JuliaFormatter

[diegozea]

No description provided.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 96.95%. Comparing base (519f6b9) to head (15d3a8b).
⚠️ Report is 1 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #185   +/-   ##
=======================================
  Coverage   96.95%   96.95%           
=======================================
  Files          64       64           
  Lines        4860     4860           
=======================================
  Hits         4712     4712           
  Misses        148      148           

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[coveralls]

coverage: 97.135%. remained the same
when pulling 15d3a8b on small-juliaformatter-run
into 519f6b9 on master.

[github-actions]

Benchmark Results (Julia v1)

Time benchmarks

	master	15d3a8b...	master / 15d3a8b...
Information/CorrectedMutualInformation/buslje09/msa	0.88 ± 0.008 s	0.877 ± 0.0081 s	1 ± 0.013
Information/CorrectedMutualInformation/buslje09/msa_large	0.0362 ± 0.00013 s	0.0361 ± 0.00011 s	1 ± 0.0047
Information/CorrectedMutualInformation/buslje09/msa_wide	0.785 ± 0.0072 s	0.783 ± 0.0039 s	1 ± 0.01
Information/MIp/PF09645	9.41 ± 0.041 ms	9.44 ± 0.033 ms	0.997 ± 0.0055
Information/frequencies!/1	0.301 ± 0.029 μs	0.29 ± 0.02 μs	1.04 ± 0.12
Information/frequencies!/2	1.51 ± 0.04 μs	1.44 ± 0.02 μs	1.05 ± 0.031
Information/highlevel/BLMI	0.0628 ± 0.00024 s	0.0643 ± 0.00017 s	0.976 ± 0.0046
Information/highlevel/buslje09	11.3 ± 0.048 ms	11.3 ± 0.056 ms	1 ± 0.0065
Information/shannon_entropy/PF09645	19.7 ± 0.39 μs	20.2 ± 0.42 μs	0.972 ± 0.028
MSA/Annotations/filtercolumns/boolean mask	9.82 ± 0.16 μs	9.9 ± 0.19 μs	0.992 ± 0.025
MSA/Annotations/filtercolumns/index array	3.52 ± 0.08 μs	3.52 ± 0.09 μs	1 ± 0.034
MSA/Base.vcat/annotated	4.34 ± 0.26 μs	4.38 ± 0.27 μs	0.991 ± 0.085
MSA/Base.vcat/unannotated	1.46 ± 0.11 μs	1.46 ± 0.12 μs	0.999 ± 0.11
MSA/Residue conversions/char2res	0.351 ± 0.64 ms	0.351 ± 0.64 ms	0.999 ± 2.6
MSA/Residue conversions/int2res	0.192 ± 0.073 ms	0.209 ± 0.84 ms	0.92 ± 3.7
MSA/Residue conversions/res2char	0.26 ± 0.011 ms	0.26 ± 0.011 ms	1 ± 0.061
MSA/Residue conversions/res2int	0.186 ± 0.11 ms	0.236 ± 0.84 ms	0.788 ± 2.9
MSA/hobohmI/pid62	0.501 ± 0.04 μs	0.501 ± 0.03 μs	1 ± 0.1
MSA/identity/matrix_Float64	17.7 ± 0.49 μs	17.9 ± 0.45 μs	0.989 ± 0.037
MSA/identity/mean	0.0882 ± 0.022 ms	0.0878 ± 0.022 ms	1 ± 0.36
MSA/read/FASTA.gz	0.045 ± 0.0087 ms	0.0452 ± 0.0084 ms	0.994 ± 0.27
MSA/read/FASTA.gz_annotated	0.0494 ± 0.0021 ms	0.0498 ± 0.0022 ms	0.993 ± 0.06
