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 #100823

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

@@ -6,6 +6,7 @@
 , curl
 , cython
 , htslib
+, libdeflate
 , lzma
 , pytest
 , samtools
@@ -27,22 +28,72 @@ buildPythonPackage rec {
   };
 
   nativeBuildInputs = [ samtools ];
-  buildInputs = [ bzip2 curl cython lzma zlib ];
+  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 ];
-  checkPhase = "py.test";
+  checkInputs = [
+    pytest
+    bcftools
+    htslib
+  ];
 
-  # tests require samtools<=1.9
-  doCheck = false;
-  preCheck = ''
+  # 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"
   ];