Test suite issues in python-pysam
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
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