# -*- coding: utf-8 -*-
from __future__ import absolute_import
from os.path import abspath, dirname, join
from cobra.io import read_sbml_model
try:
import pytest
import pytest_benchmark
except ImportError:
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"
)