Multi-arg tMRCA

Fixes #2801 #2070 #2611

Author: hyanwong

python/CHANGELOG.rst

@@ -4,6 +4,9 @@
 
 **Features**
 
+- Tree.trmca now accepts >2 nodes and returns nicer errors
+  (:user:`hyanwong`, :pr:2808, :issue:`2801`, :issue:`2070`, :issue:`2611`)
+
 - Add ``TreeSequence.genetic_relatedness_weighted`` stats method.
   (:user:`petrelharp`, :user:`brieuclehmann`, :user:`jeromekelleher`,
   :pr:`2785`, :pr:`1246`)

python/tests/test_highlevel.py

@@ -886,42 +886,60 @@ def test_minlex_postorder_multiple_roots(self):
 
 
 class TestMRCA:
+    """
+    Test both the tree.mrca and tree.tmrca methods.
+    """
+
     t = tskit.Tree.generate_balanced(3)
     #  4
     # ┏━┻┓
     # ┃  3
     # ┃ ┏┻┓
     # 0 1 2
 
-    def test_two_or_more_args(self):
-        assert self.t.mrca(2, 1) == 3
-        assert self.t.mrca(0, 1, 2) == 4
+    @pytest.mark.parametrize("args, expected", [((2, 1), 3), ((0, 1, 2), 4)])
+    def test_two_or_more_args(self, args, expected):
+        assert self.t.mrca(*args) == expected
+        assert self.t.tmrca(*args) == self.t.tree_sequence.nodes_time[expected]
 
     def test_less_than_two_args(self):
         with pytest.raises(ValueError):
             self.t.mrca(1)
+        with pytest.raises(ValueError):
+            self.t.tmrca(1)
 
     def test_no_args(self):
         with pytest.raises(ValueError):
             self.t.mrca()
+        with pytest.raises(ValueError):
+            self.t.tmrca()
 
     def test_same_args(self):
         assert self.t.mrca(0, 0, 0, 0) == 0
+        assert self.t.tmrca(0, 0, 0, 0) == self.t.tree_sequence.nodes_time[0]
 
     def test_different_tree_levels(self):
         assert self.t.mrca(0, 3) == 4
+        assert self.t.tmrca(0, 3) == self.t.tree_sequence.nodes_time[4]
 
     def test_out_of_bounds_args(self):
         with pytest.raises(ValueError):
             self.t.mrca(0, 6)
+        with pytest.raises(ValueError):
+            self.t.tmrca(0, 6)
 
     def test_virtual_root_arg(self):
         assert self.t.mrca(0, 5) == 5
+        assert np.isposinf(self.t.tmrca(0, 5))
 
     def test_multiple_roots(self):
         ts = tskit.Tree.generate_balanced(10).tree_sequence
         ts = ts.delete_intervals([ts.first().interval])
         assert ts.first().mrca(*ts.samples()) == tskit.NULL
+        # We decided to raise an error for tmrca here, rather than report inf
+        # see https://github.com/tskit-dev/tskit/issues/2801
+        with pytest.raises(ValueError, match="do not share a common ancestor"):
+            ts.first().tmrca(0, 6)
 
 
 class TestPathLength:

python/tskit/trees.py

@@ -996,7 +996,7 @@ def mrca(self, *args):
         """
         Returns the most recent common ancestor of the specified nodes.
 
-        :param int `*args`: input node IDs, must be at least 2.
+        :param int `*args`: input node IDs, at least 2 arguments are required.
         :return: The node ID of the most recent common ancestor of the
             input nodes, or :data:`tskit.NULL` if the nodes do not share
             a common ancestor in the tree.
@@ -1015,12 +1015,12 @@ def get_tmrca(self, u, v):
         # Deprecated alias for tmrca
         return self.tmrca(u, v)
 
-    def tmrca(self, u, v):
+    def tmrca(self, *args):
         """
         Returns the time of the most recent common ancestor of the specified
         nodes. This is equivalent to::
 
-            >>> tree.time(tree.mrca(u, v))
+            >>> tree.time(tree.mrca(*args))
 
         .. note::
             If you are using this method to calculate average tmrca values along the
@@ -1031,12 +1031,16 @@ def tmrca(self, u, v):
             nodes, for samples at time 0 the resulting statistics will be exactly
             twice the tmrca value.
 
-        :param int u: The first node.
-        :param int v: The second node.
-        :return: The time of the most recent common ancestor of u and v.
+        :param `*args`: input node IDs, at least 2 arguments are required.
+        :return: The time of the most recent common ancestor of all the nodes.
         :rtype: float
+        :raises ValueError: If the nodes do not share a single common ancestor in this
+            tree (i.e., if ``tree.mrca(*args) == tskit.NULL``)
         """
-        return self.get_time(self.get_mrca(u, v))
+        mrca = self.mrca(*args)
+        if mrca == tskit.NULL:
+            raise ValueError(f"Nodes {args} do not share a common ancestor in the tree")
+        return self.get_time(mrca)
 
     def get_parent(self, u):
         # Deprecated alias for parent