[Debian-med-packaging] Bug#950929: python-biom-format: FTBFS with pandas 1.0: test failures

[Andreas Tille]

Hi,

while upstream has closed the according issue #837 I was running into a
different error which is not connected to pandas but probably connected
to the change of the test framework (python3-pytest was requested).  When
trying to build I was running into

...
   dh_auto_test -O--buildsystem=pybuild
        pybuild --test --test-pytest -i python{version} -p "3.9 3.8"
I: pybuild pybuild:284: cp -r /build/python-biom-format-2.1.9/examples /build/python-biom-format-2.1.9/.pybuild/cpython3_3.9_biom-format/build
I: pybuild base:232: cd /build/python-biom-format-2.1.9/.pybuild/cpython3_3.9_biom-format/build; python3.9 -m pytest 
ERROR: usage: pytest.py [options] [file_or_dir] [file_or_dir] [...]
pytest.py: error: unrecognized arguments: --cov=biom
  inifile: /build/python-biom-format-2.1.9/pytest.ini
  rootdir: /build/python-biom-format-2.1.9

E: pybuild pybuild:353: test: plugin distutils failed with: exit code=4: cd /build/python-biom-format-2.1.9/.pybuild/cpython3_3.9_biom-format/build; python3.9 -m pytest 
I: pybuild pybuild:284: cp -r /build/python-biom-format-2.1.9/examples /build/python-biom-format-2.1.9/.pybuild/cpython3_3.8_biom-format/build
I: pybuild base:232: cd /build/python-biom-format-2.1.9/.pybuild/cpython3_3.8_biom-format/build; python3.8 -m pytest 
ERROR: usage: pytest.py [options] [file_or_dir] [file_or_dir] [...]
pytest.py: error: unrecognized arguments: --cov=biom
  inifile: /build/python-biom-format-2.1.9/pytest.ini
  rootdir: /build/python-biom-format-2.1.9

E: pybuild pybuild:353: test: plugin distutils failed with: exit code=4: cd /build/python-biom-format-2.1.9/.pybuild/cpython3_3.8_biom-format/build; python3.8 -m pytest 
        rm -fr -- /tmp/dh-xdg-rundir-cbDKiY_1
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.9 3.8" returned exit code 13
make: *** [debian/rules:19: binary] Error 25


Any help is welcome - feel free to upload yourself if you
find a fix

    Andreas.

[1] https://github.com/biocore/biom-format/issues/837

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