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"""Test functionalities of minimal medium creation and analysis."""
from typing import Callable
import pandas as pd
import pytest
from cobra.core import Model, Reaction
from cobra.medium import minimal_medium
def test_minimal_medium_linear(model: Model) -> None:
"""Test linear minimal medium."""
med = minimal_medium(model, 0.8)
assert len(med) <= 4
assert all(med > 1e-6)
def test_minimal_medium_linear_benchmark(model: Model, benchmark: Callable) -> None:
"""Benchmark linear minimal medium."""
benchmark(minimal_medium, model, 0.8)
def test_minimal_medium_mip(model: Model) -> None:
"""Test mixed-integer minimal medium."""
med = minimal_medium(model, 0.8, minimize_components=True)
assert len(med) <= 4
assert all(med > 1e-6)
# Anaerobic growth
med = minimal_medium(model, 0.1, minimize_components=True)
assert len(med) <= 3
assert all(med > 1e-6)
def test_minimal_medium_mip_benchmark(model: Model, benchmark: Callable) -> None:
"""Benchmark mixed-integer minimal medium."""
benchmark(minimal_medium, model, 0.8, True)
def test_minimal_medium_alternative_mip(model: Model) -> None:
"""Test alternative mixed-integer minimal medium."""
med = minimal_medium(model, 0.8, minimize_components=5, open_exchanges=True)
assert isinstance(med, pd.DataFrame)
assert med.shape[0] >= 5
assert med.shape[1] == 5
assert all((med > 0).sum() == 3)
assert all(med.sum(axis=1) > 1e-6)
def test_minimal_medium_exports(model: Model) -> None:
"""Test exports of a minimal medium."""
med = minimal_medium(model, 0.8, exports=True, minimize_components=True)
assert len(med) > 4
assert any(med < -1e-6)
def test_minimal_medium_open_exchanges(model: Model) -> None:
"""Test open exchanges of a minimal medium."""
model.reactions.EX_glc__D_e.bounds = 0, 0
med = minimal_medium(model, 0.8)
assert med is None
med = minimal_medium(model, 0.8, minimize_components=True)
assert med is None
med = minimal_medium(model, 0.8, open_exchanges=True)
assert len(med) >= 3
med = minimal_medium(model, 0.8, open_exchanges=100)
assert len(med) >= 3
def test_model_medium(model: Model) -> None:
"""Test proper functioning of model medium manipulations."""
# Add a dummy 'malformed' import reaction
bad_import = Reaction("bad_import")
bad_import.add_metabolites({model.metabolites.pyr_c: 1})
bad_import.bounds = (0, 42)
model.add_reactions([bad_import])
# Test basic setting and getting methods
medium = model.medium
model.medium = medium
assert model.medium == medium
# Test context management
with model:
# Ensure the bounds are correct beforehand
assert model.reactions.EX_glc__D_e.lower_bound == -10
assert model.reactions.bad_import.upper_bound == 42
assert model.reactions.EX_co2_e.lower_bound == -1000
# Make changes to the media
new_medium = model.medium
new_medium["EX_glc__D_e"] = 20
new_medium["bad_import"] = 24
del new_medium["EX_co2_e"]
# Change the medium, make sure changes work
model.medium = new_medium
assert model.reactions.EX_glc__D_e.lower_bound == -20
assert model.reactions.bad_import.upper_bound == 24
assert model.reactions.EX_co2_e.lower_bound == 0
# Make sure changes revert after the contex
assert model.reactions.EX_glc__D_e.lower_bound == -10
assert model.reactions.bad_import.upper_bound == 42
assert model.reactions.EX_co2_e.lower_bound == -1000
new_medium["bogus_rxn"] = 0
with pytest.raises(KeyError):
model.medium = new_medium
def test_medium_does_not_affect_reactant_exports(model: Model) -> None:
"""Test that the medium setter does not overwrite exports defined as reactants."""
med = model.medium
# Set a fixed export rate
model.reactions.EX_ac_e.lower_bound = 0.1
model.medium = med
assert model.reactions.EX_ac_e.lower_bound == 0.1
# should be overwritten if actually in the medium
med["EX_ac_e"] = 1
model.medium = med
assert model.reactions.EX_ac_e.lower_bound == -1
def test_medium_does_not_affect_product_exports(model: Model) -> None:
"""Test that the medium setter does not overwrite exports defined as products."""
med = model.medium
# Reverse reaction definition
model.reactions.EX_ac_e *= -1
# Set a fixed export rate
model.reactions.EX_ac_e.bounds = -1, -0.1
model.medium = med
assert model.reactions.EX_ac_e.bounds == (-1, -0.1)
# should be overwritten if actually in the medium
med["EX_ac_e"] = 1
model.medium = med
assert model.reactions.EX_ac_e.upper_bound == 1
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