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In [1]:



    


import os
os.environ['PATH'] = os.environ['PATH']+':/project/projectdirs/metatlas/bin'
sys.path.insert(0,'/project/projectdirs/metatlas/anaconda/lib/python2.7/site-packages/')



    











In [2]:



    


from cobra.test import test_all
# from matplotlib import pyplot as plt
%matplotlib notebook
test_all()



    


















    






test_add_reaction (cobra.test.unit_tests.TestCobraArrayModel) ... ok
test_add_reaction_from_other_model (cobra.test.unit_tests.TestCobraArrayModel) ... ok
test_add_reaction_orphans (cobra.test.unit_tests.TestCobraArrayModel)
test reaction addition ... ok
test_array_based_model (cobra.test.unit_tests.TestCobraArrayModel) ... ok
test_array_based_model_add (cobra.test.unit_tests.TestCobraArrayModel) ... ok
test_array_based_select (cobra.test.unit_tests.TestCobraArrayModel) ... ok
test_change_objective (cobra.test.unit_tests.TestCobraArrayModel) ... ok
test_copy (cobra.test.unit_tests.TestCobraArrayModel)
modifying copy should not modify the original ... ok
test_deepcopy (cobra.test.unit_tests.TestCobraArrayModel)
Reference structures are maintained when deepcopying ... ok
test_model_remove_reaction (cobra.test.unit_tests.TestCobraArrayModel) ... ok
test_reaction_delete (cobra.test.unit_tests.TestCobraArrayModel) ... ok
test_reaction_remove (cobra.test.unit_tests.TestCobraArrayModel) ... ok
test_remove_gene (cobra.test.unit_tests.TestCobraArrayModel) ... ok
test_foruma_element_setting (cobra.test.unit_tests.TestCobraMetabolites) ... ok
test_metabolite_formula (cobra.test.unit_tests.TestCobraMetabolites) ... ok
test_add_reaction (cobra.test.unit_tests.TestCobraModel) ... ok
test_add_reaction_from_other_model (cobra.test.unit_tests.TestCobraModel) ... ok
test_add_reaction_orphans (cobra.test.unit_tests.TestCobraModel)
test reaction addition ... ok
test_change_objective (cobra.test.unit_tests.TestCobraModel) ... ok
test_copy (cobra.test.unit_tests.TestCobraModel)
modifying copy should not modify the original ... ok
test_deepcopy (cobra.test.unit_tests.TestCobraModel)
Reference structures are maintained when deepcopying ... ok
test_model_remove_reaction (cobra.test.unit_tests.TestCobraModel) ... ok
test_reaction_delete (cobra.test.unit_tests.TestCobraModel) ... ok
test_reaction_remove (cobra.test.unit_tests.TestCobraModel) ... ok
test_remove_gene (cobra.test.unit_tests.TestCobraModel) ... ok
testAdd (cobra.test.unit_tests.TestDictList) ... ok
testAppend (cobra.test.unit_tests.TestDictList) ... ok
testContains (cobra.test.unit_tests.TestDictList) ... ok
testCopy (cobra.test.unit_tests.TestDictList) ... ok
testDeepcopy (cobra.test.unit_tests.TestDictList) ... ok
testDir (cobra.test.unit_tests.TestDictList)
