Triplets Correct and RF functions both mutate the underlying tree

[richardyz98]

From the following code snippet, we see that even though the cached edges do not change, the underlying backend networkx object has changed, with the singleton edge at the top of the tree being collapsed. Hence we believe that the behavior of the collapse_unifurcations function that is called on the (supposed) copy of the trees passed into triplets_correct and robinson_foulds somehow persists.

import cassiopeia as cas

simulated_tree_dir = "/data/yosef2/users/richardz/projects/CassiopeiaV2-Reproducibility/topologies/exponential_plus_c/400cells/no_fit/"
reconstructed_tree_dir = '/data/yosef2/users/richardz/projects/CassiopeiaV2-Reproducibility/reconstructed/exponential_plus_c/400cells/no_priors/no_fit/char40/'

ind = 0
tree = pic.load(open(f'{simulated_tree_dir}/topology{ind}.pkl', 'rb'))
print(len(tree.edges))
print(tree._CassiopeiaTree__network.number_of_edges())
print(tree.root, tree.children(tree.root))

recon_tree = cas.data.CassiopeiaTree(tree=f'{reconstructed_tree_dir}/greedy/recon{ind}')
triplets = cas.critique.triplets_correct(tree, recon_tree, min_triplets_at_depth = 50)[0]  # or rf = cas.critique.robinson_foulds(tree, recon_tree)
print(len(tree.edges))
print(tree._CassiopeiaTree__network.number_of_edges())
print(tree.root, tree.children(tree.root))