padix-key:dssp-bypass - Branch - biotite-dev/biotite

Bypass DSSP in tests and documentation

#775Merged

Comparing

padix-key:dssp-bypass

(

d374052

) with

main

(

cc408da

)

-21%

Improvements: 4

Regressions: 6

Untouched: 49

New: 0

Dropped: 0

Ignored: 0

Benchmarks

Improved

benchmark_structural_alphabet_methods[to_protein_blocks]

benchmarks/structure/benchmark_alphabet.py::benchmark_structural_alphabet_methods[to_protein_blocks]

×9.6

85.6 ms

8.9 ms

benchmark_superimpose[superimpose_homologs]

benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose_homologs]

×4.3

103.3 ms

23.8 ms

benchmark_set_structure[bcif-True]

benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[bcif-True]

+77%

51.7 ms

29.2 ms

benchmark_kmer_decomposition[None]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_kmer_decomposition[None]

+28%

195.1 µs

153 µs

Passed

benchmark_set_structure[cif-True]

benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[cif-True]

+9%

141.6 ms

130 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]

+7%

2.2 s

2 s

benchmark_score_threshold_rule[None]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_score_threshold_rule[None]

+7%

2.2 s

2.1 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]

+4%

13.4 ms

12.9 ms

benchmark_match_table[BucketKmerTable(10000)-None]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[BucketKmerTable(10000)-None]

+4%

13.4 ms

12.9 ms

benchmark_superimpose[superimpose]

benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose]

+2%

2.7 ms

2.6 ms

benchmark_match_table[KmerTable-None]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[KmerTable-None]

+2%

15.5 ms

15.3 ms

benchmark_superimpose[superimpose_structural_homologs]

benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose_structural_homologs]

+1%

41.1 ms

40.6 ms

benchmark_structural_alphabet_methods[to_3di]

benchmarks/structure/benchmark_alphabet.py::benchmark_structural_alphabet_methods[to_3di]

+1%

13.4 ms

13.3 ms

benchmark_compress

benchmarks/structure/benchmark_pdbx.py::benchmark_compress

+1%

570.1 ms

565.6 ms

benchmark_deserialize_pdbx[cif]

benchmarks/structure/benchmark_pdbx.py::benchmark_deserialize_pdbx[cif]

91.9 ms

91.7 ms

benchmark_lddt[True-chain]

benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-chain]

1.9 s

benchmark_lddt[True-residue]

benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-residue]

1.9 s

benchmark_match_table[KmerTable-11*11*1*1***111]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_table[KmerTable-11*11*1*1***111]

15.4 ms

benchmark_lddt[True-atom]

benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-atom]

1.9 s

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]

-1%

7.3 ms

7.4 ms

benchmark_lddt[True-all]

benchmarks/structure/benchmark_compare.py::benchmark_lddt[True-all]

-1%

904 ms

908.8 ms

benchmark_match_kmer_selection[BucketKmerTable(10000)-None]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_kmer_selection[BucketKmerTable(10000)-None]

-1%

549.5 µs

553.5 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]

-1%

546.3 µs

550.4 µs

benchmark_match[BucketKmerTable(10000)-None]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[BucketKmerTable(10000)-None]

-1%

579.5 µs

585.6 µs

benchmark_lddt[False-residue]

benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-residue]

-1%

306.3 ms

310.6 ms

test_pickle_and_unpickle[BucketKmerTable(10000)-None]

benchmarks/sequence/align/benchmark_kmers.py::test_pickle_and_unpickle[BucketKmerTable(10000)-None]

-1%

7.3 ms

7.4 ms

benchmark_match[KmerTable-None]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[KmerTable-None]

-1%

495.3 µs

502.8 µs

benchmark_lddt[False-atom]

benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-atom]

-2%

293.8 ms

298.4 ms

benchmark_lddt[False-chain]

benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-chain]

-2%

300.9 ms

305.6 ms

benchmark_superimpose[superimpose_without_outliers]

benchmarks/structure/benchmark_superimpose.py::benchmark_superimpose[superimpose_without_outliers]