MSA/read/FASTA_deletefullgaps	7 ± 0.37 ms	7.05 ± 0.45 ms	0.992 ± 0.082
MSA/read/FASTA_deletefullgaps_mapping	0.0918 ± 0.0053 s	0.0917 ± 0.0053 s	1 ± 0.081
MSA/read/Stockholm	0.0338 ± 0.0021 ms	0.0336 ± 0.0021 ms	1.01 ± 0.088
MSA/read/Stockholm_annotated	0.0454 ± 0.0081 ms	0.0452 ± 0.0082 ms	1 ± 0.26
MSA/read/Stockholm_mapping	0.184 ± 0.016 ms	0.185 ± 0.015 ms	0.995 ± 0.12
MSA/read/Stockholm_mapping_coords	0.0975 ± 0.028 ms	0.0982 ± 0.028 ms	0.993 ± 0.4
MSA/write/FASTA	0.234 ± 0.039 ms	0.226 ± 0.045 ms	1.04 ± 0.27
PDB/_generate_interaction_keys/defaults	29 ± 17 μs	29 ± 17 μs	1 ± 0.84
PDB/_get_matched_Cαs/hemoglobin	0.0343 ± 0.0078 ms	0.0337 ± 0.0082 ms	1.02 ± 0.34
PDB/_pdbresidues_to_mmcifdict/2vqc	0.564 ± 0.018 ms	0.581 ± 0.018 ms	0.97 ± 0.043
PDB/contact/1CBN_20_30_CB	0.201 ± 0.001 μs	0.201 ± 0.01 μs	1 ± 0.05
PDB/contact/1CBN_20_30_heavy	0.26 ± 0.001 μs	0.261 ± 0.01 μs	0.996 ± 0.038
PDB/count_alanine/1CBN	0.32 ± 0.01 μs	0.321 ± 0.001 μs	0.997 ± 0.031
PDB/distance/1CBN_20_30	0.14 ± 0.01 μs	0.14 ± 0.009 μs	1 ± 0.096
PDB/read/MMCIFFile	2.9 ± 0.038 ms	2.92 ± 0.039 ms	0.994 ± 0.019
PDB/squared_distance/1CBN_20_30_CB	0.2 ± 0.011 μs	0.21 ± 0.01 μs	0.952 ± 0.069
PDB/squared_distance/1CBN_20_30_heavy	0.251 ± 0.011 μs	0.26 ± 0.01 μs	0.965 ± 0.056
Pfam/accession mapping/acc2seqnames	0.188 ± 0.0091 ms	0.187 ± 0.0088 ms	1 ± 0.068
SIFTS/ResidueDetails/_get_details	2.13 ± 0.42 μs	1.7 ± 0.62 μs	1.25 ± 0.52
SIFTS/ResidueDetails/_is_missing	2.14 ± 0.47 μs	1.61 ± 0.44 μs	1.33 ± 0.46
SIFTS/SIFTSResidue/18gs	0.1 ± 0.001 μs	0.1 ± 0.001 μs	1 ± 0.014
SIFTS/siftsmapping/2vqc	2.22 ± 0.052 ms	2.16 ± 0.035 ms	1.03 ± 0.029
Utils/get_n_words/ascii	0.15 ± 0.001 μs	0.151 ± 0.01 μs	0.993 ± 0.066
Utils/get_n_words/utf8	0.14 ± 0.01 μs	0.15 ± 0.001 μs	0.933 ± 0.067
Utils/hascoordinates/invalid	0.08 ± 0.001 μs	0.08 ± 0 μs	1 ± 0.013
Utils/hascoordinates/valid	0.13 ± 0.001 μs	0.13 ± 0.001 μs	1 ± 0.011
Utils/list2matrix/upper	0.168 ± 0.059 ms	0.178 ± 0.063 ms	0.945 ± 0.47
Utils/list2matrix/upper_diagonal	0.236 ± 0.1 ms	0.262 ± 0.11 ms	0.903 ± 0.54
Utils/matrix2list/upper	0.0643 ± 0.02 ms	0.0685 ± 0.021 ms	0.938 ± 0.41
Utils/matrix2list/upper_diagonal	0.0649 ± 0.019 ms	0.0692 ± 0.028 ms	0.938 ± 0.46
time_to_load	0.791 ± 0.01 s	0.786 ± 0.0036 s	1.01 ± 0.014

Memory benchmarks

	master	15d3a8b...	master / 15d3a8b...
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	1
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	0.533 k allocs: 0.0794 MB	0.533 k allocs: 0.0794 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