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"""Test functionalities of flux sampling methods."""
import os
import numpy as np
import pytest
from cobra.core import Metabolite, Model, Reaction
from cobra.flux_analysis.parsimonious import pfba
from cobra.sampling import ACHRSampler, OptGPSampler, sample
def test_single_achr(model: Model) -> None:
"""Test ACHR sampling (one sample)."""
s = sample(model, 10, method="achr")
assert s.shape == (10, len(model.reactions))
def test_single_optgp(model: Model) -> None:
"""Test OptGP sampling (one sample)."""
s = sample(model, 10, processes=1)
assert s.shape == (10, len(model.reactions))
@pytest.mark.skipif("SKIP_MP" in os.environ, reason="unsafe for parallel execution")
def test_multi_optgp(model: Model) -> None: # pragma: no cover
"""Test OptGP sampling (multi sample)."""
s = sample(model, 10, processes=2)
assert s.shape == (10, len(model.reactions))
def test_wrong_method(model: Model) -> None:
"""Test method intake sanity."""
with pytest.raises(ValueError):
sample(model, 1, method="schwupdiwupp")
def test_fixed_seed(model: Model) -> None:
"""Test result of fixed seed for sampling."""
s1 = sample(model, 1, seed=42)
s2 = sample(model, 1, seed=42)
assert np.isclose(s1.TPI[0], s2.TPI[0])
def test_equality_constraint(model: Model) -> None:
"""Test equality constraint."""
model.reactions.ACALD.bounds = (-1.5, -1.5)
s = sample(model, 10)
assert np.allclose(s.ACALD, -1.5, atol=1e-6, rtol=0)
s = sample(model, 10, method="achr")
assert np.allclose(s.ACALD, -1.5, atol=1e-6, rtol=0)
def test_inequality_constraint(model: Model) -> None:
"""Test inequality constraint."""
co = model.problem.Constraint(model.reactions.ACALD.flux_expression, lb=-0.5)
model.add_cons_vars(co)
s = sample(model, 10)
assert all(s.ACALD > -0.5 - 1e-6)
s = sample(model, 10, method="achr")
assert all(s.ACALD > -0.5 - 1e-6)
def test_inhomogeneous_sanity(model: Model) -> None:
"""Test standard deviation between inhomogeneous and homogeneous sampling."""
model.reactions.ACALD.bounds = (-1.5, -1.5)
s_inhom = sample(model, 64)
model.reactions.ACALD.bounds = (-1.5 - 1e-3, -1.5 + 1e-3)
s_hom = sample(model, 64)
relative_diff = (s_inhom.std() + 1e-12) / (s_hom.std() + 1e-12)
assert 0.5 < relative_diff.abs().mean() < 2
model.reactions.ACALD.bounds = (-1.5, -1.5)
s_inhom = sample(model, 64, method="achr")
model.reactions.ACALD.bounds = (-1.5 - 1e-3, -1.5 + 1e-3)
s_hom = sample(model, 64, method="achr")
relative_diff = (s_inhom.std() + 1e-12) / (s_hom.std() + 1e-12)
assert 0.5 < relative_diff.abs().mean() < 2
def test_complicated_model() -> None:
"""Test a complicated model.
Difficult model since the online mean calculation is numerically
unstable, so many samples weakly violate the equality constraints.
"""
model = Model("flux_split")
reaction1 = Reaction("V1")
reaction2 = Reaction("V2")
reaction3 = Reaction("V3")
reaction1.bounds = (0, 6)
reaction2.bounds = (0, 8)
reaction3.bounds = (0, 10)
A = Metabolite("A")
reaction1.add_metabolites({A: -1})
reaction2.add_metabolites({A: -1})
reaction3.add_metabolites({A: 1})
model.add_reactions([reaction1, reaction2, reaction3])
optgp = OptGPSampler(model, 1, seed=42)
achr = ACHRSampler(model, seed=42)
optgp_samples = optgp.sample(100)
achr_samples = achr.sample(100)
assert any(optgp_samples.corr().abs() < 1.0)
assert any(achr_samples.corr().abs() < 1.0)
# > 95% are valid
assert sum(optgp.validate(optgp_samples) == "v") > 95
assert sum(achr.validate(achr_samples) == "v") > 95
def test_single_point_space(model: Model) -> None:
"""Test the reduction of the sampling space to one point."""
pfba_sol = pfba(model)
pfba_const = model.problem.Constraint(
sum(model.variables), ub=pfba_sol.objective_value
)
model.add_cons_vars(pfba_const)
model.reactions.Biomass_Ecoli_core.lower_bound = pfba_sol.fluxes.Biomass_Ecoli_core
with pytest.raises(ValueError):
sample(model, 1)
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