makes sure tab complete will work ... ok
testExtend (cobra.test.unit_tests.TestDictList) ... ok
testIadd (cobra.test.unit_tests.TestDictList) ... ok
testIndependent (cobra.test.unit_tests.TestDictList) ... ok
testIndex (cobra.test.unit_tests.TestDictList) ... ok
testInitCopy (cobra.test.unit_tests.TestDictList) ... ok
testInsert (cobra.test.unit_tests.TestDictList) ... ok
testPickle (cobra.test.unit_tests.TestDictList) ... ok
testQuery (cobra.test.unit_tests.TestDictList) ... ok
testRemoval (cobra.test.unit_tests.TestDictList) ... ok
testSet (cobra.test.unit_tests.TestDictList) ... ok
testSlice (cobra.test.unit_tests.TestDictList) ... ok
testSortandReverse (cobra.test.unit_tests.TestDictList) ... ok
testUnion (cobra.test.unit_tests.TestDictList) ... ok
testGPR (cobra.test.unit_tests.TestReactions) ... ok
testGPR_modification (cobra.test.unit_tests.TestReactions) ... ok
test_add (cobra.test.unit_tests.TestReactions) ... ok
test_add_metabolite (cobra.test.unit_tests.TestReactions) ... ok
test_build_from_string (cobra.test.unit_tests.TestReactions) ... ok
test_copy (cobra.test.unit_tests.TestReactions) ... ok
test_iadd (cobra.test.unit_tests.TestReactions) ... ok
test_mass_balance (cobra.test.unit_tests.TestReactions) ... ok
test_mul (cobra.test.unit_tests.TestReactions) ... ok
test_sub (cobra.test.unit_tests.TestReactions) ... ok
test_subtract_metabolite (cobra.test.unit_tests.TestReactions) ... ok
test_attributes (cobra.test.solvers.cglpkTester) ... ok
test_change_coefficient (cobra.test.solvers.cglpkTester) ... ok
test_creation (cobra.test.solvers.cglpkTester) ... ok
test_independent_creation (cobra.test.solvers.cglpkTester) ... ok
test_inequality (cobra.test.solvers.cglpkTester) ... ok
test_low_level_control (cobra.test.solvers.cglpkTester) ... ok
test_quadratic (cobra.test.solvers.cglpkTester) ... skipped 'no qp support'
test_set_objective_sense (cobra.test.solvers.cglpkTester) ... ok
test_solve_feasible (cobra.test.solvers.cglpkTester) ... ok
test_solve_infeasible (cobra.test.solvers.cglpkTester) ... ok
test_solve_minimize (cobra.test.solvers.cglpkTester) ... ok
test_solve_mip (cobra.test.solvers.cglpkTester) ... ok
test_double_gene_deletion (cobra.test.flux_analysis.TestCobraFluxAnalysis) ... ok
test_double_reaction_deletion (cobra.test.flux_analysis.TestCobraFluxAnalysis) ... ok
test_find_blocked_reactions (cobra.test.flux_analysis.TestCobraFluxAnalysis) ... ok
test_flux_variability (cobra.test.flux_analysis.TestCobraFluxAnalysis) ... ok
test_gapfilling (cobra.test.flux_analysis.TestCobraFluxAnalysis) ... ok
test_loopless (cobra.test.flux_analysis.TestCobraFluxAnalysis) ... ok
test_pFBA (cobra.test.flux_analysis.TestCobraFluxAnalysis) ... ok
test_phenotype_phase_plane (cobra.test.flux_analysis.TestCobraFluxAnalysis) ... 









