Raise ValueError for unknown method in pedigree_kinship

Author: timothymillar

sgkit/stats/pedigree.py

@@ -567,6 +567,8 @@ def pedigree_kinship(
 
     Raises
     ------
+    ValueError
+        If an unknown method is specified.
     ValueError
         If the pedigree contains a directed loop.
     ValueError
@@ -613,7 +615,8 @@ def pedigree_kinship(
     "Computation of the inverse additive relationship matrix for autopolyploid
     and multiple-ploidy populations." Theoretical and Applied Genetics 131: 851-860.
     """
-    assert method in {"diploid", "Hamilton-Kerr"}
+    if method not in {"diploid", "Hamilton-Kerr"}:
+        raise ValueError("Unknown method '{}'".format(method))
     ds = define_variable_if_absent(ds, variables.parent, parent, parent_indices)
     variables.validate(ds, {parent: variables.parent_spec})
     parent = da.asarray(ds[parent].data, chunks=ds[parent].shape)

sgkit/tests/test_pedigree.py

@@ -486,3 +486,16 @@ def test_pedigree_kinship__raise_on_parents_dimension(method):
         ValueError, match="Parent matrix must have shape \(samples, 2\)"  # noqa: W605
     ):
         pedigree_kinship(ds, method=method).compute()
+
+
+def test_pedigree_kinship__raise_on_invalid_method():
+    ds = sg.simulate_genotype_call_dataset(n_variant=1, n_sample=5)
+    ds["parent_id"] = ["samples", "parents"], [
+        [".", "."],
+        [".", "."],
+        ["S0", "S1"],
+        ["S1", "."],
+        ["S2", "S3"],
+    ]
+    with pytest.raises(ValueError, match="Unknown method 'unknown'"):
+        pedigree_kinship(ds, method="unknown")