Source code for test_geometric

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

"""Test functionalities of Geometric FBA."""

from __future__ import absolute_import

import numpy as np
import pytest
from pandas import Series

from cobra.core import Metabolite, Model, Reaction, Solution
from cobra.flux_analysis import geometric_fba


@pytest.fixture(scope="module")
[docs]def geometric_fba_model(): """ Generate geometric FBA model as described in [1]_ References ---------- .. [1] Smallbone, Kieran & Simeonidis, Vangelis. (2009). Flux balance analysis: A geometric perspective. Journal of theoretical biology.258. 311-5. 10.1016/j.jtbi.2009.01.027. """ test_model = Model('geometric_fba_paper_model') test_model.add_metabolites(Metabolite('A')) test_model.add_metabolites(Metabolite('B')) v_1 = Reaction('v1', upper_bound=1.0) v_1.add_metabolites({test_model.metabolites.A: 1.0}) v_2 = Reaction('v2', lower_bound=-1000.0) v_2.add_metabolites({test_model.metabolites.A: -1.0, test_model.metabolites.B: 1.0}) v_3 = Reaction('v3', lower_bound=-1000.0) v_3.add_metabolites({test_model.metabolites.A: -1.0, test_model.metabolites.B: 1.0}) v_4 = Reaction('v4', lower_bound=-1000.0) v_4.add_metabolites({test_model.metabolites.A: -1.0, test_model.metabolites.B: 1.0}) v_5 = Reaction('v5') v_5.add_metabolites({test_model.metabolites.A: 0.0, test_model.metabolites.B: -1.0}) test_model.add_reactions([v_1, v_2, v_3, v_4, v_5]) test_model.objective = 'v5' return test_model
[docs]def test_geometric_fba_benchmark(model, benchmark, all_solvers): """Benchmark geometric_fba.""" model.solver = all_solvers benchmark(geometric_fba, model, processes=1)
[docs]def test_geometric_fba(geometric_fba_model, all_solvers): """Test geometric_fba.""" geometric_fba_model.solver = all_solvers geometric_fba_sol = geometric_fba(geometric_fba_model, processes=1) expected = Series({'v1': 1.0, 'v2': 0.33, 'v3': 0.33, 'v4': 0.33, 'v5': 1.0}, index=['v1', 'v2', 'v3', 'v4', 'v5']) assert np.allclose(geometric_fba_sol.fluxes, expected, atol=1E-02)