[Debian-med-packaging] Bug#978032: python-cobra: autopkgtest regression in testing

[Andreas Tille]

Hi Adrian,

On Mon, Jan 25, 2021 at 12:07:27AM +0200, Adrian Bunk wrote:
> > ______________ ERROR at setup of TestManipulation.test_escape_ids ______________
> > 
> > filename = '/usr/lib/python3/dist-packages/cobra/test/data/textbook.xml.gz'
> > number = <class 'float'>
> > f_replace = {'F_GENE': <function _f_gene at 0x7f75f8c3cc10>,
> > 'F_GENE_REV': <function _f_gene_rev at 0x7f75f8c3cca0>, 'F_GROUP':
> > <function _f_group at 0x7f75f8c3cf70>, 'F_GROUP_REV': <function
> > _f_group_rev at 0x7f75f8531040>, ...}
> > kwargs = {}
> > doc = <libsbml.SBMLDocument; proxy of <Swig Object of type
> > 'SBMLDocument *' at 0x7f75f402cc60> >
> > cobra_error = CobraSBMLError('Something went wrong reading the SBML
> > model. Most likely the SBML model is not valid. Please check
> > tha...ame)`\nIf the model is valid and cannot be read please open an
> > issue at https://github.com/opencobra/cobrapy/issues .')
> 
> This is also a FTBFS.
> 
> Trying to upgrade to 0.20.0 for checking whether that would help:
> After some minor adjustments the first blocker is missing
> diskcache (#940625).

I've pushed a (not fully functional - cheating in dh_auto_test for the
moment) packaging for diskcache[1] (will try to fix that test issue soon
and upload to new).  Unfortunately with the updated python-cobra I get
lots of mostly sbml related errors.  The summary is

=========================== short test summary info ============================
FAILED cobra/test/test_manipulation.py::TestManipulation::test_remove_genes
ERROR cobra/test/test_manipulation.py::TestManipulation::test_escape_ids - co...
ERROR cobra/test/test_manipulation.py::TestManipulation::test_rename_gene - c...
ERROR cobra/test/test_manipulation.py::TestManipulation::test_gene_knockout_computation
ERROR cobra/test/test_manipulation.py::TestManipulation::test_sbo_annotation
ERROR cobra/test/test_manipulation.py::TestManipulation::test_validate_formula_compartment
ERROR cobra/test/test_manipulation.py::TestManipulation::test_validate_mass_balance
ERROR cobra/test/test_manipulation.py::TestManipulation::test_prune_unused_mets_output_type
ERROR cobra/test/test_manipulation.py::TestManipulation::test_prune_unused_mets_functionality
ERROR cobra/test/test_manipulation.py::TestManipulation::test_prune_unused_rxns_output_type
ERROR cobra/test/test_manipulation.py::TestManipulation::test_prune_unused_rxns_functionality
ERROR cobra/test/test_medium.py::TestModelMedium::test_model_medium - cobra.i...
ERROR cobra/test/test_medium.py::TestTypeDetection::test_external_compartment
ERROR cobra/test/test_medium.py::TestTypeDetection::test_multi_external - cob...
ERROR cobra/test/test_medium.py::TestTypeDetection::test_exchange - cobra.io....
ERROR cobra/test/test_medium.py::TestTypeDetection::test_demand - cobra.io.sb...
ERROR cobra/test/test_medium.py::TestTypeDetection::test_sink - cobra.io.sbml...
ERROR cobra/test/test_medium.py::TestTypeDetection::test_sbo_terms - cobra.io...
ERROR cobra/test/test_medium.py::TestMinimalMedia::test_medium_linear - cobra...
ERROR cobra/test/test_medium.py::TestMinimalMedia::test_medium_mip - cobra.io...
ERROR cobra/test/test_medium.py::TestMinimalMedia::test_medium_alternative_mip
ERROR cobra/test/test_medium.py::TestMinimalMedia::test_benchmark_medium_linear
ERROR cobra/test/test_medium.py::TestMinimalMedia::test_benchmark_medium_mip
ERROR cobra/test/test_medium.py::TestMinimalMedia::test_medium_exports - cobr...
ERROR cobra/test/test_medium.py::TestMinimalMedia::test_open_exchanges - cobr...
ERROR cobra/test/test_medium.py::TestErrorsAndExceptions::test_no_boundary_reactions
ERROR cobra/test/test_medium.py::TestErrorsAndExceptions::test_no_names_or_boundary_reactions
ERROR cobra/test/test_medium.py::TestErrorsAndExceptions::test_bad_exchange
=================== 1 failed, 5 warnings, 27 errors in 4.09s ===================
E: pybuild pybuild:353: test: plugin distutils failed with: exit code=1: cd /build/python-cobra-0.20.0/.pybuild/cpython3_3.9_cobra/build; python3.9 -m pytest 


I'm not sure whether this is related to libsbml 5.19 upgrade (I admit I failed to
realise that upgrading libsbml might mean a transition since I lived under the
impression that libsbml has no rdepends. :-()  I will ask cobra upstream about
this.

Kind regards

       Andreas.


[1]  https://salsa.debian.org/python-team/packages/diskcache

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