Remove error states related to samples and individuals with no nodes

Author: benjeffery

python/tests/test_highlevel.py

@@ -5505,7 +5505,7 @@ def test_basic_individual_nodes(self, tmp_path):
         tables.nodes.add_row(flags=tskit.NODE_IS_SAMPLE, time=0, individual=1)
         ts = tables.tree_sequence()
 
-        result = ts.individual_nodes()
+        result = ts.individual_nodes
         assert result.shape == (2, 2)
         assert np.array_equal(result, [[0, 1], [2, 3]])
 
@@ -5529,7 +5529,7 @@ def test_variable_ploidy(self, tmp_path):
 
         ts = tables.tree_sequence()
 
-        result = ts.individual_nodes()
+        result = ts.individual_nodes
 
         assert result.shape == (3, 3)
 
@@ -5544,17 +5544,18 @@ def test_no_individuals(self):
         ts = tables.tree_sequence()
 
         with pytest.raises(ValueError, match="Tree sequence has no individuals"):
-            _ = ts.individual_nodes()
+            _ = ts.individual_nodes
 
-    def test_no_samples_with_individuals(self):
+    def test_no_nodes_with_individuals(self):
         tables = tskit.TableCollection(sequence_length=100)
         tables.individuals.add_row(flags=0, location=(0, 0), metadata=b"")
         # Node without individual reference
         tables.nodes.add_row(flags=tskit.NODE_IS_SAMPLE, time=0)
         ts = tables.tree_sequence()
 
-        with pytest.raises(ValueError, match="No nodes refer to individuals"):
-            _ = ts.individual_nodes()
+        result = ts.individual_nodes
+        expected = np.array([[]])
+        assert np.array_equal(result, expected)
 
     def test_individual_with_no_nodes(self):
         tables = tskit.TableCollection(sequence_length=100)
@@ -5564,18 +5565,17 @@ def test_individual_with_no_nodes(self):
         tables.nodes.add_row(flags=tskit.NODE_IS_SAMPLE, time=0, individual=0)
         ts = tables.tree_sequence()
 
-        with pytest.raises(
-            ValueError, match="Individual 1 not associated with any nodes"
-        ):
-            _ = ts.individual_nodes()
+        result = ts.individual_nodes
+        expected = np.array([[0], [-1]])
+        assert np.array_equal(result, expected)
 
     def test_mixed_sample_status(self):
         tables = tskit.TableCollection(sequence_length=100)
         tables.individuals.add_row(flags=0, location=(0, 0), metadata=b"")
         tables.nodes.add_row(flags=tskit.NODE_IS_SAMPLE, time=0, individual=0)
         tables.nodes.add_row(flags=0, time=0, individual=0)
         ts = tables.tree_sequence()
-        with pytest.raises(
-            ValueError, match="has nodes that are sample and non-samples"
-        ):
-            _ = ts.individual_nodes()
+
+        result = ts.individual_nodes
+        expected = np.array([[0, 1]])
+        assert np.array_equal(result, expected)

python/tskit/trees.py

@@ -10476,12 +10476,11 @@ def ld_matrix(
             mode=mode,
         )
 
+    @property
     def individual_nodes(self):
         """
         Return an array of node IDs for each individual in the tree sequence.
-        Errors if the tree sequence has no individuals, if individuals have
-        nodes that are both samples and non-samples, or if an individual
-        has no samples.
+        Errors if the tree sequence has no individuals.
 
         :return: Array of shape (num_individuals, max_ploidy) containing node IDs.
             Values of -1 indicate unused slots for individuals with ploidy
@@ -10491,25 +10490,11 @@ def individual_nodes(self):
         if self.num_individuals == 0:
             raise ValueError("Tree sequence has no individuals")
 
-        max_ploidy = 0
-        for i in range(self.num_individuals):
-            ind = self.individual(i)
-            max_ploidy = max(max_ploidy, len(ind.nodes))
-        if max_ploidy == 0:
-            raise ValueError("No nodes refer to individuals")
-
+        max_ploidy = max(len(i.nodes) for i in self.individuals())
         # Initialize output array with -1 (indicating no node)
         result = np.full((self.num_individuals, max_ploidy), -1, dtype=np.int32)
 
-        for i in range(self.num_individuals):
-            ind = self.individual(i)
-            if len(ind.nodes) == 0:
-                raise ValueError(f"Individual {i} not associated with any nodes")
-            is_sample = {self.node(u).is_sample() for u in ind.nodes}
-            if len(is_sample) != 1:
-                raise ValueError(
-                    f"Individual {ind.id} has nodes that are sample and non-samples"
-                )
+        for i, ind in enumerate(self.individuals()):
             for j, node_id in enumerate(ind.nodes):
                 result[i, j] = node_id