def test_construction():
tax = test_taxonomy()
nr, mr = tax.reactions, tax.metabolites
com = Community(tax)
assert len(com.taxa) == 4
assert len(com.taxonomy) == 4
assert len(com.reactions) > tax.reactions.sum()
assert len(com.metabolites) > tax.metabolites.sum()
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_abundance_cutoff():
tax = test_taxonomy(n=3)
tax["abundance"] = [1.0, 2.0, 1e-6]
com = Community(tax)
assert len(com.taxa) == 2
assert len(com.taxonomy) == 2
def test_benchmark_construction(benchmark):
tax = test_taxonomy(3)
benchmark(Community, tax)