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"""Test functionalities of Geometric FBA."""
from typing import Callable, List
import numpy as np
import pandas as pd
import pytest
from cobra.core import Metabolite, Model, Reaction
from cobra.flux_analysis import geometric_fba
@pytest.fixture(scope="module")
def geometric_fba_model() -> 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
def test_geometric_fba_benchmark(
model: Model, benchmark: Callable, all_solvers: List[str]
) -> None:
"""Benchmark geometric_fba."""
model.solver = all_solvers
benchmark(geometric_fba, model, processes=1)
def test_geometric_fba(geometric_fba_model: Model, all_solvers: List[str]) -> None:
"""Test geometric_fba."""
geometric_fba_model.solver = all_solvers
geometric_fba_sol = geometric_fba(geometric_fba_model, processes=1)
expected = pd.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)
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