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Fix usage of `mkdssp>=4`

#764Merged
Comparing
padix-key:dssp
(
d1a1a58
) with
main
(
ac856a2
)
CodSpeed Performance Gauge
0%
Untouched
59

Benchmarks

Passed

benchmark_kmer_decomposition[None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_kmer_decomposition[None]
CodSpeed Performance Gauge
+1%
153 µs151 µs
benchmark_lddt[False-atom]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-atom]
CodSpeed Performance Gauge
0%
313.5 ms312.4 ms
benchmark_deserialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py::benchmark_deserialize_pdbx[bcif]
CodSpeed Performance Gauge
0%
118.7 ms118.5 ms
benchmark_get_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[bcif-False]
CodSpeed Performance Gauge
0%
19.6 ms19.6 ms
benchmark_match_kmer_selection[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_kmer_selection[KmerTable-None]
CodSpeed Performance Gauge
0%
463.8 µs463.1 µs
benchmark_lddt[False-chain]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-chain]
CodSpeed Performance Gauge
0%
319.6 ms319.2 ms
benchmark_match[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[KmerTable-None]
CodSpeed Performance Gauge
0%
495.4 µs494.7 µs
benchmark_lddt[False-residue]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-residue]
CodSpeed Performance Gauge
0%
325 ms324.6 ms
benchmark_indexing_from_kmer_selection[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmer_selection[None-BucketKmerTable(100000)]
CodSpeed Performance Gauge
0%
9.4 ms9.3 ms
benchmark_match_table[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[KmerTable-11*11*1*1***111]
CodSpeed Performance Gauge
0%
14.9 ms14.9 ms
benchmark_match_table[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[KmerTable-None]
CodSpeed Performance Gauge
0%
15.2 ms15.2 ms
test_pickle_and_unpickle[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::test_pickle_and_unpickle[KmerTable-11*11*1*1***111]
CodSpeed Performance Gauge
0%
38.8 ms38.8 ms
test_pickle_and_unpickle[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::test_pickle_and_unpickle[BucketKmerTable(10000)-11*11*1*1***111]
CodSpeed Performance Gauge
0%
7.3 ms7.3 ms
benchmark_score_threshold_rule[11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_score_threshold_rule[11*11*1*1***111]
CodSpeed Performance Gauge
0%
2 s2 s
benchmark_match_table[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[BucketKmerTable(10000)-11*11*1*1***111]
CodSpeed Performance Gauge
0%
12.9 ms12.9 ms
benchmark_lddt[True-residue]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-residue]
CodSpeed Performance Gauge
0%
1.9 s1.9 s
benchmark_lddt[True-atom]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-atom]
CodSpeed Performance Gauge
0%
1.9 s1.9 s
benchmark_lddt[True-chain]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-chain]
CodSpeed Performance Gauge
0%
1.9 s1.9 s
benchmark_match_table[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[BucketKmerTable(10000)-None]
CodSpeed Performance Gauge
0%
12.9 ms12.9 ms
test_pickle_and_unpickle[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py::test_pickle_and_unpickle[KmerTable-None]
CodSpeed Performance Gauge
0%
39 ms39 ms
test_pickle_and_unpickle[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::test_pickle_and_unpickle[BucketKmerTable(10000)-None]
CodSpeed Performance Gauge
0%
7.4 ms7.4 ms
benchmark_indexing_from_kmer_selection[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmer_selection[None-KmerTable]
CodSpeed Performance Gauge
0%
12.4 ms12.4 ms
benchmark_lddt[True-all]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-all]
CodSpeed Performance Gauge
0%
882.6 ms883.2 ms
benchmark_match[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[KmerTable-11*11*1*1***111]
CodSpeed Performance Gauge
0%
538.7 µs539.1 µs
benchmark_match_kmer_selection[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_kmer_selection[BucketKmerTable(10000)-11*11*1*1***111]
CodSpeed Performance Gauge
0%
541.8 µs542.2 µs
benchmark_set_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[cif-False]
CodSpeed Performance Gauge
0%
104.3 ms104.4 ms
benchmark_indexing_from_sequences[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_sequences[11*11*1*1***111-KmerTable]
CodSpeed Performance Gauge
0%
17.3 ms17.3 ms
benchmark_match[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[BucketKmerTable(10000)-11*11*1*1***111]
CodSpeed Performance Gauge
0%
621.3 µs622 µs
benchmark_score_threshold_rule[None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_score_threshold_rule[None]
CodSpeed Performance Gauge
0%
2 s2 s
benchmark_indexing_from_sequences[11*11*1*1***111-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_sequences[11*11*1*1***111-BucketKmerTable(100000)]
CodSpeed Performance Gauge
0%
14.2 ms14.2 ms
benchmark_indexing_from_sequences[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_sequences[None-BucketKmerTable(100000)]
CodSpeed Performance Gauge
0%
9.6 ms9.6 ms
benchmark_indexing_from_kmers[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmers[None-KmerTable]
CodSpeed Performance Gauge
0%
13.4 ms13.4 ms
benchmark_set_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[bcif-False]
CodSpeed Performance Gauge
0%
7.8 ms7.8 ms
benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]
CodSpeed Performance Gauge
0%
10.3 ms10.3 ms
benchmark_indexing_from_sequences[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_sequences[None-KmerTable]
CodSpeed Performance Gauge
0%
12.6 ms12.7 ms
benchmark_match_kmer_selection[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_kmer_selection[KmerTable-11*11*1*1***111]
CodSpeed Performance Gauge
0%
460 µs461 µs
benchmark_superimpose[superimpose]
benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose]
CodSpeed Performance Gauge
0%
2.4 ms2.4 ms
benchmark_match_kmer_selection[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_kmer_selection[BucketKmerTable(10000)-None]
CodSpeed Performance Gauge
0%
542.7 µs544.4 µs
benchmark_get_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[cif-False]
CodSpeed Performance Gauge
0%
59.8 ms60 ms
benchmark_kmer_decomposition[11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_kmer_decomposition[11*11*1*1***111]
CodSpeed Performance Gauge
0%
185.6 µs186.2 µs
benchmark_superimpose[superimpose_without_outliers]
benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose_without_outliers]
CodSpeed Performance Gauge
0%
17.2 ms17.2 ms
benchmark_serialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py::benchmark_serialize_pdbx[cif]
CodSpeed Performance Gauge
0%
201.3 ms202.1 ms
benchmark_indexing_from_kmer_selection[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmer_selection[11*11*1*1***111-KmerTable]
CodSpeed Performance Gauge
0%
12.4 ms12.5 ms
benchmark_match[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[BucketKmerTable(10000)-None]
CodSpeed Performance Gauge
0%
574 µs576.5 µs
benchmark_indexing_from_kmers[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmers[11*11*1*1***111-KmerTable]
CodSpeed Performance Gauge
0%
13.4 ms13.5 ms
benchmark_structural_alphabet_methods[to_protein_blocks]
benchmarks/structure/benchmark_alphabet.py::benchmark_structural_alphabet_methods[to_protein_blocks]
CodSpeed Performance Gauge
0%
8.9 ms8.9 ms
benchmark_superimpose[superimpose_homologs]
benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose_homologs]
CodSpeed Performance Gauge
0%
23.9 ms24 ms
benchmark_indexing_from_kmer_selection[11*11*1*1***111-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmer_selection[11*11*1*1***111-BucketKmerTable(100000)]
CodSpeed Performance Gauge
0%
9.3 ms9.4 ms
benchmark_compress
benchmarks/structure/benchmark_pdbx.py::benchmark_compress
CodSpeed Performance Gauge
0%
677.2 ms680.5 ms
benchmark_deserialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py::benchmark_deserialize_pdbx[cif]
CodSpeed Performance Gauge
-1%
107 ms107.6 ms
benchmark_structural_alphabet_methods[to_3di]
benchmarks/structure/benchmark_alphabet.py::benchmark_structural_alphabet_methods[to_3di]
CodSpeed Performance Gauge
-1%
13.2 ms13.3 ms
benchmark_lddt[False-all]
benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-all]
CodSpeed Performance Gauge
-1%
227.4 ms228.8 ms
benchmark_indexing_from_kmers[11*11*1*1***111-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmers[11*11*1*1***111-BucketKmerTable(100000)]
CodSpeed Performance Gauge
-1%
10.3 ms10.4 ms
benchmark_superimpose[superimpose_structural_homologs]
benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose_structural_homologs]
CodSpeed Performance Gauge
-1%
39.8 ms40 ms
benchmark_serialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py::benchmark_serialize_pdbx[bcif]
CodSpeed Performance Gauge
-1%
106.9 ms107.6 ms
benchmark_get_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[cif-True]
CodSpeed Performance Gauge
-1%
125.9 ms127.1 ms
benchmark_set_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[cif-True]
CodSpeed Performance Gauge
-1%
128 ms129.3 ms
benchmark_get_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[bcif-True]
CodSpeed Performance Gauge
-1%
83.8 ms84.9 ms
benchmark_set_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[bcif-True]
CodSpeed Performance Gauge
-3%
29.7 ms30.4 ms

Commits

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Base
main
ac856a2
-0.23%
Fix usage of `mkdssp>=4`
d1a1a58
7 months ago
by padix-key
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