--deselect tests/AlignmentFile_test.py::TestIO::testSAM2BAM \
--deselect tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile \
--deselect tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile \
--deselect tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader \
--deselect tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader \
--deselect tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing \
tests/
'';
pythonImportsCheck = [
"pysam"
"pysam.bcftools"
"pysam.libchtslib"
"pysam.libcutils"
"pysam.libcvcf"
];
meta = with lib; {
description = "A python module for reading, manipulating and writing genome data sets";
homepage = "https://pysam.readthedocs.io/";
maintainers = with maintainers; [ unode ];
license = licenses.mit;
platforms = [ "i686-linux" "x86_64-linux" ];
};
}