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Robinson foulds bug fix #283

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gloriayma wants to merge 5 commits into from
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Robinson foulds bug fix #283

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e9e9046
add reconstruct_ancestral_characters helper, which works on an nx dig…
gloriayma Nov 4, 2025
d1a0aed
add get_mutations_along_edge_nx helper in utils.py, rewrite calculate…
gloriayma Nov 13, 2025
7e5df4e
Fix Robinson-Foulds bug: leaf check (degree == 1) mistakenly flags ro…
gloriayma Dec 4, 2025
6ee8e02
Revert "add get_mutations_along_edge_nx helper in utils.py, rewrite c…
gloriayma Dec 4, 2025
95b538a
Revert "add reconstruct_ancestral_characters helper, which works on a…
gloriayma Dec 4, 2025
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4 changes: 2 additions & 2 deletions src/cassiopeia/critique/compare.py
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Original file line number Diff line number Diff line change
Expand Up @@ -117,8 +117,8 @@ def triplets_correct(

def _robinson_foulds_bitset(tree1: nx.DiGraph, tree2: nx.DiGraph):
"""Compute the unrooted Robinson–Foulds distance using bitsets."""
leaves1 = sorted([n for n in tree1 if tree1.degree[n] == 1])
leaves2 = sorted([n for n in tree2 if tree2.degree[n] == 1])
leaves1 = sorted([n for n in tree1 if tree1.out_degree(n) == 0])
leaves2 = sorted([n for n in tree2 if tree2.out_degree(n) == 0])
if set(leaves1) != set(leaves2):
raise ValueError("Trees must have identical leaf sets.")

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