Avoid deprecation warnings

Curewntly getting "FutureWarning: This property is a deprecated alias for Tree.tree_sequence.num_nodes and will be removed in the future"

python/tests/__init__.py

@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2018-2022 Tskit Developers
+# Copyright (c) 2018-2023 Tskit Developers
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -53,7 +53,7 @@ def __init__(self, num_nodes):
 
     @classmethod
     def from_tree(cls, tree):
-        ret = PythonTree(tree.num_nodes)
+        ret = PythonTree(tree.tree_sequence.num_nodes)
         ret.left, ret.right = tree.get_interval()
         ret.site_list = list(tree.sites())
         ret.index = tree.get_index()

python/tests/test_genotype_matching_fb.py

@@ -174,8 +174,8 @@ def stupid_compress_dict(self):
         # Retain the old T_index, because the internal T that's passed up the tree will
         # retain this ordering.
         old_T_index = copy.deepcopy(self.T_index)
-        self.T_index = np.zeros(tree.num_nodes, dtype=int) - 1
-        self.N = np.zeros(tree.num_nodes, dtype=int)
+        self.T_index = np.zeros(tree.tree_sequence.num_nodes, dtype=int) - 1
+        self.N = np.zeros(tree.tree_sequence.num_nodes, dtype=int)
         self.T.clear()
 
         # First, create T root.
@@ -345,7 +345,7 @@ def update_tree(self):
                     vt.tree_node = -1
                 vt.value_index = -1
 
-        self.N = np.zeros(self.tree.num_nodes, dtype=int)
+        self.N = np.zeros(self.tree.tree_sequence.num_nodes, dtype=int)
         node_map = {st.tree_node: st for st in self.T}
 
         for u in self.tree.samples():