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Implement KmerTable and BucketKmerTable in Rust#859

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padix-key wants to merge 4 commits intobiotite-dev:rustfrom
padix-key:rust-kmertable
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Implement KmerTable and BucketKmerTable in Rust#859
padix-key wants to merge 4 commits intobiotite-dev:rustfrom
padix-key:rust-kmertable

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@padix-key
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Currently KmerTable and BucketKmerTable are implemented in Cython. However the code is a bit cumbersome, has some degree of code duplication and, since pointer handling is involved, memory safety could pose an issue. All these problems can be mitigated by using a Rust implementation instead.

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codspeed-hq bot commented Jan 30, 2026

Merging this PR will not alter performance

✅ 63 untouched benchmarks
🆕 7 new benchmarks

Performance Changes

Benchmark BASE HEAD Efficiency
🆕 benchmark_set_structure_with_bonds N/A 13 ms N/A
🆕 benchmark_get_structure_with_bonds N/A 55.4 ms N/A
🆕 benchmark_get_structure N/A 4 ms N/A
🆕 benchmark_read N/A 2.2 ms N/A
🆕 benchmark_set_structure N/A 11.5 ms N/A
🆕 benchmark_get_coord N/A 585 µs N/A
🆕 benchmark_get_remark N/A 170.6 µs N/A

Comparing padix-key:rust-kmertable (0e745c6) with main (5fde24b)1

Open in CodSpeed

Footnotes

  1. No successful run was found on rust (dcb748d) during the generation of this report, so main (5fde24b) was used instead as the comparison base. There might be some changes unrelated to this pull request in this report.

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