Add python changelog and tests

Author: benjeffery

c/CHANGELOG.rst

@@ -5,7 +5,7 @@
 **Breaking changes**
 
 - ``tsk_treeseq_init`` now requires that mutation parents in the table collection
-  are correct and consistent with the topology of the tree at the mutation site.
+  are correct and consistent with the topology of the tree at each mutation site.
   Returns ``TSK_ERR_BAD_MUTATION_PARENT`` if this is not the case, or 
   ``TSK_ERR_MUTATION_PARENT_AFTER_CHILD`` if the mutations are not in an order
   compatible with the correct mutation parent.

python/CHANGELOG.rst

@@ -2,6 +2,15 @@
 [0.6.5] - 2025-0X-XX
 --------------------
 
+**Breaking Changes**
+
+- For a tree seqeunce to be valid mutation parents in the table collection
+  must be correct and consistent with the topology of the tree at each mutation site.
+  ``TableCollection.tree_sequence()`` will raise a ``_tskit.LibraryError`` if this
+  is not the case.
+  (:user:`benjeffery`, :issue:`2729`, :issue:`2732`, :pr:`3212`).
+
+
 **Features**
 
 - ``TreeSequence.map_to_vcf_model`` now also returns the transformed positions and

python/tests/test_highlevel.py

@@ -2692,6 +2692,104 @@ def test_impute_unknown_mutations_time(self, ts):
         ):
             ts.impute_unknown_mutations_time(method="foobar")
 
+    @pytest.mark.parametrize(
+        "mutations, error",
+        [
+            ([], None),
+            (
+                [{"node": 0, "parent": -1}, {"node": 1, "parent": -1}],
+                None,
+            ),  # On parallel branches, no parents
+            (
+                [
+                    {"node": 4, "parent": -1},
+                    {"node": 0, "parent": 0},
+                    {"node": 1, "parent": 0},
+                ],
+                None,
+            ),  # On parallel branches, legal parent
+            (
+                [{"node": 0, "parent": -1}, {"node": 0, "parent": 0}],
+                None,
+            ),  # On same node
+            (
+                [{"node": 0, "parent": -1}, {"node": 0, "parent": -1}],
+                "not consistent with the topology",
+            ),  # On same node without parents
+            (
+                [
+                    {"node": 3, "parent": -1},
+                    {"node": 0, "parent": 0},
+                    {"node": 1, "parent": 0},
+                ],
+                "not consistent with the topology",
+            ),  # On parallel branches, parent on parallel branches
+            (
+                [
+                    {"node": 5, "parent": -1},
+                    {"node": 0, "parent": 0},
+                    {"node": 1, "parent": 0},
+                ],
+                "not consistent with the topology",
+            ),  # On parallel branches, parent high on parallel
+            (
+                [
+                    {"node": 3, "parent": -1},
+                    {"node": 0, "parent": 0},
+                    {"node": 7, "parent": 0},
+                ],
+                "not consistent with the topology",
+            ),  # On parallel branches, parent on different root
+            (
+                [
+                    {"node": 0, "parent": -1},
+                    {"node": 1, "parent": 0},
+                ],
+                "not consistent with the topology",
+            ),  # parent on parallel branch
+            (
+                [
+                    {"node": 6, "parent": -1},
+                    {"node": 6, "parent": 0},
+                ],
+                None,
+            ),  # parent above root
+            (
+                [
+                    {"node": 6, "parent": -1},
+                    {"node": 6, "parent": -1},
+                ],
+                "not consistent with the topology",
+            ),  # parent above root, no parents
+        ],
+    )
+    def test_mutation_parent_errors(self, mutations, error):
+        tables = tskit.TableCollection(sequence_length=1)
+        tables.nodes.add_row(time=0, flags=tskit.NODE_IS_SAMPLE)
+        tables.nodes.add_row(time=0, flags=tskit.NODE_IS_SAMPLE)
+        tables.nodes.add_row(time=0, flags=tskit.NODE_IS_SAMPLE)
+        tables.nodes.add_row(time=0, flags=tskit.NODE_IS_SAMPLE)
+        tables.nodes.add_row(time=1)
+        tables.nodes.add_row(time=1)
+        tables.nodes.add_row(time=2)
+        tables.nodes.add_row(time=3)
+        tables.edges.add_row(left=0, right=1, parent=4, child=0)
+        tables.edges.add_row(left=0, right=1, parent=4, child=1)
+        tables.edges.add_row(left=0, right=1, parent=5, child=2)
+        tables.edges.add_row(left=0, right=1, parent=5, child=3)
+        tables.edges.add_row(left=0, right=1, parent=6, child=4)
+        tables.edges.add_row(left=0, right=1, parent=6, child=5)
+        tables.sites.add_row(position=0.5, ancestral_state="A")
+
+        for mut in mutations:
+            tables.mutations.add_row(**{"derived_state": "G", "site": 0, **mut})
+
+        if error is not None:
+            with pytest.raises(_tskit.LibraryError, match=error):
+                tables.tree_sequence()
+        else:
+            tables.tree_sequence()
+
 
 class TestSimplify:
     # This class was factored out of the old TestHighlevel class 2022-12-13,