Hi, I'm observing test suite issues in python-pysam that IMHO are not related to the htslib / samtools update I did yesterday (possibly a bit to fast to unstable ... but hmmm, that's out now). I'm trying to compare the current test results with the results from the current python-pysam version in unstable [1].
For instance my Build in Git shows an error tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works FAILED which is also in [1]. Thus I grepped in both logs and found: python-pysam_0.15.4.1+ds-1_amd64.build:tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works FAILED python-pysam_0.15.4.1+ds-1_amd64.build:tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected FAILED python-pysam_0.15.4.1+ds-1_amd64.build:tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works FAILED python-pysam_0.15.4.1+ds-1_amd64.build:tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected FAILED python-pysam_0.15.4.1+ds-1_amd64.build-tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused python-pysam_0.15.4.1+ds-1_amd64.build:FAILED python-pysam_0.15.4.1+ds-1_amd64.build-tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused python-pysam_0.15.4.1+ds-1_amd64.build:FAILED python-pysam_0.15.4.1+ds-1_amd64.build-tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused python-pysam_0.15.4.1+ds-1_amd64.build:FAILED python-pysam_0.15.4.1+ds-1_amd64.build-tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused python-pysam_0.15.4.1+ds-1_amd64.build:FAILED python-pysam_0.15.4.1+ds-1_amd64.build-tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused python-pysam_0.15.4.1+ds-1_amd64.build:FAILED python-pysam_0.15.4.1+ds-1_amd64.build-tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused python-pysam_0.15.4.1+ds-1_amd64.build:FAILED python-pysam_0.15.4.1+ds-1_amd64.build-tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused python-pysam_0.15.4.1+ds-1_amd64.build:FAILED python-pysam_0.15.4.1+ds-1_amd64.build-tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused python-pysam_0.15.4.1+ds-1_amd64.build:FAILED python-pysam_0.15.4.1+ds-1_amd64.build:tests/AlignmentFile_test.py::TestIO::testBAM2SAM FAILED python-pysam_0.15.4.1+ds-1_amd64.build-tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM [E::hts_open_format] Failed to open file "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/example_empty_with_header.bam" : No such file or directory python-pysam_0.15.4.1+ds-1_amd64.build:FAILED python-pysam_0.15.4.1+ds-1_amd64.build:tests/AlignmentFile_test.py::TestIO::testSAM2BAM FAILED python-pysam_0.15.4.1+ds-1_amd64.build:tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile FAILED python-pysam_0.15.4.1+ds-1_amd64.build:tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile FAILED python-pysam_0.15.4.1+ds-1_amd64.build:tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader FAILED python-pysam_0.15.4.1+ds-1_amd64.build-tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader [E::hts_open_format] Failed to open file "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/rg_with_tab.bam" : No such file or directory python-pysam_0.15.4.1+ds-1_amd64.build:FAILED python-pysam_0.15.4.1+ds-1_amd64.build:tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing FAILED python-pysam_0.16.0.1+ds-1_amd64.build:tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works FAILED python-pysam_0.16.0.1+ds-1_amd64.build:tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected FAILED python-pysam_0.16.0.1+ds-1_amd64.build:tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works FAILED python-pysam_0.16.0.1+ds-1_amd64.build:tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected FAILED python-pysam_0.16.0.1+ds-1_amd64.build:tests/AlignmentFile_test.py::TestIO::testBAM2BAM FAILED python-pysam_0.16.0.1+ds-1_amd64.build:tests/AlignmentFile_test.py::TestIO::testBAM2SAM FAILED python-pysam_0.16.0.1+ds-1_amd64.build:tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject FAILED python-pysam_0.16.0.1+ds-1_amd64.build:tests/AlignmentFile_test.py::TestIO::testOpenFromFilename FAILED python-pysam_0.16.0.1+ds-1_amd64.build:tests/AlignmentFile_test.py::TestIO::testSAM2BAM FAILED python-pysam_0.16.0.1+ds-1_amd64.build:tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile FAILED python-pysam_0.16.0.1+ds-1_amd64.build:tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate FAILED python-pysam_0.16.0.1+ds-1_amd64.build:tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile FAILED python-pysam_0.16.0.1+ds-1_amd64.build:tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader FAILED python-pysam_0.16.0.1+ds-1_amd64.build:tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader FAILED python-pysam_0.16.0.1+ds-1_amd64.build:tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing FAILED python-pysam_0.16.0.1+ds-1_amd64.build:tests/compile_test.py::BAMTest::testCount FAILED In total version 0.15.4 in unstable has ======== 20 failed, 907 passed, 10 skipped, 4 warnings in 44.59 seconds ======== while my preparation in Git has only ======== 16 failed, 911 passed, 10 skipped, 4 warnings in 38.50 seconds ======== which seems slightly better. I admit I'd feel better if we would solve those 16 failed tests and clarify why these are failing and whether we can do something about this or need to ignore these. The former tests simply have passed since we were "cheating" (see [2]) and I would prefer to stop this if possible. Any hints - also for single tests - would be welcome. Kind regards Andreas. [1] https://buildd.debian.org/status/fetch.php?pkg=python-pysam&arch=amd64&ver=0.15.4%2Bds-3&stamp=1588965556&raw=0 [2] https://salsa.debian.org/med-team/python-pysam/-/commit/4e497c19c91bf4c4ddea1c47c57211f7d7a4cf98 -- http://fam-tille.de
