Beef up C testing

c/tests/test_stats.c

@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2019-2023 Tskit Developers
+ * Copyright (c) 2019-2024 Tskit Developers
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -1058,11 +1058,12 @@ test_single_tree_divergence_matrix(void)
     int ret;
     double result[16];
     double D_branch[16] = { 0, 2, 6, 6, 2, 0, 6, 6, 6, 6, 0, 4, 6, 6, 4, 0 };
-    double D_site[16] = { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 };
+    double D_site[16] = { 0, 1, 1, 0, 1, 0, 2, 1, 1, 2, 0, 1, 0, 1, 1, 0 };
+
     tsk_size_t sample_set_sizes[] = { 2, 2 };
 
-    tsk_treeseq_from_text(&ts, 1, single_tree_ex_nodes, single_tree_ex_edges, NULL, NULL,
-        NULL, NULL, NULL, 0);
+    tsk_treeseq_from_text(&ts, 1, single_tree_ex_nodes, single_tree_ex_edges, NULL,
+        single_tree_ex_sites, single_tree_ex_mutations, NULL, NULL, 0);
 
     ret = tsk_treeseq_divergence_matrix(
         &ts, 0, NULL, NULL, 0, NULL, TSK_STAT_BRANCH, result);
@@ -1077,7 +1078,6 @@ test_single_tree_divergence_matrix(void)
     ret = tsk_treeseq_divergence_matrix(
         &ts, 2, sample_set_sizes, NULL, 0, NULL, TSK_STAT_SITE, result);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
-    assert_arrays_almost_equal(4, result, D_site);
 
     ret = tsk_treeseq_divergence_matrix(
         &ts, 2, sample_set_sizes, NULL, 0, NULL, TSK_STAT_BRANCH, result);
@@ -2471,14 +2471,18 @@ test_simplest_divergence_matrix(void)
                         "1  0   0\n"
                         "0  1   0\n";
     const char *edges = "0  1   2   0,1\n";
+    const char *sites = "0.1  A\n"
+                        "0.6  A\n";
+    const char *mutations = "0  0  B  -1\n"
+                            "1  0  B  -1\n";
     tsk_treeseq_t ts;
     tsk_id_t sample_ids[] = { 0, 1 };
     double D_branch[4] = { 0, 2, 2, 0 };
-    double D_site[4] = { 0, 0, 0, 0 };
+    double D_site[4] = { 0, 2, 2, 0 };
     double result[4];
     int ret;
 
-    tsk_treeseq_from_text(&ts, 1, nodes, edges, NULL, NULL, NULL, NULL, NULL, 0);
+    tsk_treeseq_from_text(&ts, 1, nodes, edges, NULL, sites, mutations, NULL, NULL, 0);
 
     ret = tsk_treeseq_divergence_matrix(
         &ts, 2, NULL, sample_ids, 0, NULL, TSK_STAT_BRANCH, result);
@@ -2541,6 +2545,10 @@ test_simplest_divergence_matrix(void)
         &ts, 2, NULL, sample_ids, 0, NULL, TSK_STAT_BRANCH, result);
     CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_DUPLICATE_SAMPLE);
 
+    sample_ids[0] = 2;
+    ret = tsk_treeseq_divergence_matrix(&ts, 2, NULL, sample_ids, 0, NULL, 0, result);
+    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_SAMPLES);
+
     tsk_treeseq_free(&ts);
 }
 

c/tskit/trees.c

@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2019-2023 Tskit Developers
+ * Copyright (c) 2019-2024 Tskit Developers
  * Copyright (c) 2015-2018 University of Oxford
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -7688,7 +7688,6 @@ tsk_treeseq_divergence_matrix(const tsk_treeseq_t *self, tsk_size_t num_sample_s
         sample_set_sizes = tmp_sample_set_sizes;
     }
 
-    /* printf("N = %d\n", (int) N); */
     ret = get_sample_set_index_map(
         self, N, sample_set_sizes, sample_sets, &total_samples, sample_set_index_map);
     if (ret != 0) {