fix: use fixture for self comparison test

Author: andrewkern

python/tests/test_tree_stats.py

@@ -2311,16 +2311,29 @@ def test_shapes(self, proportion):
 class TestBranchGeneticRelatedness(TestGeneticRelatedness, TopologyExamplesMixin):
     mode = "branch"
 
-    def test_single_sample_set_self_comparison(self):
+    def test_single_sample_set_self_comparison(self, ts_12_highrecomb_fixture):
         # Test for issue #3055 - self-comparisons with single sample set
-        ts = msprime.simulate(sample_size=10, Ne=10000, length=1000, random_seed=42)
+        ts = ts_12_highrecomb_fixture
         # Single sample set with self-comparison
         result = ts.genetic_relatedness([[0]], indexes=[(0, 0)], mode="branch")
         assert result.shape == (1,)
         # Should work for multiple samples in single set too
         result = ts.genetic_relatedness([[0, 1, 2]], indexes=[(0, 0)], mode="branch")
         assert result.shape == (1,)
 
+    def test_single_sample_set_invalid_indexes(self, ts_12_highrecomb_fixture):
+        # Test that invalid indexes raise ValueError with single sample set
+        ts = ts_12_highrecomb_fixture
+        # Index out of bounds (only have 1 sample set, but trying to access index 1)
+        with pytest.raises(ValueError, match="Index out of bounds"):
+            ts.genetic_relatedness([[0]], indexes=[(0, 1)], mode="branch")
+        # Negative index
+        with pytest.raises(ValueError, match="Index out of bounds"):
+            ts.genetic_relatedness([[0]], indexes=[(-1, 0)], mode="branch")
+        # Both indexes out of bounds
+        with pytest.raises(ValueError, match="Index out of bounds"):
+            ts.genetic_relatedness([[0, 1]], indexes=[(2, 2)], mode="branch")
+
     @pytest.mark.parametrize("polarised", [True, False])
     def test_simple_tree_noncentred(self, polarised):
         # 2.00┊   4   ┊
@@ -2385,6 +2398,19 @@ def test_single_sample_set_self_comparison(self, ts_12_highrecomb_fixture):
         result = ts.genetic_relatedness([[0, 1, 2]], indexes=[(0, 0)], mode="node")
         assert result.shape == (ts.num_nodes, 1)
 
+    def test_single_sample_set_invalid_indexes(self, ts_12_highrecomb_fixture):
+        # Test that invalid indexes raise ValueError with single sample set
+        ts = ts_12_highrecomb_fixture
+        # Index out of bounds (only have 1 sample set, but trying to access index 1)
+        with pytest.raises(ValueError, match="Index out of bounds"):
+            ts.genetic_relatedness([[0]], indexes=[(0, 1)], mode="node")
+        # Negative index
+        with pytest.raises(ValueError, match="Index out of bounds"):
+            ts.genetic_relatedness([[0]], indexes=[(-1, 0)], mode="node")
+        # Both indexes out of bounds
+        with pytest.raises(ValueError, match="Index out of bounds"):
+            ts.genetic_relatedness([[0, 1]], indexes=[(2, 2)], mode="node")
+
 
 class TestSiteGeneticRelatedness(TestGeneticRelatedness, MutatedTopologyExamplesMixin):
     mode = "site"
@@ -2404,6 +2430,19 @@ def test_single_sample_set_self_comparison(self, ts_12_highrecomb_fixture):
         )
         assert result.shape == (2,)
 
+    def test_single_sample_set_invalid_indexes(self, ts_12_highrecomb_fixture):
+        # Test that invalid indexes raise ValueError with single sample set
+        ts = ts_12_highrecomb_fixture
+        # Index out of bounds (only have 1 sample set, but trying to access index 1)
+        with pytest.raises(ValueError, match="Index out of bounds"):
+            ts.genetic_relatedness([[0]], indexes=[(0, 1)], mode="site")
+        # Negative index
+        with pytest.raises(ValueError, match="Index out of bounds"):
+            ts.genetic_relatedness([[0]], indexes=[(-1, 0)], mode="site")
+        # Both indexes out of bounds
+        with pytest.raises(ValueError, match="Index out of bounds"):
+            ts.genetic_relatedness([[0, 1]], indexes=[(2, 2)], mode="site")
+
     def test_match_K_c0(self):
         # This test checks that ts.genetic_relatedness() matches K_c0
         # from Speed & Balding (2014) https://www.nature.com/articles/nrg3821