Bump version to 3.6.0 and update release notes for bug fix in get_n_words

[diegozea]

No description provided.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 96.95%. Comparing base (acd8e29) to head (080512d).
⚠️ Report is 1 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #186   +/-   ##
=======================================
  Coverage   96.95%   96.95%           
=======================================
  Files          64       64           
  Lines        4860     4860           
=======================================
  Hits         4712     4712           
  Misses        148      148           

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[github-actions]

Benchmark Results (Julia v1)

Time benchmarks

	master	080512d...	master / 080512d...
Information/CorrectedMutualInformation/buslje09/msa	0.876 ± 0.0081 s	0.877 ± 0.0087 s	0.999 ± 0.014
Information/CorrectedMutualInformation/buslje09/msa_large	0.0361 ± 0.00011 s	0.0361 ± 0.00013 s	0.998 ± 0.0046
Information/CorrectedMutualInformation/buslje09/msa_wide	0.783 ± 0.0037 s	0.783 ± 0.0053 s	0.999 ± 0.0082
Information/MIp/PF09645	9.41 ± 0.034 ms	9.41 ± 0.042 ms	1 ± 0.0057
Information/frequencies!/1	0.291 ± 0.03 μs	0.291 ± 0.02 μs	1 ± 0.12
Information/frequencies!/2	1.44 ± 0.02 μs	1.46 ± 0.03 μs	0.986 ± 0.024
Information/highlevel/BLMI	0.0627 ± 0.0002 s	0.0632 ± 0.0027 s	0.992 ± 0.043
Information/highlevel/buslje09	11.3 ± 0.052 ms	11.3 ± 0.05 ms	0.998 ± 0.0064
Information/shannon_entropy/PF09645	19.9 ± 0.4 μs	19.5 ± 0.41 μs	1.02 ± 0.03
MSA/Annotations/filtercolumns/boolean mask	10.5 ± 0.19 μs	10.4 ± 0.21 μs	1 ± 0.027
MSA/Annotations/filtercolumns/index array	3.52 ± 0.09 μs	3.52 ± 0.071 μs	1 ± 0.033
MSA/Base.vcat/annotated	4.31 ± 0.23 μs	4.36 ± 0.22 μs	0.989 ± 0.073
MSA/Base.vcat/unannotated	1.46 ± 0.1 μs	1.47 ± 0.09 μs	0.993 ± 0.091
MSA/Residue conversions/char2res	0.349 ± 0.78 ms	0.35 ± 0.65 ms	0.999 ± 2.9
MSA/Residue conversions/int2res	0.175 ± 0.086 ms	0.18 ± 0.084 ms	0.973 ± 0.66
MSA/Residue conversions/res2char	0.258 ± 0.013 ms	0.259 ± 0.013 ms	0.998 ± 0.07
MSA/Residue conversions/res2int	0.169 ± 0.13 ms	0.172 ± 0.12 ms	0.982 ± 1
MSA/hobohmI/pid62	0.521 ± 0.02 μs	0.511 ± 0.031 μs	1.02 ± 0.073
MSA/identity/matrix_Float64	17.6 ± 0.4 μs	17.6 ± 0.36 μs	0.998 ± 0.031
MSA/identity/mean	0.0876 ± 0.022 ms	0.0875 ± 0.023 ms	1 ± 0.36
MSA/read/FASTA.gz	0.0483 ± 0.0095 ms	0.0476 ± 0.0096 ms	1.02 ± 0.29