    




















    
















    






ok
test_single_gene_deletion (cobra.test.flux_analysis.TestCobraFluxAnalysis) ... ok
test_single_reaction_deletion (cobra.test.flux_analysis.TestCobraFluxAnalysis) ... ok
test_summary_methods (cobra.test.flux_analysis.TestCobraFluxAnalysis) ... ok
test_read (cobra.test.io_tests.TestCobraIOPickle) ... ok
test_read_nonexistent (cobra.test.io_tests.TestCobraIOPickle) ... ok
test_write (cobra.test.io_tests.TestCobraIOPickle) ... ok
test_write_empty (cobra.test.io_tests.TestCobraIOPickle) ... ok
test_read (cobra.test.io_tests.TestCobraIOSBMLcobra) ... ok
test_read_nonexistent (cobra.test.io_tests.TestCobraIOSBMLcobra) ... ok
test_write (cobra.test.io_tests.TestCobraIOSBMLcobra) ... ok
test_write_empty (cobra.test.io_tests.TestCobraIOSBMLcobra) ... ok
test_read (cobra.test.io_tests.TestCobraIOSBMLfbc1) ... expected failure
test_read_nonexistent (cobra.test.io_tests.TestCobraIOSBMLfbc1) ... ok
test_write (cobra.test.io_tests.TestCobraIOSBMLfbc1) ... expected failure
test_write_empty (cobra.test.io_tests.TestCobraIOSBMLfbc1) ... ok
test_read (cobra.test.io_tests.TestCobraIOSBMLfbc2) ... ok
test_read_nonexistent (cobra.test.io_tests.TestCobraIOSBMLfbc2) ... ok
test_write (cobra.test.io_tests.TestCobraIOSBMLfbc2) ... ok
test_write_empty (cobra.test.io_tests.TestCobraIOSBMLfbc2) ... ok
test_read (cobra.test.io_tests.TestCobraIOSBMLfbc2Bz2) ... ok
test_read_nonexistent (cobra.test.io_tests.TestCobraIOSBMLfbc2Bz2) ... ok
test_write (cobra.test.io_tests.TestCobraIOSBMLfbc2Bz2) ... ok
test_write_empty (cobra.test.io_tests.TestCobraIOSBMLfbc2Bz2) ... ok
test_read (cobra.test.io_tests.TestCobraIOSBMLfbc2Gz) ... ok
test_read_nonexistent (cobra.test.io_tests.TestCobraIOSBMLfbc2Gz) ... ok
test_write (cobra.test.io_tests.TestCobraIOSBMLfbc2Gz) ... ok
test_write_empty (cobra.test.io_tests.TestCobraIOSBMLfbc2Gz) ... ok
test_read (cobra.test.io_tests.TestCobraIOcPickle) ... ok
test_read_nonexistent (cobra.test.io_tests.TestCobraIOcPickle) ... ok
test_write (cobra.test.io_tests.TestCobraIOcPickle) ... ok
test_write_empty (cobra.test.io_tests.TestCobraIOcPickle) ... ok
test_read (cobra.test.io_tests.TestCobraIOjson) ... ok
test_read_nonexistent (cobra.test.io_tests.TestCobraIOjson) ... ok
test_write (cobra.test.io_tests.TestCobraIOjson) ... ok
test_write_empty (cobra.test.io_tests.TestCobraIOjson) ... ok
test_read (cobra.test.io_tests.TestCobraIOmat) ... ok
test_read_nonexistent (cobra.test.io_tests.TestCobraIOmat) ... ok
test_write (cobra.test.io_tests.TestCobraIOmat) ... ok
test_write_empty (cobra.test.io_tests.TestCobraIOmat) ... ok
test_bad_valiation (cobra.test.io_tests.TestCobraSBMLValidation) ... ok
test_dual (cobra.test.design.TestDesignAlgorithms) ... ok
test_dual_integer_vars_as_lp (cobra.test.design.TestDesignAlgorithms) ... ok
test_dual_integer_vars_as_mip (cobra.test.design.TestDesignAlgorithms) ... ok
test_optknock (cobra.test.design.TestDesignAlgorithms) ... ok
test_SBO_annotation (cobra.test.manipulation.TestManipulation) ... ok
test_canonical_form (cobra.test.manipulation.TestManipulation) ... ok
test_canonical_form_minimize (cobra.test.manipulation.TestManipulation) ... ok
test_escape_ids (cobra.test.manipulation.TestManipulation) ... ok
test_gene_knockout_computation (cobra.test.manipulation.TestManipulation) ... ok
test_modify_reversible (cobra.test.manipulation.TestManipulation) ... ok
test_remove_genes (cobra.test.manipulation.TestManipulation) ... ok
test_validate_formula_compartment (cobra.test.manipulation.TestManipulation) ... ok
test_validate_mass_balance (cobra.test.manipulation.TestManipulation) ... ok
test_validate_reaction_bounds (cobra.test.manipulation.TestManipulation) ... ok

----------------------------------------------------------------------
Ran 129 tests in 6.579s

OK (skipped=1, expected failures=2)










    
Out[2]:








False

Documentation

https://cobrapy.readthedocs.io/en/stable/index.html





In [ ]:

Specifying a solver

/ https://cobrapy.readthedocs.io/en/stable/solvers.html





In [ ]:

Content source: metabolite-atlas/metatlas

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