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"""Unit test the ReactionSummary class."""
import pytest
from cobra.flux_analysis import flux_variability_analysis, pfba
from cobra.summary import ReactionSummary
def test_reaction_summary_interface(model, opt_solver):
"""Test that a summary can be created successfully."""
model.solver = opt_solver
reaction = model.reactions.get_by_id("FUM")
ReactionSummary(
reaction=reaction,
model=model,
)
ReactionSummary(
reaction=reaction,
model=model,
solution=pfba(model),
)
ReactionSummary(
reaction=reaction,
model=model,
fva=0.95,
)
ReactionSummary(
reaction=reaction,
model=model,
fva=flux_variability_analysis(model, reaction_list=["FUM"]),
)
def test_reaction_summary_to_frame(model, opt_solver):
"""Test that the summary's method ``to_frame`` can be called."""
model.solver = opt_solver
summary = model.reactions.get_by_id("FUM").summary()
summary.to_frame()
@pytest.mark.parametrize(
"kwargs",
[
{},
{"names": True},
{"float_format": ".1f"},
{"threshold": 1e-2},
{"column_width": 20},
],
)
def test_reaction_summary_to_string(model, opt_solver, kwargs):
"""Test that the summary's method ``to_string`` can be called."""
model.solver = opt_solver
summary = model.reactions.get_by_id("FUM").summary()
summary.to_string(**kwargs)
@pytest.mark.parametrize(
"kwargs", [{}, {"names": True}, {"float_format": ".1f"}, {"threshold": 1e-2}]
)
def test_reaction_summary_to_html(model, opt_solver, kwargs):
"""Test that the summary's method ``to_html`` can be called."""
model.solver = opt_solver
summary = model.reactions.get_by_id("FUM").summary()
summary.to_html(**kwargs)
@pytest.mark.parametrize(
"reaction_id, expected", [("ACALD", 0.0), ("FUM", 5.06), ("PFK", 7.48)]
)
def test_reaction_summary_flux(model, reaction_id: str, expected: float) -> None:
"""Test that the reported flux in the summary is reasonable."""
result = ReactionSummary(
reaction=model.reactions.get_by_id(reaction_id), model=model
)
assert result.to_frame().at[reaction_id, "flux"] == pytest.approx(
expected, abs=1e-2
)
@pytest.mark.parametrize(
"reaction_id, min_flux, max_flux",
[("ACALD", -1.27, 0.0), ("FUM", 0.79, 7.38), ("PFK", 2.58, 16.38)],
)
def test_reaction_summary_flux_fva(
model, reaction_id: str, min_flux: float, max_flux: float
) -> None:
"""Test that the reported flux ranges in the summary are reasonable."""
result = ReactionSummary(
reaction=model.reactions.get_by_id(reaction_id), model=model, fva=0.95
)
assert result.to_frame().at[reaction_id, "minimum"] == pytest.approx(
min_flux, abs=1e-2
)
assert result.to_frame().at[reaction_id, "maximum"] == pytest.approx(
max_flux, abs=1e-2
)
@pytest.mark.parametrize("reaction_id", ["ACALD", "FUM", "PFK"])
def test_reaction_summary_flux_in_context(model, reaction_id: str) -> None:
"""Test that the reaction summary inside and outside of a context are equal."""
with model:
context_summary = model.reactions.get_by_id(reaction_id).summary()
outside_summary = model.reactions.get_by_id(reaction_id).summary()
assert context_summary.to_frame()["flux"].values == pytest.approx(
outside_summary.to_frame()["flux"].values, abs=model.tolerance
)
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