Source code for test_array

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

"""Test functions of array.py"""

from __future__ import absolute_import

import numpy as np
import pytest

from cobra.util import create_stoichiometric_matrix


try:
    import scipy
except ImportError:
[docs] scipy = None
[docs]def test_dense_matrix(model): S = create_stoichiometric_matrix(model, array_type='dense', dtype=int) assert S.dtype == int assert np.allclose(S.max(), [59]) S_df = create_stoichiometric_matrix( model, array_type='DataFrame', dtype=int) assert S_df.values.dtype == int assert np.all(S_df.columns == [r.id for r in model.reactions]) assert np.all(S_df.index == [m.id for m in model.metabolites]) assert np.allclose(S_df.values, S) S = create_stoichiometric_matrix(model, array_type='dense', dtype=float) solution = model.optimize() mass_balance = S.dot(solution.fluxes) assert np.allclose(mass_balance, 0)
@pytest.mark.skipif(not scipy, reason='Sparse array methods require scipy')
[docs]def test_sparse_matrix(model): sparse_types = ['dok', 'lil'] solution = model.optimize() for sparse_type in sparse_types: S = create_stoichiometric_matrix(model, array_type=sparse_type) mass_balance = S.dot(solution.fluxes) assert np.allclose(mass_balance, 0)