fixup! Testing corner cases.

tskit-dev · Apr 23, 2020 · a81bcd3 · a81bcd3
1 parent 365296f
commit a81bcd3
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Showing 5 changed files with 84 additions and 4 deletions.
diff --git a/_msprimemodule.c b/_msprimemodule.c
@@ -2016,7 +2016,6 @@ MutationModel_init(MutationModel *self, PyObject *args, PyObject *kwds)
             "transition matrix must be a square matrix with num_alleles rows");
         goto out;
     }
-    assert(shape[0] == PyObject_Size(py_transition_matrix));
 
     /* Note: it's important we zero out mutation_model here because
      * we can error before we can mutation_model_alloc, leaving the

diff --git a/lib/tests/tests.c b/lib/tests/tests.c
@@ -4742,15 +4742,51 @@ test_single_tree_mutgen_do_nothing_mutations(void)
     ret = mutgen_generate(&mutgen, &tables, MSP_DISCRETE_SITES | MSP_KEEP_SITES);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
     CU_ASSERT_TRUE(tsk_table_collection_equals(&tables, &copy));
+    mutgen_free(&mutgen);
 
     ret = mutgen_alloc(&mutgen, rng, &rate_map, &mut_model, 100);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
     ret = mutgen_generate(&mutgen, &tables, MSP_DISCRETE_SITES);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
     CU_ASSERT_EQUAL_FATAL(tables.mutations.num_rows, 0);
     CU_ASSERT_EQUAL_FATAL(tables.sites.num_rows, 0);
+    mutgen_free(&mutgen);
+
+    interval_map_free(&rate_map);
+    mutation_model_free(&mut_model);
+    tsk_table_collection_free(&tables);
+    tsk_table_collection_free(&copy);
+    gsl_rng_free(rng);
+}
+
+static void
+test_single_tree_mutgen_many_mutations(void)
+{
+    int ret = 0;
+    mutgen_t mutgen;
+    gsl_rng *rng = gsl_rng_alloc(gsl_rng_default);
+    tsk_table_collection_t tables;
+    interval_map_t rate_map;
+    mutation_model_t mut_model;
+
+    CU_ASSERT_FATAL(rng != NULL);
+    ret = mutation_model_factory(&mut_model, ALPHABET_BINARY);
+    CU_ASSERT_EQUAL_FATAL(ret, 0);
+    ret = interval_map_alloc_single(&rate_map, 1, 100);
+    CU_ASSERT_EQUAL_FATAL(ret, 0);
 
+    ret = tsk_table_collection_init(&tables, 0);
+    CU_ASSERT_EQUAL_FATAL(ret, 0);
+    insert_single_tree(&tables, ALPHABET_BINARY);
+
+    ret = mutgen_alloc(&mutgen, rng, &rate_map, &mut_model, 0);
+    CU_ASSERT_EQUAL_FATAL(ret, 0);
+    ret = mutgen_generate(&mutgen, &tables, MSP_DISCRETE_SITES);
+    CU_ASSERT_EQUAL_FATAL(ret, 0);
+    ret = mutgen_generate(&mutgen, &tables, MSP_DISCRETE_SITES | MSP_KEEP_SITES);
+    CU_ASSERT_EQUAL_FATAL(ret, MSP_ERR_MUTATION_GENERATION_OUT_OF_ORDER);
     mutgen_free(&mutgen);
+
     interval_map_free(&rate_map);
     mutation_model_free(&mut_model);
     tsk_table_collection_free(&tables);
@@ -5135,7 +5171,16 @@ test_mutation_model_errors(void)
     CU_ASSERT_EQUAL_FATAL(ret, MSP_ERR_BAD_ROOT_PROBABILITIES);
     mutation_model_free(&model);
 
+    /* Sums to 1, but bad values */
+    dist[0] = -1;
+    dist[1] = 2;
+    ret = mutation_model_alloc(&model, 2, (char **) (uintptr_t) alleles,
+            dist, matrix);
+    CU_ASSERT_EQUAL_FATAL(ret, MSP_ERR_BAD_ROOT_PROBABILITIES);
+    mutation_model_free(&model);
+
     dist[0] = 1.1;
+    dist[1] = 0.5;
     ret = mutation_model_alloc(&model, 2, (char **) (uintptr_t) alleles,
             dist, matrix);
     CU_ASSERT_EQUAL_FATAL(ret, MSP_ERR_BAD_ROOT_PROBABILITIES);
@@ -5168,7 +5213,16 @@ test_mutation_model_errors(void)
     CU_ASSERT_EQUAL_FATAL(ret, MSP_ERR_BAD_TRANSITION_MATRIX);
     mutation_model_free(&model);
 
