From cba692251592364865392adfd27479060e57054f Mon Sep 17 00:00:00 2001 From: Yan Wong Date: Fri, 6 Jan 2023 17:23:00 +0000 Subject: [PATCH] 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 | 4 ++-- python/tests/test_genotype_matching_fb.py | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/python/tests/__init__.py b/python/tests/__init__.py index 1f064b6a8d..f069f04f2e 100644 --- a/python/tests/__init__.py +++ b/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() diff --git a/python/tests/test_genotype_matching_fb.py b/python/tests/test_genotype_matching_fb.py index 88dd7a754d..984b3ce13a 100644 --- a/python/tests/test_genotype_matching_fb.py +++ b/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():