On Fri, 2020-10-02 at 12:01 +0200, Andreas Tille wrote: > 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::testPresentOptio > nalFields [W::find_file_url] Failed to open reference " > https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7":
this url error appears multiple times. Returns for now a 404, so issue should be forwarded to upstream. Though, as in debian should pass without network, I think those tests should be skipped. Maybe some other tests failure are related (using downloaded file?) Olivier > 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::testPresentOp > tionalFields [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::testPresentOption > alFields [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::testPresentOpti > onalFields [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::testWriteUncompres > sedBAMFile FAILED > python-pysam_0.15.4.1+ds- > 1_amd64.build:tests/AlignmentFile_test.py::TestDeNovoConstruction::te > stBAMWholeFile FAILED > python-pysam_0.15.4.1+ds- > 1_amd64.build:tests/AlignmentFile_test.py::TestEmptyHeader::testEmpty > Header 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_t > ext_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::testFetchFromClose > dFileObject FAILED > python-pysam_0.16.0.1+ds- > 1_amd64.build:tests/AlignmentFile_test.py::TestIO::testOpenFromFilena > me 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::testWriteUncompres > sedBAMFile FAILED > python-pysam_0.16.0.1+ds- > 1_amd64.build:tests/AlignmentFile_test.py::TestIteratorRowAllBAM::tes > tIterate FAILED > python-pysam_0.16.0.1+ds- > 1_amd64.build:tests/AlignmentFile_test.py::TestDeNovoConstruction::te > stBAMWholeFile FAILED > python-pysam_0.16.0.1+ds- > 1_amd64.build:tests/AlignmentFile_test.py::TestEmptyHeader::testEmpty > Header FAILED > python-pysam_0.16.0.1+ds- > 1_amd64.build:tests/AlignmentFile_test.py::TestHeaderWithProgramOptio > ns::testHeader FAILED > python-pysam_0.16.0.1+ds- > 1_amd64.build:tests/StreamFiledescriptors_test.py::StreamTest::test_t > ext_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 > -- Olivier Sallou Univ Rennes, Inria, CNRS, IRISA Irisa, Campus de Beaulieu F-35042 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