+    /* Sums to 1, but bad values */
+    matrix[0] = -1;
+    matrix[1] = 2;
+    ret = mutation_model_alloc(&model, 2, (char **) (uintptr_t) alleles,
+            dist, matrix);
+    CU_ASSERT_EQUAL_FATAL(ret, MSP_ERR_BAD_TRANSITION_MATRIX);
+    mutation_model_free(&model);
+
     matrix[0] = 1.1;
+    matrix[1] = 1.0;
     ret = mutation_model_alloc(&model, 2, (char **) (uintptr_t) alleles,
             dist, matrix);
     CU_ASSERT_EQUAL_FATAL(ret, MSP_ERR_BAD_TRANSITION_MATRIX);
@@ -5374,6 +5428,7 @@ main(int argc, char **argv)
         {"test_single_tree_mutgen_interval", test_single_tree_mutgen_interval},
         {"test_single_tree_mutgen_empty_site", test_single_tree_mutgen_empty_site},
         {"test_single_tree_mutgen_do_nothing_mutations", test_single_tree_mutgen_do_nothing_mutations},
+        {"test_single_tree_mutgen_many_mutations", test_single_tree_mutgen_many_mutations},
 
         {"test_genic_selection_trajectory", test_genic_selection_trajectory},
         {"test_sweep_genic_selection_bad_parameters",

diff --git a/msprime/mutations.py b/msprime/mutations.py
@@ -94,7 +94,7 @@ def __init__(self):
 
 class InfiniteSites(MutationModel):
     # This mutation model is defined for backwards compatability, and is a remnant
-    # avoid confusion. The class should be formally deprecated and removed at
+    # of an earlier design. The class should be formally deprecated and removed at
     # some point.
     def __init__(self, alphabet=BINARY):
         self.alphabet = alphabet

diff --git a/tests/test_mutations.py b/tests/test_mutations.py
@@ -94,6 +94,9 @@ def validate_model(self, model):
         self.assertEqual(sum(model.root_distribution), 1.0)
         for j in range(num_alleles):
             self.assertEqual(sum(model.transition_matrix[j]), 1.0)
+        s = model.__str__()
+        self.assertIsInstance(s, str)
+        self.assertTrue(s.startswith("Mutation model with alleles"))
 
     def validate_stationary(self, model):
         # for most models, the root distribution should be the
@@ -868,9 +871,7 @@ def verify_model(self, model, verify_roots=True):
                     self.chisquare(row, sum(row) * p)
 
     def example_models(self):
-        print("MM")
         yield msprime.BinaryMutations()
-        print("JK")
         yield msprime.JukesCantor()
         model = msprime.MutationModel(
                 alleles=[b"abc", b"", b"x"],

diff --git a/tests/test_provenance.py b/tests/test_provenance.py
@@ -198,6 +198,31 @@ def test_mutate(self):
             'msprime.mutations.BinaryMutations'
         )
 
+    def test_mutate_model(self):
+        ts = msprime.simulate(5, random_seed=1)
+        ts = msprime.mutate(ts, model=msprime.JukesCantor())
+        decoded = self.decode(ts.provenance(1).record)
+        self.assertEqual(decoded.schema_version, "1.0.0")
+        self.assertEqual(decoded.parameters.command, "mutate")
+        self.assertEqual(
+            decoded.parameters.model['__class__'],
+            'msprime.mutations.JukesCantor'
+        )
+
+    def test_mutate_map(self):
+        ts = msprime.simulate(5, random_seed=1)
+        rate_map = msprime.MutationMap(position=[0, 0.5, 1], rate=[0, 1, 0])
+        ts = msprime.mutate(ts, rate=rate_map)
+        decoded = self.decode(ts.provenance(1).record)
+        self.assertEqual(decoded.schema_version, "1.0.0")
+        self.assertEqual(decoded.parameters.command, "mutate")
+        self.assertEqual(
+            decoded.parameters.rate['__class__'],
+            'msprime.mutations.MutationMap'
+        )
+        self.assertEqual(decoded.parameters.rate["position"], rate_map.position)
+        self.assertEqual(decoded.parameters.rate["rate"], rate_map.rate)
+
     def test_mutate_numpy(self):
         ts = msprime.simulate(5, random_seed=1)
         ts = msprime.mutate(