[Debian-med-packaging] Bug#919928: htslib breaks python-pysam autopkgtest

[Paul Gevers]

Source: htslib, python-pysam
Control: found -1 htslib/1.9-10
Control: found -1 python-pysam/0.15.1+ds-1
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: breaks needs-update

Dear maintainers,

With a recent upload of htslib the autopkgtest of python-pysam fails in
testing when that autopkgtest is run with the binary packages of htslib
from unstable. It passes when run with only packages from testing. In
tabular form:
                       pass            fail
htslib                 from testing    1.9-10
python-pysam           from testing    0.15.1+ds-1
all others             from testing    from testing

I copied some of the output at the bottom of this report.

Currently this regression is blocking the migration of htslib to testing
[1]. Due to the nature of this issue, I filed this bug report against
both packages. Can you please investigate the situation and reassign the
bug to the right package? If needed, please change the bug's severity.

More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation

Paul

[1] https://qa.debian.org/excuses.php?package=htslib

https://ci.debian.net/data/autopkgtest/testing/amd64/p/python-pysam/1739216/log.gz

=================================== FAILURES
===================================
_____________ TestIndexing.test_indexing_to_custom_location_works
______________

self = <tabix_test.TestIndexing
testMethod=test_indexing_to_custom_location_works>

    def test_indexing_to_custom_location_works(self):
        '''test indexing a file with a non-default location.'''

        index_path = get_temp_filename(suffix='custom.tbi')
        pysam.tabix_index(self.tmpfilename, preset="gff",
                          index=index_path, force=True)
>       self.assertTrue(checkBinaryEqual(index_path, self.filename_idx))
E       AssertionError: False is not true

tests/tabix_test.py:89: AssertionError
____________ TestIndexing.test_indexing_with_explict_columns_works
_____________

self = <tabix_test.TestIndexing
testMethod=test_indexing_with_explict_columns_works>

    def test_indexing_with_explict_columns_works(self):
        '''test indexing via preset.'''

        pysam.tabix_index(self.tmpfilename,
                          seq_col=0,
                          start_col=3,
                          end_col=4,
                          line_skip=0,
                          zerobased=False)
        self.assertTrue(checkBinaryEqual(
>           self.tmpfilename + ".tbi", self.filename_idx))
E       AssertionError: False is not true

tests/tabix_test.py:102: AssertionError
_________________ TestIndexing.test_indexing_with_preset_works
_________________

self = <tabix_test.TestIndexing testMethod=test_indexing_with_preset_works>

    def test_indexing_with_preset_works(self):
        '''test indexing via preset.'''

        pysam.tabix_index(self.tmpfilename, preset="gff")
        self.assertTrue(checkBinaryEqual(
>           self.tmpfilename + ".tbi", self.filename_idx))
E       AssertionError: False is not true

tests/tabix_test.py:81: AssertionError

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