Migrate remaining k-mer functionalities to Rust

[padix-key]

Pursuing #688, this PR migrates the remaining k-mer related functionalities to Rust. This includes

• KmerAlphabet
• KmerSelector
• Permutation
• SimilarityRule

Benchmarks ensured that the new implementations run at least approximately as fast as the legacy Cython implementation.

[codspeed-hq]

Merging this PR will improve performance by 23.99%

⚠️ Different runtime environments detected

Some benchmarks with significant performance changes were compared across different runtime environments,
which may affect the accuracy of the results.

Open the report in CodSpeed to investigate

⚡ 12 improved benchmarks
✅ 91 untouched benchmarks
⏩ 4 skipped benchmarks¹

Performance Changes

	Benchmark	BASE	HEAD	Efficiency
⚡	benchmark_score_threshold_rule[11*11*1*1***111]	1.9 s	1.2 s	+56.1%
⚡	benchmark_score_threshold_rule[None]	2 s	1.3 s	+56.05%
⚡	benchmark_kmer_decomposition[11*11*1*1***111]	171.8 µs	134 µs	+28.28%
⚡	benchmark_kmer_decomposition[None]	122.9 µs	96.8 µs	+27%
⚡	benchmark_similar_kmers	292.8 µs	240.8 µs	+21.59%
⚡	benchmark_indexing_from_sequences[11*11*1*1***111-BucketKmerTable(100000)]	17.3 ms	14.3 ms	+20.79%
⚡	benchmark_indexing_from_sequences[11*11*1*1***111-KmerTable]	18 ms	15 ms	+19.5%
⚡	benchmark_indexing_from_sequences[None-BucketKmerTable(100000)]	7.8 ms	6.7 ms	+15.39%
⚡	benchmark_match[BucketKmerTable(10000)-None]	423.6 µs	368.2 µs	+15.04%
⚡	benchmark_indexing_from_sequences[None-KmerTable]	8.6 ms	7.5 ms	+14.03%
⚡	benchmark_match[KmerTable-None]	333.7 µs	295 µs	+13.13%
⚡	benchmark_match_kmer_selection[BucketKmerTable(10000)-None]	354.3 µs	320 µs	+10.71%

Tip

Curious why this is faster? Comment @codspeedbot explain why this is faster on this PR, or directly use the CodSpeed MCP with your agent.

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_{Comparing padix-key:rust-kmer-misc (2d86546) with main (9e9f6a1)}

Footnotes

1. 4 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. ↩