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Use positional argument in np.reshape to keep working with newer numpy

#850Merged
Comparing
sdvillal:fix-numpy-reshape-compat
(
3f70f84
) with
main
(
693a9cb
)
CodSpeed Performance Gauge
-14%
Improvements
1
Regressions
1
(
1
)
Untouched
61

Benchmarks

Improved

benchmark_get_assembly
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
+36%
900.8 ms663.9 ms

Passed

benchmark_get_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
+4%
60.8 ms58.6 ms
benchmark_deserialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
+4%
109.5 ms105.8 ms
benchmark_structural_alphabet_methods[to_3di]
benchmarks/structure/benchmark_alphabet.py
CodSpeed Performance Gauge
+3%
10.3 ms10 ms
benchmark_set_structure[cif-False]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
+3%
106.5 ms103.7 ms
benchmark_serialize_pdbx[cif]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
+2%
204.3 ms199.4 ms
benchmark_set_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
+2%
130.8 ms127.7 ms
benchmark_indexing_from_kmer_selection[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
+2%
9.4 ms9.1 ms
benchmark_get_structure[cif-True]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
+2%
127.7 ms124.8 ms
benchmark_indexing_from_kmer_selection[11*11*1*1***111-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
+2%
9.4 ms9.2 ms
benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
+2%
10.3 ms10.1 ms
benchmark_indexing_from_kmers[11*11*1*1***111-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
+2%
10.4 ms10.2 ms
benchmark_indexing_from_kmer_selection[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
+2%
12.5 ms12.3 ms
benchmark_indexing_from_kmer_selection[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
+2%
12.5 ms12.3 ms
benchmark_indexing_from_kmers[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
+2%
13.5 ms13.3 ms
benchmark_set_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
+2%
30.4 ms30 ms
benchmark_score_threshold_rule[None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
+2%
2 s2 s
benchmark_indexing_from_kmers[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
+1%
13.4 ms13.2 ms
benchmark_score_threshold_rule[11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
+1%
2 s2 s
benchmark_set_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
+1%
8.1 ms8 ms
benchmark_get_sequences[fasta_path1-ProteinSequence]
benchmarks/sequence/benchmark_fasta.py
CodSpeed Performance Gauge
+1%
8.8 ms8.7 ms
benchmark_lddt[False-all]
benchmarks/structure/benchmark_compare.py
CodSpeed Performance Gauge
+1%
229.4 ms227.2 ms
benchmark_get_structure[bcif-True]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
+1%
82.4 ms81.7 ms
benchmark_get_a3m_alignments
benchmarks/sequence/benchmark_fasta.py
CodSpeed Performance Gauge
+1%
579.7 ms575 ms
benchmark_match_kmer_selection[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
+1%
546.7 µs542.5 µs
benchmark_lddt[False-atom]
benchmarks/structure/benchmark_compare.py
CodSpeed Performance Gauge
+1%
313.6 ms311.3 ms
benchmark_lddt[False-chain]
benchmarks/structure/benchmark_compare.py
CodSpeed Performance Gauge
+1%
320.2 ms317.9 ms
benchmark_lddt[False-residue]
benchmarks/structure/benchmark_compare.py
CodSpeed Performance Gauge
+1%
325.5 ms323.2 ms
benchmark_match_kmer_selection[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
+1%
545.9 µs542.1 µs
benchmark_match_kmer_selection[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
+1%
463.8 µs460.8 µs
benchmark_superimpose[superimpose_without_outliers]
benchmarks/structure/benchmark_superimpose.py
CodSpeed Performance Gauge
0%
17.4 ms17.3 ms
benchmark_superimpose[superimpose_structural_homologs]
benchmarks/structure/benchmark_superimpose.py
CodSpeed Performance Gauge
0%
32.6 ms32.4 ms
benchmark_indexing_from_sequences[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
9.5 ms9.5 ms
benchmark_compress
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
703 ms701.6 ms
benchmark_kmer_decomposition[11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
186.6 µs186.2 µs
benchmark_serialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
112.1 ms111.9 ms
benchmark_match_kmer_selection[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
462.8 µs462.2 µs
benchmark_match_table[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
13 ms13 ms
benchmark_get_sequences[fasta_path0-NucleotideSequence]
benchmarks/sequence/benchmark_fasta.py
CodSpeed Performance Gauge
0%
185.5 ms185.4 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_sequences[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
17.6 ms17.6 ms
benchmark_get_structure[bcif-False]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
18.5 ms18.4 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
benchmark_deserialize_pdbx[bcif]
benchmarks/structure/benchmark_pdbx.py
CodSpeed Performance Gauge
0%
110.7 ms110.7 ms
benchmark_indexing_from_sequences[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
12.6 ms12.6 ms
test_pickle_and_unpickle[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
7.4 ms7.4 ms
test_pickle_and_unpickle[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
38.9 ms38.9 ms
test_pickle_and_unpickle[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
39 ms39.1 ms
benchmark_match[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
574.8 µs575.5 µs
benchmark_superimpose[superimpose]
benchmarks/structure/benchmark_superimpose.py
CodSpeed Performance Gauge
0%
2.5 ms2.5 ms
benchmark_lddt[True-all]
benchmarks/structure/benchmark_compare.py
CodSpeed Performance Gauge
0%
883.3 ms885 ms
benchmark_match[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
542.3 µs543.5 µs
benchmark_match[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
625.8 µs627.6 µs
benchmark_lddt[True-residue]
benchmarks/structure/benchmark_compare.py
CodSpeed Performance Gauge
0%
1.9 s1.9 s
benchmark_lddt[True-atom]
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_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_match[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
0%
491.7 µs493.9 µs
benchmark_match_table[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
-1%
15.1 ms15.2 ms
benchmark_match_table[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
-1%
15 ms15.1 ms
benchmark_kmer_decomposition[None]
benchmarks/sequence/align/benchmark_kmers.py
CodSpeed Performance Gauge
-1%
146.7 µs148.9 µs
benchmark_structural_alphabet_methods[to_protein_blocks]
benchmarks/structure/benchmark_alphabet.py
CodSpeed Performance Gauge
-7%
6.4 ms6.9 ms
benchmark_superimpose[superimpose_homologs]
benchmarks/structure/benchmark_superimpose.py
Regression
CodSpeed Performance Gauge
-14%
24.4 ms28.3 ms

Commits

Click on a commit to change the comparison range
Base
main
693a9cb
-13.58%
Use positional argument to keep working with newer numpy
3f70f84
9 days ago
by sdvillal
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