[Debian-med-packaging] Bug#912586: python-cobra still fails it's autopkg tests

[Andreas Tille]

Control: tags -1 help

Hi,

I tried to find the reason for the autopkgtest failure.  It is running
the same tests as on build time.  These tests are fine:

cobra/test/test_manipulation.py ...........                              [ 14%]
cobra/test/test_medium.py ..............                                 [ 32%]
cobra/test/test_io/test_io_order.py ...........................          [ 68%]
cobra/test/test_io/test_json.py x.x                                      [ 72%]
cobra/test/test_io/test_mat.py ss                                        [ 75%]
cobra/test/test_io/test_pickle.py .s.s                                   [ 80%]
cobra/test/test_io/test_sbml.py sss                                      [ 84%]
cobra/test/test_io/test_sbml3.py ..........                              [ 97%]
cobra/test/test_io/test_yaml.py .x                                       [100%]


However, if I install python3-cobra on my local machine and do

   cd python-cobra/debian/tests/
   make py3-test | grep -i fail
../../cobra/test/test_io/test_json.py::test_validate_json <- ../../../../../../usr/lib/python3/dist-packages/cobra/test/test_io/test_json.py xfail [ 69%]
../../cobra/test/test_io/test_json.py::test_save_json_model <- ../../../../../../usr/lib/python3/dist-packages/cobra/test/test_io/test_json.py xfail [ 72%]
../../cobra/test/test_io/test_yaml.py::test_save_yaml_model <- ../../../../../../usr/lib/python3/dist-packages/cobra/test/test_io/test_yaml.py xfail [100%]
=============== 64 passed, 9 skipped, 3 xfailed in 14.10 seconds ===============

I checked the relevant test sources


$ grep -B1 -A3 test_validate_json cobra/test/test_io/test_json.py 
@pytest.mark.xfail(reason="schema outdated")
def test_validate_json(data_directory):
    """Validate file according to JSON-schema."""
    jsonschema = pytest.importorskip("jsonschema")
    with open(join(data_directory, "mini.json"),
$ grep -B1 -A3 test_save_json_model cobra/test/test_io/test_json.py 
@pytest.mark.xfail(reason="schema outdated")
def test_save_json_model(tmpdir, mini_model):
    """Test the writing of JSON model."""
    jsonschema = pytest.importorskip("jsonschema")
    output_file = tmpdir.join("mini.json")
$ grep -B1 -A3 test_save_yaml_model cobra/test/test_io/test_yaml.py 
@pytest.mark.xfail(reason="schema outdated")
def test_save_yaml_model(tmpdir, mini_model):
    jsonschema = pytest.importorskip("jsonschema")
    """Test the writing of YAML model."""
    output_file = tmpdir.join("mini.yml")


all test failures seem to be caused by outdated schemas.  Unfortunately
I have no idea what schema is searched for and why it is valid at package
build time while outdated on installed machine.

I somehow suspect that the problem is

  jsonschema = pytest.importorskip("jsonschema")

which is unique to all these three failing tests (and does not occure in
any other test).

Does anybody have a clue?

Kind regards

       Andreas.

-- 
http://fam-tille.de