Implement is_empty method

Fixes #2640

Author: hyanwong

python/tests/test_topology.py

@@ -1764,6 +1764,85 @@ def test_multiple_trees(self):
         self.verify(ts, no_root_ts)
 
 
+class TestEmptyTrees(TopologyTestCase):
+    """
+    Tests for different sorts of "empty" trees
+    """
+
+    @pytest.mark.parametrize("check_roots", [None, True, False])
+    def test_no_nodes(self, check_roots):
+        tables = tskit.TableCollection(1)
+        tree = tables.tree_sequence().first()
+        assert tree.is_empty(check_roots=check_roots)
+
+    @pytest.mark.parametrize("check_roots", [None, True, False])
+    @pytest.mark.parametrize("root_threshold", [1, 2, 3])
+    def test_normal(self, check_roots, root_threshold):
+        tree = tskit.Tree.generate_balanced(2, root_threshold=root_threshold)
+        if check_roots and root_threshold > 2:
+            assert tree.is_empty(check_roots=check_roots)
+        else:
+            assert not tree.is_empty(check_roots=check_roots)
+
+    @pytest.mark.parametrize("check_roots", [None, True, False])
+    @pytest.mark.parametrize("root_threshold", [1, 2])
+    def test_stick(self, check_roots, root_threshold):
+        ts = tskit.Tree.generate_balanced(2).tree_sequence
+        stick_tree = ts.simplify([0], keep_unary=True).first(
+            root_threshold=root_threshold
+        )
+        if check_roots and root_threshold > 1:
+            assert stick_tree.is_empty(check_roots=check_roots)
+        else:
+            assert not stick_tree.is_empty(check_roots=check_roots)
+
+    @pytest.mark.parametrize("check_roots", [None, True, False])
+    @pytest.mark.parametrize("root_threshold", [1, 2])
+    def test_upsidedown_stick(self, check_roots, root_threshold):
+        ts = tskit.Tree.generate_balanced(2).tree_sequence
+        tables = ts.simplify([0], keep_unary=True).dump_tables()
+        # swap flags so that non-sample is dangling off sample
+        tables.nodes.flags = 1 - tables.nodes.flags
+        upsidedown_stick_tree = tables.tree_sequence().first(
+            root_threshold=root_threshold
+        )
+        if check_roots and root_threshold > 1:
+            assert upsidedown_stick_tree.is_empty(check_roots=check_roots)
+        else:
+            assert not upsidedown_stick_tree.is_empty(check_roots=check_roots)
+
+    @pytest.mark.parametrize("check_roots", [None, True, False])
+    @pytest.mark.parametrize("root_threshold", [1, 2])
+    def test_multiroot_non_empty(self, check_roots, root_threshold):
+        tables = tskit.Tree.generate_balanced(2).tree_sequence.dump_tables()
+        tables.edges.truncate(1)
+        multiroot_tree = tables.tree_sequence().first(root_threshold=root_threshold)
+        assert multiroot_tree.num_roots == (2 if root_threshold == 1 else 0)
+        if check_roots and root_threshold > 1:
+            assert multiroot_tree.is_empty(check_roots=check_roots)
+        else:
+            assert not multiroot_tree.is_empty(check_roots=check_roots)
+
+    @pytest.mark.parametrize("check_roots", [True, False])
+    @pytest.mark.parametrize("root_threshold", [1, 2])
+    def test_empty(self, check_roots, root_threshold):
+        tables = tskit.Tree.generate_balanced(2).tree_sequence.dump_tables()
+        tables.delete_intervals([[0, 1]])
+        # check that sites & mutations make no difference
+        s = tables.sites.add_row(position=0.5, ancestral_state="0")
+        s = tables.mutations.add_row(site=s, derived_state="1", node=0)
+        tree = tables.tree_sequence().first(root_threshold=root_threshold)
+        assert tree.is_empty(check_roots=check_roots)
+
+    def test_dead_branch(self):
+        tables = tskit.Tree.generate_balanced(2).tree_sequence.dump_tables()
+        tables.nodes.flags = np.zeros_like(tables.nodes.flags)
+        tables.nodes.add_row(flags=tskit.NODE_IS_SAMPLE)
+        tree = tables.tree_sequence().first()
+        assert not tree.is_empty(check_roots=False)
+        assert tree.is_empty(check_roots=True)
+
+
 class TestEmptyTreeSequences(TopologyTestCase):
     """
     Tests covering tree sequences that have zero edges.

python/tskit/trees.py

@@ -851,6 +851,35 @@ def seek(self, position):
             raise ValueError("Position out of bounds")
         self._ll_tree.seek(position)
 
+    def is_empty(self, check_roots=None) -> bool:
+        """
+        Check if this tree is "empty" (i.e. has no topology). A tree is empty if it has
+        no edges. However, it may also be considered empty if it contains edges which
+        represent :ref:`dead branches<sec_data_model_tree_dead_leaves_and_branches>`
+        (i.e. not reachable from the :meth:`~Tree.roots` of the tree). To consider such
+        a tree as empty too, which is more involved, specify ``check_roots=True``.
+
+        Note that this is purely a property of the topology. An "empty" tree can still
+        contain sites and there may even be mutations on those sites.
+
+        :param bool check_roots: Should we also consider a tree empty if it has
+            topology but the topology is unconnected to any of the roots of the tree?
+            Default: ``None`` treated as ``False``.
+        :return: ``True`` if this tree is empty, ``False`` otherwise.
+        """
+        if self.num_edges == 0:
+            return True
+
+        if not check_roots:
+            return False
+
+        # Exhaustively check the roots: it's not simply enough to check that the roots
+        # are all samples, as they could still have children
+        for u in self.roots:
+            if self.num_children(u) != 0:
+                return False
+        return True
+
     def rank(self) -> tskit.Rank:
         """
         Produce the rank of this tree in the enumeration of all leaf-labelled