[Debian-med-packaging] Bug#920250: python-pysam ftbfs from source (test failures)

[Matthias Klose]

Package: src:python-pysam
Version: 0.15.2+ds-1
Severity: serious
Tags: sid buster

=================================== 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
=============================== warnings summary ===============================
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367
  /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning:
Cython directive 'language_level' not set, using 2 for now (Py2). This will
change in a later release! File:
/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/_compile_test.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython2_2.7_pysam/build/tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator

/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/AlignmentFile_test.py:1459:
UserWarning: no BGZF EOF marker; file may be truncated
    ignore_truncation=True)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
======== 3 failed, 906 passed, 17 skipped, 2 warnings in 60.36 seconds =========
E: pybuild pybuild:338: test: plugin distutils failed with: exit code=1: cd
/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build;
python2.7 -m pytest tests
dh_auto_test: pybuild --test --test-pytest -i python{version} -p 2.7 returned
exit code 13
make[1]: *** [debian/rules:32: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.2+ds'
make: *** [debian/rules:24: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2