Re: Test suite issues in python-pysam
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
Reply to: