feat: O(n) order_cherries using parental indices#94
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Neclow merged 1 commit intosbhattlab:mainfrom Aug 6, 2025
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GitHub: from ~12.5ms (#93) to 9.5ms! |
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No need to use
sort_by_keyforrow_idxswhich is O(n log n), we can simply use the parental indices, which should be continuous (e.g., n, .., 2(n-1)) to reorder the rows in the ancestry matrix.Also reduces the size of Fenwick trees to n_leaves - 1 instead of n_leaves (last element not needed).
Provided ~25% speed-ups on my machine (for n = 100000, from_newick went from ~9 ms to ~7 ms)