Source code for cobra.test

# -*- coding: utf-8 -*-

from __future__ import absolute_import

from os.path import abspath, dirname, join

from import read_sbml_model

    import pytest
    import pytest_benchmark
except ImportError:
[docs] pytest = None
try: from cPickle import load as _load except ImportError: from pickle import load as _load
[docs]cobra_directory = abspath(join(dirname(abspath(__file__)), ".."))
[docs]cobra_location = abspath(join(cobra_directory, ".."))
[docs]data_dir = join(cobra_directory, "test", "data", "")
[docs]def create_test_model(model_name="salmonella"): """Returns a cobra model for testing model_name: str One of 'ecoli', 'textbook', or 'salmonella', or the path to a pickled cobra.Model """ if model_name == "ecoli": ecoli_sbml = join(data_dir, "iJO1366.xml.gz") return read_sbml_model(ecoli_sbml) elif model_name == "textbook": textbook_sbml = join(data_dir, "textbook.xml.gz") return read_sbml_model(textbook_sbml) elif model_name == "mini": mini_sbml = join(data_dir, "mini_fbc2.xml") return read_sbml_model(mini_sbml) elif model_name == "salmonella": salmonella_pickle = join(data_dir, "salmonella.pickle") model_name = salmonella_pickle with open(model_name, "rb") as infile: return _load(infile)
[docs]def test_all(args=None): """alias for running all unit-tests on installed cobra""" if pytest: args = args if args else [] return pytest.main( ["--pyargs", "cobra", "--benchmark-skip", "-v", "-rs"] + args ) else: raise ImportError( "missing package pytest and pytest_benchmark" " required for testing"