Count edges in the tree.

Use for a crude upper bound on number of nodes in a traversal.

Author: jeromekelleher

c/tests/test_trees.c

@@ -5039,7 +5039,10 @@ test_virtual_root_properties(void)
     CU_ASSERT_EQUAL_FATAL(depth, -1);
 
     CU_ASSERT_EQUAL_FATAL(tsk_tree_get_time(&t, t.virtual_root, &time), 0)
-    CU_ASSERT_TRUE(isinf(time));
+    /* Workaround problems in IEEE floating point macros. We may want to
+     * add tsk_isinf (like tsk_isnan) at some point, but not worth it just
+     * for this test case */
+    CU_ASSERT_TRUE(isinf((float) time));
 
     CU_ASSERT_EQUAL_FATAL(tsk_tree_get_mrca(&t, t.virtual_root, 0, &node), 0)
     CU_ASSERT_EQUAL(node, t.virtual_root);

python/tests/test_topology.py

@@ -6556,6 +6556,8 @@ def verify(self, ts):
         tree2 = tskit.Tree(ts)
         tree2.first()
         for interval, tree1 in tsutil.algorithm_R(ts, root_threshold=1):
+            root_reachable_nodes = len(tree2.preorder())
+            assert tree1.max_nodes >= root_reachable_nodes
             assert interval == tree2.interval
             assert tree1.roots() == tree2.roots
             # Definition here is the set unique path ends from samples
@@ -6592,6 +6594,9 @@ def verify(self, ts):
             assert interval_py == tree_lib.interval
             assert interval_leg == tree_lib.interval
 
+            root_reachable_nodes = len(tree_lib.preorder())
+            assert tree_py.max_nodes >= root_reachable_nodes
+
             # Definition here is the set unique path ends from samples
             # that subtend at least k samples
             roots = set()

python/tests/tsutil.py

@@ -1184,6 +1184,7 @@ def __init__(self, n, root_threshold=1):
         self.left_sib = np.zeros(n + 1, dtype=np.int32) - 1
         self.right_sib = np.zeros(n + 1, dtype=np.int32) - 1
         self.num_samples = np.zeros(n + 1, dtype=np.int32)
+        self.num_edges = 0
 
     def __str__(self):
         s = "id\tparent\tlchild\trchild\tlsib\trsib\tnsamp\n"
@@ -1196,6 +1197,12 @@ def __str__(self):
             )
         return s
 
+    @property
+    def max_nodes(self):
+        # This gives a crude upper bound on the number of possible nodes in a
+        # traversal.
+        return self.num_edges + sum(self.num_samples[root] for root in self.roots())
+
     def roots(self):
         roots = []
         u = self.left_child[-1]
@@ -1245,6 +1252,7 @@ def remove_root(self, root):
         self.remove_branch(-1, root)
 
     def remove_edge(self, edge):
+        self.num_edges -= 1
         self.remove_branch(edge.parent, edge.child)
 
         u = edge.parent
@@ -1260,6 +1268,7 @@ def remove_edge(self, edge):
             self.insert_root(edge.child)
 
     def insert_edge(self, edge):
+        self.num_edges += 1
         u = edge.parent
         while u != -1:
             path_end = u