MSA/read/FASTA.gz_annotated	0.0508 ± 0.0017 ms	0.0499 ± 0.0017 ms	1.02 ± 0.048
MSA/read/FASTA_deletefullgaps	7.3 ± 0.34 ms	7.05 ± 1.6 ms	1.04 ± 0.24
MSA/read/FASTA_deletefullgaps_mapping	0.0928 ± 0.008 s	0.0929 ± 0.0042 s	0.999 ± 0.097
MSA/read/Stockholm	0.0337 ± 0.0025 ms	0.0337 ± 0.0025 ms	1 ± 0.1
MSA/read/Stockholm_annotated	0.0455 ± 0.0086 ms	0.0456 ± 0.0087 ms	0.998 ± 0.27
MSA/read/Stockholm_mapping	0.186 ± 0.016 ms	0.187 ± 0.016 ms	0.995 ± 0.12
MSA/read/Stockholm_mapping_coords	0.101 ± 0.028 ms	0.103 ± 0.028 ms	0.977 ± 0.38
MSA/write/FASTA	0.228 ± 0.034 ms	0.214 ± 0.029 ms	1.06 ± 0.21
PDB/_generate_interaction_keys/defaults	28.9 ± 17 μs	29.2 ± 18 μs	0.99 ± 0.84
PDB/_get_matched_Cαs/hemoglobin	0.033 ± 0.0088 ms	0.0331 ± 0.0084 ms	0.997 ± 0.37
PDB/_pdbresidues_to_mmcifdict/2vqc	0.581 ± 0.02 ms	0.561 ± 0.022 ms	1.04 ± 0.054
PDB/contact/1CBN_20_30_CB	0.22 ± 0.001 μs	0.2 ± 0.001 μs	1.1 ± 0.0074
PDB/contact/1CBN_20_30_heavy	0.251 ± 0.001 μs	0.251 ± 0.01 μs	1 ± 0.04
PDB/count_alanine/1CBN	0.331 ± 0.001 μs	0.341 ± 0.001 μs	0.971 ± 0.0041
PDB/distance/1CBN_20_30	0.14 ± 0.009 μs	0.131 ± 0.01 μs	1.07 ± 0.11
PDB/read/MMCIFFile	2.96 ± 0.041 ms	2.91 ± 0.045 ms	1.02 ± 0.021
PDB/squared_distance/1CBN_20_30_CB	0.191 ± 0.01 μs	0.191 ± 0.01 μs	1 ± 0.074
PDB/squared_distance/1CBN_20_30_heavy	0.26 ± 0.01 μs	0.26 ± 0.01 μs	1 ± 0.054
Pfam/accession mapping/acc2seqnames	0.185 ± 0.0095 ms	0.187 ± 0.01 ms	0.988 ± 0.074
SIFTS/ResidueDetails/_get_details	1.71 ± 0.3 μs	1.67 ± 0.32 μs	1.02 ± 0.26
SIFTS/ResidueDetails/_is_missing	1.69 ± 0.28 μs	1.79 ± 0.36 μs	0.944 ± 0.25
SIFTS/SIFTSResidue/18gs	0.1 ± 0 μs	0.101 ± 0.01 μs	0.99 ± 0.098
SIFTS/siftsmapping/2vqc	2.21 ± 0.053 ms	2.24 ± 0.045 ms	0.991 ± 0.031
Utils/get_n_words/ascii	0.16 ± 0.01 μs	0.15 ± 0.01 μs	1.07 ± 0.097
Utils/get_n_words/utf8	0.15 ± 0.001 μs	0.14 ± 0.001 μs	1.07 ± 0.01
Utils/hascoordinates/invalid	0.081 ± 0.01 μs	0.08 ± 0.01 μs	1.01 ± 0.18
Utils/hascoordinates/valid	0.13 ± 0.001 μs	0.13 ± 0.001 μs	1 ± 0.011
Utils/list2matrix/upper	0.162 ± 0.042 ms	0.162 ± 0.033 ms	0.998 ± 0.33
Utils/list2matrix/upper_diagonal	0.244 ± 0.083 ms	0.248 ± 0.07 ms	0.985 ± 0.43
Utils/matrix2list/upper	0.0719 ± 0.0069 ms	0.0726 ± 0.0093 ms	0.99 ± 0.16
Utils/matrix2list/upper_diagonal	0.0718 ± 0.011 ms	0.0728 ± 0.0099 ms	0.987 ± 0.2
time_to_load	0.777 ± 0.0079 s	0.775 ± 0.0032 s	1 ± 0.011

