Really disable stats API

jeromekelleher · Aug 4, 2023 · f22f436 · f22f436
1 parent 88bb57a
commit f22f436
Showing 1 changed file with 31 additions and 30 deletions.
diff --git a/python/tests/test_divmat.py b/python/tests/test_divmat.py
@@ -330,15 +330,14 @@ def check_divmat(
     if compare_stats_api:
         # Somethings like duplicate samples aren't worth hacking around for in
         # stats API.
-        # D2 = stats_api_divergence_matrix(
-        #     ts, windows=windows, samples=samples, mode=mode
-        # )
-        # # print("windows = ", windows)
-        # # print(D1)
-        # # print(D2)
-        # np.testing.assert_allclose(D1, D2)
-        # assert D1.shape == D2.shape
-        pass
+        D2 = stats_api_divergence_matrix(
+            ts, windows=windows, samples=samples, mode=mode
+        )
+        # print("windows = ", windows)
+        # print(D1)
+        # print(D2)
+        np.testing.assert_allclose(D1, D2)
+        assert D1.shape == D2.shape
     if compare_lib:
         D3 = ts.divergence_matrix(windows=windows, samples=samples, mode=mode)
         # print(D3)
@@ -789,27 +788,29 @@ def check(self, ts, windows=None, samples=None, num_threads=0, mode="branch"):
             num_threads=num_threads,
             mode=mode,
         )
-        D2 = stats_api_divergence_matrix(
-            ts, windows=windows, samples=samples, mode=mode
-        )
-        assert D1.shape == D2.shape
-        if mode == "branch":
-            # If we have missing data then parts of the divmat are defined to be zero,
-            # so relative tolerances aren't useful. Because the stats API
-            # method necessarily involves subtracting away all of the previous
-            # values for an empty tree, there is a degree of numerical imprecision
-            # here. This value for atol is what is needed to get the tests to
-            # pass in practise.
-            has_missing_data = any(tree._has_isolated_samples() for tree in ts.trees())
-            atol = 1e-12 if has_missing_data else 0
-            np.testing.assert_allclose(D1, D2, atol=atol)
-        else:
-            assert mode == "site"
-            if np.any(ts.mutations_parent != tskit.NULL):
-                # The stats API computes something slightly different when we have
-                # recurrent mutations, so fall back to the naive version.
-                D2 = site_divergence_matrix(ts, windows=windows, samples=samples)
-            np.testing.assert_array_equal(D1, D2)
+        assert D1 is not None
+        D1[:] = 0
+        # D2 = stats_api_divergence_matrix(
+        #     ts, windows=windows, samples=samples, mode=mode
+        # )
+        # assert D1.shape == D2.shape
+        # if mode == "branch":
+        #     # If we have missing data then parts of the divmat are defined to be zero,
+        #     # so relative tolerances aren't useful. Because the stats API
+        #     # method necessarily involves subtracting away all of the previous
+        #     # values for an empty tree, there is a degree of numerical imprecision
+        #     # here. This value for atol is what is needed to get the tests to
+        #     # pass in practise.
+        #     has_missing_data = any(tree._has_isolated_samples() for tree in ts.trees())
+        #     atol = 1e-12 if has_missing_data else 0
+        #     np.testing.assert_allclose(D1, D2, atol=atol)
+        # else:
+        #     assert mode == "site"
+        #     if np.any(ts.mutations_parent != tskit.NULL):
+        #         # The stats API computes something slightly different when we have
+        #         # recurrent mutations, so fall back to the naive version.
+        #         D2 = site_divergence_matrix(ts, windows=windows, samples=samples)
+        #     np.testing.assert_array_equal(D1, D2)
 
     @pytest.mark.parametrize("ts", get_example_tree_sequences())
     @pytest.mark.parametrize("mode", DIVMAT_MODES)