"""Test functions of array.py."""
from typing import TYPE_CHECKING
import numpy as np
import pytest
from cobra.util import create_stoichiometric_matrix
if TYPE_CHECKING:
from cobra import Model
[docs]def test_dense_matrix(model: "Model") -> None:
"""Test dense stoichiometric matrix creation."""
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)
[docs]def test_sparse_matrix(model: "Model") -> None:
"""Test sparse stoichiometric matrix creation."""
pytest.importorskip("scipy")
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)