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Remove Tree and TreeNode class - #944
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September 22, 2026 20:53
Merging this PR will improve performance by 50.54%
|
| Benchmark | BASE |
HEAD |
Efficiency | |
|---|---|---|---|---|
| ⚡ | benchmark_set_structure[cif-False] |
92.9 ms | 31.6 ms | ×2.9 |
| ⚡ | benchmark_set_structure[cif-True] |
103.5 ms | 41.7 ms | ×2.5 |
| ⚡ | benchmark_connect[connect_via_distances] |
3.2 ms | 1.7 ms | +86.5% |
| ⚡ | benchmark_serialize_pdbx[cif] |
177.7 ms | 120.4 ms | +47.58% |
| ⚡ | benchmark_infer_bond_types |
1,203 µs | 827.2 µs | +45.44% |
| ⚡ | benchmark_clustering[neighbor_joining] |
557.7 µs | 394 µs | +41.54% |
| ⚡ | benchmark_set_structure |
9.4 ms | 7 ms | +35.58% |
| ⚡ | benchmark_set_structure_with_bonds |
9.6 ms | 7.2 ms | +34.53% |
| 👁 | benchmark_match_kmer_selection[KmerTable-None] |
246.2 µs | 278.6 µs | -11.64% |
| 👁 | benchmark_match[KmerTable-None] |
294 µs | 327.6 µs | -10.28% |
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Comparing padix-key:phylo-networkx (5139a12) with main (1aaf784)
Footnotes
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14 benchmarks were skipped, so the baseline results were used instead. If they were deleted from the codebase, click here and archive them to remove them from the performance reports. ↩
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Trees are now represented as rooted `networkx.DiGraph` objects with integer leaf nodes and a `distance` edge attribute, replacing the Cython `Tree` and `TreeNode` classes. UPGMA and neighbor joining are implemented in Rust, with UPGMA tracking the row minima to avoid rescanning the entire distance matrix. The Newick parser is iterative, hence deeply nested trees no longer hit the recursion limit. Closes biotite-dev#903, closes biotite-dev#397
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This PR migrates
biotite.sequence.phylo.neighbor_joining,biotite.sequence.phylo.upgmaandbiotite.sequence.align.align_multipletonetworkx.DiGraph, makingTree/TreeNodeobsolete. HenceTree/TreeNodeare removed.Furthermore the functions above are refactored from Cython modules into Python and Rust modules. As these are the only remaining Cython modules, the Cython setup is removed from Biotite.
Resolves #903.