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Make `filter_intersection()` more efficient

#849Merged
Comparing
padix-key:filter-intersection
(
47f27b8
) with
main
(
531a9c8
)
CodSpeed Performance Gauge
0%
Untouched
63

Benchmarks

Passed

benchmark_kmer_decomposition[None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
+2%
149.8 µs147.5 µs
benchmark_match_table[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
+1%
15.2 ms15 ms
benchmark_match_table[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
+1%
15.2 ms15.1 ms
benchmark_set_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
+1%
30.4 ms30.3 ms
benchmark_match_kmer_selection[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
464.5 µs462.6 µs
benchmark_match_kmer_selection[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
546.6 µs544.8 µs
benchmark_serialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
204.6 ms204 ms
benchmark_match_kmer_selection[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
546 µs544.5 µs
benchmark_match_kmer_selection[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
464 µs462.8 µs
benchmark_deserialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
109 ms108.8 ms
benchmark_lddt[False-chain]
benchmarks/structure/benchmark_compare.py
CodSpeed Performance Gauge
0%
320.8 ms320.2 ms
benchmark_lddt[False-residue]
benchmarks/structure/benchmark_compare.py
CodSpeed Performance Gauge
0%
326.1 ms325.5 ms
benchmark_serialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
112 ms111.8 ms
benchmark_superimpose[superimpose_without_outliers]
benchmarks/structure/benchmark_superimpose.py
CodSpeed Performance Gauge
0%
17.4 ms17.4 ms
benchmark_set_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
8.1 ms8.1 ms
benchmark_superimpose[superimpose_homologs]
benchmarks/structure/benchmark_superimpose.py
CodSpeed Performance Gauge
0%
24.4 ms24.4 ms
benchmark_get_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
127.6 ms127.5 ms
benchmark_indexing_from_kmer_selection[11*11*1*1***111-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
9.4 ms9.4 ms
benchmark_structural_alphabet_methods[to_protein_blocks]
benchmarks/structure/benchmark_alphabet.py
CodSpeed Performance Gauge
0%
6.4 ms6.4 ms
benchmark_kmer_decomposition[11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
184.8 µs184.6 µs
benchmark_get_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
60.6 ms60.6 ms
benchmark_get_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
82.5 ms82.4 ms
benchmark_get_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
18.5 ms18.4 ms
benchmark_score_threshold_rule[None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
2 s2 s
benchmark_indexing_from_kmers[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
13.5 ms13.4 ms
benchmark_indexing_from_kmers[11*11*1*1***111-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
10.4 ms10.4 ms
benchmark_indexing_from_kmers[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
13.5 ms13.5 ms
benchmark_indexing_from_sequences[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
12.6 ms12.6 ms
benchmark_compress
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
701 ms700.7 ms
benchmark_indexing_from_sequences[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
17.6 ms17.6 ms
benchmark_indexing_from_sequences[11*11*1*1***111-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
14.5 ms14.5 ms
benchmark_indexing_from_kmer_selection[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
12.5 ms12.5 ms
benchmark_indexing_from_kmer_selection[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
12.5 ms12.5 ms
benchmark_score_threshold_rule[11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
2 s2 s
benchmark_set_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
130.6 ms130.6 ms
test_pickle_and_unpickle[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
7.4 ms7.4 ms
test_pickle_and_unpickle[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
7.4 ms7.4 ms
benchmark_lddt[True-atom]
benchmarks/structure/benchmark_compare.py
CodSpeed Performance Gauge
0%
1.9 s1.9 s
benchmark_match_table[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
13 ms13 ms
benchmark_get_assembly
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
900.5 ms900.7 ms
benchmark_superimpose[superimpose_structural_homologs]
benchmarks/structure/benchmark_superimpose.py
CodSpeed Performance Gauge
0%
32.5 ms32.5 ms
benchmark_lddt[True-residue]
benchmarks/structure/benchmark_compare.py
CodSpeed Performance Gauge
0%
1.9 s1.9 s
benchmark_lddt[True-chain]
benchmarks/structure/benchmark_compare.py
CodSpeed Performance Gauge
0%
1.9 s1.9 s
benchmark_lddt[True-all]
benchmarks/structure/benchmark_compare.py
CodSpeed Performance Gauge
0%
882.7 ms883.3 ms
test_pickle_and_unpickle[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
39 ms39 ms
benchmark_indexing_from_kmer_selection[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
9.4 ms9.4 ms
benchmark_match_table[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
12.9 ms12.9 ms
benchmark_set_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
106.2 ms106.3 ms
benchmark_get_sequences[fasta_path0-NucleotideSequence]
benchmarks/sequence/benchmark_fasta.py
CodSpeed Performance Gauge
0%
185 ms185.2 ms
test_pickle_and_unpickle[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
38.8 ms38.9 ms
benchmark_indexing_from_sequences[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
9.5 ms9.5 ms
benchmark_structural_alphabet_methods[to_3di]
benchmarks/structure/benchmark_alphabet.py
CodSpeed Performance Gauge
0%
10.3 ms10.3 ms
benchmark_match[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
624.2 µs625.2 µs
benchmark_lddt[False-atom]
benchmarks/structure/benchmark_compare.py
CodSpeed Performance Gauge
0%
313 ms313.6 ms
benchmark_match[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
573.6 µs574.8 µs
benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
10.3 ms10.3 ms
benchmark_superimpose[superimpose]
benchmarks/structure/benchmark_superimpose.py
CodSpeed Performance Gauge
0%
2.5 ms2.5 ms
benchmark_deserialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
110.8 ms111.1 ms
benchmark_match[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
492.3 µs493.7 µs
benchmark_match[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
540.1 µs541.7 µs
benchmark_get_a3m_alignments
benchmarks/sequence/benchmark_fasta.py
CodSpeed Performance Gauge
0%
579.7 ms581.6 ms
benchmark_get_sequences[fasta_path1-ProteinSequence]
benchmarks/sequence/benchmark_fasta.py
CodSpeed Performance Gauge
0%
8.9 ms8.9 ms
benchmark_lddt[False-all]
benchmarks/structure/benchmark_compare.py
CodSpeed Performance Gauge
-1%
227.8 ms229.4 ms

Commits

Click on a commit to change the comparison range
Base
main
531a9c8
+0.06%
Make `filter_intersection()` more efficient
47f27b8
5 days ago
by padix-key
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