Test failure

[smoretti]

Hi

I have issues while running python setup.py test, with glpksol in the $PATH:
An idea?

Regards

running test
running egg_info
writing requirements to gim3e.egg-info/requires.txt
writing gim3e.egg-info/PKG-INFO
writing top-level names to gim3e.egg-info/top_level.txt
writing dependency_links to gim3e.egg-info/dependency_links.txt
reading manifest file 'gim3e.egg-info/SOURCES.txt'
writing manifest file 'gim3e.egg-info/SOURCES.txt'
running build_ext
/software/lib64/python2.7/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
test_convert_objective_to_constraint (gim3e.test.unit_tests.TestGim3eCore) ... ERROR
test_convert_to_irreversible (gim3e.test.unit_tests.TestGim3eCore) ... cobra/core/Reaction.py:192 UserWarning: Setting reaction reversibility is ignored
ERROR
test_evaluate_penalties (gim3e.test.unit_tests.TestGim3eCore) ... ERROR
test_irreversible_flux_variability_analysis (gim3e.test.unit_tests.TestGim3eCore) ... ERROR
test_optimize_turnover_metabolite (gim3e.test.unit_tests.TestGim3eCore) ... ERROR
test_solve_feasible (gim3e.test.unit_tests.TestGim3eCore) ... ERROR
test_solve_milp_feasible (gim3e.test.unit_tests.TestGim3eCore) ... ERROR

ERROR: test_convert_objective_to_constraint (gim3e.test.unit_tests.TestGim3eCore)

Traceback (most recent call last):
File "/builddir/build/BUILD/gim3e-master/gim3e/test/unit_tests.py", line 156, in test_convert_objective_to_constraint
tolerance_integer = gim3e.integer_tolerances[the_solver]
KeyError: None

ERROR: test_convert_to_irreversible (gim3e.test.unit_tests.TestGim3eCore)

Traceback (most recent call last):
File "/builddir/build/BUILD/gim3e-master/gim3e/test/unit_tests.py", line 131, in test_convert_to_irreversible
gene_from_reaction = [x.id for x in the_reaction.get_gene()]
AttributeError: 'Reaction' object has no attribute 'get_gene'

ERROR: test_evaluate_penalties (gim3e.test.unit_tests.TestGim3eCore)

Traceback (most recent call last):
File "/builddir/build/BUILD/gim3e-master/gim3e/test/unit_tests.py", line 212, in test_evaluate_penalties
tolerance_integer = gim3e.integer_tolerances[the_solver]
KeyError: None

ERROR: test_irreversible_flux_variability_analysis (gim3e.test.unit_tests.TestGim3eCore)

Traceback (most recent call last):
File "/builddir/build/BUILD/gim3e-master/gim3e/test/unit_tests.py", line 187, in test_irreversible_flux_variability_analysis
tolerance_integer = gim3e.integer_tolerances[the_solver]
KeyError: None

ERROR: test_optimize_turnover_metabolite (gim3e.test.unit_tests.TestGim3eCore)

Traceback (most recent call last):
File "/builddir/build/BUILD/gim3e-master/gim3e/test/unit_tests.py", line 92, in test_optimize_turnover_metabolite
tolerance_integer = gim3e.integer_tolerances[the_solver]
KeyError: None

ERROR: test_solve_feasible (gim3e.test.unit_tests.TestGim3eCore)

Traceback (most recent call last):
File "/builddir/build/BUILD/gim3e-master/gim3e/test/unit_tests.py", line 55, in test_solve_feasible
tolerance_integer = gim3e.integer_tolerances[the_solver]
KeyError: None

ERROR: test_solve_milp_feasible (gim3e.test.unit_tests.TestGim3eCore)

Traceback (most recent call last):
File "/builddir/build/BUILD/gim3e-master/gim3e/test/unit_tests.py", line 73, in test_solve_milp_feasible
tolerance_integer = gim3e.integer_tolerances[the_solver]
KeyError: None

---

Ran 7 tests in 1.929s

FAILED (errors=7)
No working solvers detected.
No working solvers detected.
No working solvers detected.
No working solvers detected.
No working solvers detected.
No working solvers detected.

Python 2.7.5
COBRApy 0.4.1
glpk 4.59.1