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"""Unit test the model summary."""
import pytest
from cobra.flux_analysis import flux_variability_analysis, pfba
from cobra.summary import ModelSummary
def test_model_summary_interface(model, opt_solver):
"""Test that a summary can be created successfully."""
model.solver = opt_solver
ModelSummary(
model=model,
)
ModelSummary(
model=model,
solution=pfba(model),
)
ModelSummary(
model=model,
fva=0.95,
)
ModelSummary(
model=model,
fva=flux_variability_analysis(
model, reaction_list=["CYTBD", "NADH16", "SUCDi"]
),
)
def test_model_summary_to_frame(model, opt_solver):
"""Test that the summary's method ``to_frame`` can be called."""
model.solver = opt_solver
summary = model.summary()
summary.to_frame()
@pytest.mark.parametrize(
"kwargs",
[
{},
{"names": True},
{"float_format": ".1f"},
{"threshold": 1e-2},
{"column_width": 20},
],
)
def test_model_summary_to_string(model, opt_solver, kwargs):
"""Test that the summary's method ``to_string`` can be called."""
model.solver = opt_solver
summary = model.summary()
summary.to_string(**kwargs)
@pytest.mark.parametrize(
"kwargs", [{}, {"names": True}, {"float_format": ".1f"}, {"threshold": 1e-2}]
)
def test_model_summary_to_html(model, opt_solver, kwargs):
"""Test that the summary's method ``to_html`` can be called."""
model.solver = opt_solver
summary = model.summary()
summary.to_html(**kwargs)
def test_model_summary_to_frame_previous_solution(model, opt_solver):
"""Test that the summary correctly uses an existing solution."""
model.solver = opt_solver
solution = pfba(model)
rxn = model.reactions.EX_glc__D_e
solution.fluxes[rxn.id] = -123
summary = model.summary(solution=solution)
assert summary.to_frame().at[rxn.id, "flux"] == 123
def test_model_summary_flux(model, opt_solver):
"""Test that the summary has expected fluxes."""
model.solver = opt_solver
summary = model.summary()
assert summary.uptake_flux.at["EX_o2_e", "flux"] == pytest.approx(21.8, abs=1e-02)
assert summary.secretion_flux.at["EX_h2o_e", "flux"] == pytest.approx(
-29.18, abs=1e-02
)
def test_model_summary_fva(model, opt_solver):
"""Test that the exchange summary is within expected bounds."""
model.solver = opt_solver
summary = model.summary(fva=0.95)
assert summary.to_frame().at["EX_o2_e", "flux"] == pytest.approx(21.8, abs=1e-02)
assert summary.to_frame().at["EX_o2_e", "minimum"] == pytest.approx(19.9, abs=1e-02)
assert summary.to_frame().at["EX_o2_e", "maximum"] == pytest.approx(
23.71, abs=1e-02
)
assert summary.to_frame().at["EX_h2o_e", "flux"] == pytest.approx(-29.18, abs=1e-02)
assert summary.to_frame().at["EX_h2o_e", "minimum"] == pytest.approx(
-30.72, abs=1e-02
)
assert summary.to_frame().at["EX_h2o_e", "maximum"] == pytest.approx(-25, abs=1e-02)
def test_model_summary_flux_in_context(model, opt_solver):
"""Test that the model summary inside and outside of a context are equal."""
model.solver = opt_solver
copy = model.copy()
with model:
model.reactions.EX_glc__D_e.bounds = (0, 1000)
model.reactions.EX_ac_e.bounds = (-10, 1000)
context_summary = model.summary()
copy.reactions.EX_glc__D_e.bounds = (0, 1000)
copy.reactions.EX_ac_e.bounds = (-10, 1000)
outside_summary = copy.summary()
assert context_summary.to_frame()["flux"].values == pytest.approx(
outside_summary.to_frame()["flux"].values, abs=model.tolerance
)
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