def test_db(tmp_path):
manifest = load_qiime_manifest(db)
tax = md.test_taxonomy()
manifest.file = tax.file[0]
built = build_database(manifest, str(tmp_path), rank="species")
assert built.shape[0] == 3
for fi in built.file:
assert (tmp_path / fi).exists()
built = build_database(manifest, str(tmp_path / "db.zip"))
assert (tmp_path / "db.zip").exists()
def test_qiime_model():
manifest = qf.load_qiime_manifest(models)
assert "sample_id" in manifest.columns
for i in manifest.sample_id:
com = qf.load_qiime_model(models, i)
assert len(com.abundances) == 3
assert com.optimize().growth_rate == approx(0.874, 0.001)
with raises(ValueError):
qf.load_qiime_model(models, "blub")
with raises(ValueError):
qf.load_qiime_model(db, "blub")
def test_bad_manifest():
with raises(ValueError):
manifest = qf.load_qiime_manifest(medium)
def test_good_manifest(arti):
manifest = qf.load_qiime_manifest(arti)
assert "file" in manifest.columns