def test_qiime_community():
tax = mm.data.test_taxonomy()
tax["species"] = tax["id"].str.replace("_", " ")
tax["abundance"] = [1, 2, 3, 4]
del tax["file"]
com = mm.Community(tax, db, progress=False)
assert len(com.abundances) == 3
m = com.build_metrics
assert m[0] == 3
assert m[1] == 4
assert m[2] == approx(0.75)
assert m[3] == approx(0.6)
def test_zip_build(tmp_path, rank):
manifest = mm.data.test_taxonomy()
with raises(ValueError):
dman = mw.build_database(manifest, str(tmp_path), rank=rank,
progress=False)
for co in ["kingdom", "phylum", "class", "order", "family"]:
manifest[co] = "fake"
dman = mw.build_database(manifest, str(tmp_path / "test.zip"), rank=rank,
progress=False)
assert dman.shape[0] == 1
assert path.exists(str(tmp_path / "test.zip"))
tax = mm.data.test_taxonomy()
com = mm.Community(tax, str(tmp_path / "test.zip"), progress=False)
m = com.build_metrics
assert m[0] == 4
assert m[1] == 4
assert m[2] == 1.0
assert m[3] == 1.0
def linear_community():
"""A simple community containing 4 species."""
return micom.Community(micom.data.test_taxonomy(),
progress=False,
solver="glpk")
def community():
"""A simple community containing 4 species."""
return micom.Community(micom.data.test_taxonomy(), progress=False)