-2%

16.5 ms

16.7 ms

benchmark_match[KmerTable-11*11*1*1***111]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[KmerTable-11*11*1*1***111]

-2%

537.9 µs

549.1 µs

benchmark_match_kmer_selection[KmerTable-None]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_match_kmer_selection[KmerTable-None]

-2%

460.5 µs

470.6 µs

benchmark_match[BucketKmerTable(10000)-11*11*1*1***111]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_match[BucketKmerTable(10000)-11*11*1*1***111]

-2%

617.7 µs

631.8 µs

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]

-3%

458.4 µs

470.5 µs

benchmark_kmer_decomposition[11*11*1*1***111]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_kmer_decomposition[11*11*1*1***111]

-3%

183.6 µs

188.8 µs

benchmark_lddt[False-all]

benchmarks/structure/benchmark_compare.py::benchmark_lddt[False-all]

-3%

212.3 ms

218.3 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]

-3%

37.5 ms

38.9 ms

test_pickle_and_unpickle[KmerTable-None]

benchmarks/sequence/align/benchmark_kmers.py::test_pickle_and_unpickle[KmerTable-None]

-4%

37.6 ms

39 ms

benchmark_serialize_pdbx[cif]

benchmarks/structure/benchmark_pdbx.py::benchmark_serialize_pdbx[cif]

-5%

167.1 ms

176 ms

benchmark_set_structure[bcif-False]

benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[bcif-False]

-5%

10.5 ms

11.1 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)]

-6%

8.9 ms

9.4 ms

benchmark_indexing_from_kmer_selection[None-BucketKmerTable(100000)]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmer_selection[None-BucketKmerTable(100000)]

-6%

8.8 ms

9.4 ms

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)]

-7%

13.5 ms

14.4 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)]

-7%

9.7 ms

10.4 ms

benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]

-7%

9.7 ms

10.4 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]

-9%

15.9 ms

17.4 ms

benchmark_indexing_from_sequences[None-BucketKmerTable(100000)]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_sequences[None-BucketKmerTable(100000)]

-9%

8.9 ms

9.8 ms

benchmark_deserialize_pdbx[bcif]

benchmarks/structure/benchmark_pdbx.py::benchmark_deserialize_pdbx[bcif]

-9%

99.8 ms

110.1 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]

-10%

11.3 ms

12.5 ms

benchmark_indexing_from_kmer_selection[None-KmerTable]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmer_selection[None-KmerTable]

-10%

11.3 ms

12.5 ms

benchmark_get_structure[bcif-False]

benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[bcif-False]

-10%

19.2 ms

21.3 ms

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]

-10%

12.1 ms

13.5 ms

benchmark_indexing_from_kmers[None-KmerTable]

benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_kmers[None-KmerTable]

-10%

12.1 ms

13.4 ms

benchmark_set_structure[cif-False]Regression

benchmarks/structure/benchmark_pdbx.py::benchmark_set_structure[cif-False]

-10%

97.1 ms

108 ms

benchmark_get_structure[cif-False]Regression

benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[cif-False]

-11%

52 ms

58.5 ms

benchmark_get_structure[cif-True]Regression

benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[cif-True]

-11%

106.9 ms

120.7 ms

benchmark_get_structure[bcif-True]Regression

benchmarks/structure/benchmark_pdbx.py::benchmark_get_structure[bcif-True]

-12%

74.6 ms

84.8 ms

benchmark_serialize_pdbx[bcif]Regression

benchmarks/structure/benchmark_pdbx.py::benchmark_serialize_pdbx[bcif]

-14%

73.3 ms

84.9 ms

benchmark_indexing_from_sequences[None-KmerTable]Regression

benchmarks/sequence/align/benchmark_kmers.py::benchmark_indexing_from_sequences[None-KmerTable]

-21%

10.1 ms

12.8 ms

Commits

Click on a commit to change the comparison range

Base

main

cc408da

-21%

Update Python version in build environment

d374052

20 days ago

by padix-key

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