Memory benchmarks

	master	080512d...	master / 080512d...
Information/CorrectedMutualInformation/buslje09/msa	0.766 M allocs: 0.032 GB	0.766 M allocs: 0.032 GB	1
Information/CorrectedMutualInformation/buslje09/msa_large	0.0901 M allocs: 5.03 MB	0.0901 M allocs: 5.03 MB	1
Information/CorrectedMutualInformation/buslje09/msa_wide	0.742 M allocs: 30.3 MB	0.742 M allocs: 30.3 MB	1
Information/MIp/PF09645	20.3 k allocs: 0.819 MB	20.3 k allocs: 0.819 MB	1
Information/frequencies!/1	0 allocs: 0 B	0 allocs: 0 B
Information/frequencies!/2	0 allocs: 0 B	0 allocs: 0 B
Information/highlevel/BLMI	19.9 k allocs: 1.19 MB	19.9 k allocs: 1.19 MB	0.999
Information/highlevel/buslje09	0.0377 M allocs: 2.3 MB	0.0377 M allocs: 2.3 MB	1
Information/shannon_entropy/PF09645	0.047 k allocs: 12.2 kB	0.047 k allocs: 12.2 kB	1
MSA/Annotations/filtercolumns/boolean mask	18 allocs: 5.22 kB	18 allocs: 5.22 kB	1
MSA/Annotations/filtercolumns/index array	16 allocs: 1.62 kB	16 allocs: 1.62 kB	1
MSA/Base.vcat/annotated	0.143 k allocs: 6.58 kB	0.143 k allocs: 6.58 kB	1
MSA/Base.vcat/unannotated	0.064 k allocs: 2.7 kB	0.064 k allocs: 2.7 kB	1
MSA/Residue conversions/char2res	3 allocs: 4.1 MB	3 allocs: 4.1 MB	1
MSA/Residue conversions/int2res	3 allocs: 4.1 MB	3 allocs: 4.1 MB	1
MSA/Residue conversions/res2char	3 allocs: 2.05 MB	3 allocs: 2.05 MB	1
MSA/Residue conversions/res2int	3 allocs: 4.1 MB	3 allocs: 4.1 MB	1
MSA/hobohmI/pid62	31 allocs: 1.77 kB	31 allocs: 1.77 kB	1
MSA/identity/matrix_Float64	0.249 k allocs: 11.8 kB	0.249 k allocs: 11.8 kB	1
MSA/identity/mean	1.23 k allocs: 0.0517 MB	1.23 k allocs: 0.0517 MB	1
MSA/read/FASTA.gz	0.443 k allocs: 0.0752 MB	0.443 k allocs: 0.0752 MB	1
MSA/read/FASTA.gz_annotated	0.536 k allocs: 0.0794 MB	0.533 k allocs: 0.0793 MB	1
MSA/read/FASTA_deletefullgaps	13.6 k allocs: 17.4 MB	13.6 k allocs: 17.4 MB	1
MSA/read/FASTA_deletefullgaps_mapping	1.64 M allocs: 0.0795 GB	1.64 M allocs: 0.0795 GB	1
MSA/read/Stockholm	0.402 k allocs: 0.033 MB	0.402 k allocs: 0.033 MB	1
MSA/read/Stockholm_annotated	0.562 k allocs: 0.0413 MB	0.559 k allocs: 0.0413 MB	1
MSA/read/Stockholm_mapping	2.08 k allocs: 0.104 MB	2.08 k allocs: 0.104 MB	1
MSA/read/Stockholm_mapping_coords	1.64 k allocs: 0.0812 MB	1.64 k allocs: 0.0812 MB	1
MSA/write/FASTA	0.303 k allocs: 14.1 kB	0.303 k allocs: 14.1 kB	1
PDB/_generate_interaction_keys/defaults	0.497 k allocs: 0.0581 MB	0.497 k allocs: 0.0581 MB	1
PDB/_get_matched_Cαs/hemoglobin	0.584 k allocs: 0.0438 MB	0.584 k allocs: 0.0438 MB	1
PDB/_pdbresidues_to_mmcifdict/2vqc	8.56 k allocs: 1.12 MB	8.56 k allocs: 1.12 MB	1
PDB/contact/1CBN_20_30_CB	4 allocs: 0.281 kB	4 allocs: 0.281 kB	1
PDB/contact/1CBN_20_30_heavy	4 allocs: 0.281 kB	4 allocs: 0.281 kB	1
PDB/count_alanine/1CBN	0 allocs: 0 B	0 allocs: 0 B
PDB/distance/1CBN_20_30	0 allocs: 0 B	0 allocs: 0 B
PDB/read/MMCIFFile	0.039 M allocs: 2.9 MB	0.039 M allocs: 2.9 MB	1
PDB/squared_distance/1CBN_20_30_CB	4 allocs: 0.281 kB	4 allocs: 0.281 kB	1
PDB/squared_distance/1CBN_20_30_heavy	4 allocs: 0.281 kB	4 allocs: 0.281 kB	1
Pfam/accession mapping/acc2seqnames	4.32 k allocs: 0.319 MB	4.32 k allocs: 0.319 MB	1
SIFTS/ResidueDetails/_get_details	25 allocs: 1.45 kB	25 allocs: 1.45 kB	1
SIFTS/ResidueDetails/_is_missing	25 allocs: 1.45 kB	25 allocs: 1.45 kB	1
SIFTS/SIFTSResidue/18gs	4 allocs: 0.125 kB	4 allocs: 0.125 kB	1
SIFTS/siftsmapping/2vqc	5.94 k allocs: 0.88 MB	5.94 k allocs: 0.88 MB	1
Utils/get_n_words/ascii	5 allocs: 0.203 kB	5 allocs: 0.203 kB	1
Utils/get_n_words/utf8	5 allocs: 0.219 kB	5 allocs: 0.219 kB	1
Utils/hascoordinates/invalid	0 allocs: 0 B	0 allocs: 0 B
Utils/hascoordinates/valid	0 allocs: 0 B	0 allocs: 0 B
Utils/list2matrix/upper	3 allocs: 1.91 MB	3 allocs: 1.91 MB	1
Utils/list2matrix/upper_diagonal	6 allocs: 2.86 MB	6 allocs: 2.86 MB	1
Utils/matrix2list/upper	3 allocs: 0.952 MB	3 allocs: 0.952 MB	1
Utils/matrix2list/upper_diagonal	3 allocs: 0.956 MB	3 allocs: 0.956 MB	1
time_to_load	0.149 k allocs: 11.1 kB	0.149 k allocs: 11.1 kB	1

[coveralls]

coverage: 97.135%. remained the same
when pulling 080512d on bump-version-3-6-0
into acd8e29 on master.