def test_fix_medium(tmp_path):
data = md.test_data()
built = build(data, db, str(tmp_path), cutoff=0)
bad_medium = medium.iloc[0:2, :]
fixed = fix_medium(built, str(tmp_path), bad_medium, 0.5, 0.001, 10)
assert fixed.shape[0] > 3
assert "description" in fixed.columns
def test_tradeoff(tmp_path):
data = md.test_data()
built = build(data, db, str(tmp_path), cutoff=0)
rates = tradeoff(built, str(tmp_path), medium)
assert "growth_rate" in rates.columns
assert "tradeoff" in rates.columns
assert rates.dropna().shape[0] < rates.shape[0]
def test_media(tmp_path):
data = md.test_data()
built = build(data, db, str(tmp_path), cutoff=0)
media = minimal_media(built, str(tmp_path), 0.5)
assert media.shape[0] > 3
assert "flux" in media.columns
assert "reaction" in media.columns
def test_grow(tmp_path):
data = md.test_data()
built = build(data, db, str(tmp_path), cutoff=0)
grown = grow(built, str(tmp_path), medium, 0.5)
assert len(grown) == 3
assert "growth_rate" in grown.growth_rates.columns
assert "flux" in grown.exchanges.columns
with pytest.raises(OptimizationError):
grow(built, str(tmp_path), medium, 1.5)
def test_build(tmp_path):
data = md.test_data()
built = build(data, db, str(tmp_path), cutoff=0)
assert built.shape[0] == 4
assert "sample_id" in built.columns
assert "found_fraction" in built.columns
assert "file" in built.columns
for fi in built.file:
assert (tmp_path / fi).exists()
def build(abundance: biom.Table,
taxonomy: pd.Series,
models: JSONDirectory,
threads: int = 1,
cutoff: float = 0.0001,
strict: bool = False,
solver: str = "auto") -> CommunityModelDirectory:
"""Build the community models."""
if solver == "auto":
solver = None
tax = build_spec(abundance, taxonomy, models, cutoff, strict)
out = CommunityModelDirectory()
out_folder = str(out.model_files.path_maker(model_id="test")).replace(
"test.pickle", "")
model_folder = str(models.json_files.path_maker(model_id="test")).replace(
"test.json", "")
mw.build(tax, model_folder, out_folder, cutoff, threads, solver)
os.rename(os.path.join(out_folder, "manifest.csv"),
out.manifest.path_maker())
return out
def tradeoff_data(tmp_path):
"""Generate some growth simulation data."""
data = md.test_data()
built = build(data, md.test_db, str(tmp_path), cutoff=0)
rates = tradeoff(built, str(tmp_path), medium)
return rates
def growth_data(tmp_path):
"""Generate some growth simulation data."""
data = md.test_data()
built = build(data, md.test_db, str(tmp_path), cutoff=0)
grown = grow(built, str(tmp_path), medium, 0.5)
return grown