[Debian-med-packaging] Bug#972812: python-cobra: FTBFS with Python 3.9 as supported

[Graham Inggs]

Source: python-cobra
Version: 0.18.1-2
Severity: serious
Tags: ftbfs sid bullseye
User: debian-python at lists.debian.org
Usertags: python3.9

Hi Maintainer

Python-cobra FTBFS with Python 3.9 as a supported Python version.

I've copied what I hope is the relevant part of the log below.

Regards
Graham


[1] https://buildd.debian.org/status/package.php?p=python-cobra


________________________ ERROR collecting test session _________________________
/usr/lib/python3/dist-packages/_pytest/config/__init__.py:447: in
_importconftest
    return self._conftestpath2mod[conftestpath]
E   KeyError: local('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_cobra/build/cobra/test/conftest.py')

During handling of the above exception, another exception occurred:
/usr/lib/python3/dist-packages/_pytest/config/__init__.py:453: in
_importconftest
    mod = conftestpath.pyimport()
/usr/lib/python3/dist-packages/py/_path/local.py:704: in pyimport
    __import__(modname)
cobra/__init__.py:40: in <module>
    from cobra import io
cobra/io/__init__.py:8: in <module>
    from cobra.io.sbml import read_sbml_model, write_sbml_model, \
cobra/io/sbml.py:41: in <module>
    import libsbml
/usr/lib/python3/dist-packages/libsbml/libsbml.py:22: in <module>
    import _libsbml
E   ModuleNotFoundError: No module named '_libsbml'

During handling of the above exception, another exception occurred:
/usr/lib/python3/dist-packages/py/_path/common.py:383: in visit
    for x in Visitor(fil, rec, ignore, bf, sort).gen(self):
/usr/lib/python3/dist-packages/py/_path/common.py:435: in gen
    for p in self.gen(subdir):
/usr/lib/python3/dist-packages/py/_path/common.py:424: in gen
    dirs = self.optsort([p for p in entries
/usr/lib/python3/dist-packages/py/_path/common.py:425: in <listcomp>
    if p.check(dir=1) and (rec is None or rec(p))])
/usr/lib/python3/dist-packages/_pytest/main.py:667: in _recurse
    ihook = self.gethookproxy(dirpath)
/usr/lib/python3/dist-packages/_pytest/main.py:482: in gethookproxy
    my_conftestmodules = pm._getconftestmodules(fspath)
/usr/lib/python3/dist-packages/_pytest/config/__init__.py:431: in
_getconftestmodules
    mod = self._importconftest(conftestpath.realpath())
/usr/lib/python3/dist-packages/_pytest/config/__init__.py:470: in
_importconftest
    raise ConftestImportFailure(conftestpath, sys.exc_info())
E   _pytest.config.ConftestImportFailure:
(local('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_cobra/build/cobra/test/conftest.py'),
(<class 'ModuleNotFoundError'>, ModuleNotFoundError("No module named
'_libsbml'"), <traceback object at 0x7fdc96838fc0>))