Enhance type annotations for parse_file functions across multiple modules

[diegozea]

No description provided.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 96.97%. Comparing base (04de5ee) to head (e916df8).
⚠️ Report is 1 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #188   +/-   ##
=======================================
  Coverage   96.97%   96.97%           
=======================================
  Files          64       64           
  Lines        4861     4861           
=======================================
  Hits         4714     4714           
  Misses        147      147           

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[github-actions]

Benchmark Results (Julia v1)

Time benchmarks

	master	e916df8...	master / e916df8...
Information/CorrectedMutualInformation/buslje09/msa	0.879 ± 0.012 s	0.879 ± 0.011 s	1 ± 0.018
Information/CorrectedMutualInformation/buslje09/msa_large	0.0362 ± 0.00016 s	0.0362 ± 0.00017 s	1 ± 0.0064
Information/CorrectedMutualInformation/buslje09/msa_wide	0.785 ± 0.0081 s	0.785 ± 0.0049 s	1 ± 0.012
Information/MIp/PF09645	9.46 ± 0.053 ms	9.6 ± 0.067 ms	0.986 ± 0.0088
Information/frequencies!/1	0.29 ± 0.039 μs	0.28 ± 0.03 μs	1.04 ± 0.18
Information/frequencies!/2	1.86 ± 0.09 μs	1.45 ± 0.02 μs	1.28 ± 0.064
Information/highlevel/BLMI	0.0643 ± 0.00021 s	0.0626 ± 0.00025 s	1.03 ± 0.0054
Information/highlevel/buslje09	11.3 ± 0.053 ms	11.3 ± 0.057 ms	0.999 ± 0.0068
Information/shannon_entropy/PF09645	20 ± 0.46 μs	19.5 ± 0.42 μs	1.03 ± 0.032
MSA/Annotations/filtercolumns/boolean mask	9.83 ± 0.2 μs	9.85 ± 0.21 μs	0.998 ± 0.03
MSA/Annotations/filtercolumns/index array	3.52 ± 0.071 μs	3.52 ± 0.09 μs	1 ± 0.033
MSA/Base.vcat/annotated	4.31 ± 0.28 μs	4.34 ± 0.26 μs	0.993 ± 0.088
MSA/Base.vcat/unannotated	1.47 ± 0.09 μs	1.49 ± 0.09 μs	0.987 ± 0.085
MSA/Residue conversions/char2res	0.351 ± 0.84 ms	0.35 ± 0.83 ms	1 ± 3.4
MSA/Residue conversions/int2res	0.185 ± 0.7 ms	0.187 ± 0.11 ms	0.987 ± 3.8
MSA/Residue conversions/res2char	0.259 ± 0.014 ms	0.259 ± 0.013 ms	1 ± 0.075
MSA/Residue conversions/res2int	0.166 ± 0.15 ms	0.179 ± 0.67 ms	0.923 ± 3.6
MSA/hobohmI/pid62	0.521 ± 0.03 μs	0.501 ± 0.06 μs	1.04 ± 0.14
MSA/identity/matrix_Float64	17.5 ± 0.42 μs	17.7 ± 0.55 μs	0.992 ± 0.039
MSA/identity/mean	0.088 ± 0.022 ms	0.0883 ± 0.022 ms	0.996 ± 0.35
MSA/read/FASTA.gz	0.0465 ± 0.0088 ms	0.0466 ± 0.009 ms	0.998 ± 0.27
MSA/read/FASTA.gz_annotated	0.0497 ± 0.0017 ms	0.0503 ± 0.0023 ms	0.99 ± 0.057
MSA/read/FASTA_deletefullgaps	7.19 ± 1.7 ms	6.97 ± 1 ms	1.03 ± 0.29
MSA/read/FASTA_deletefullgaps_mapping	0.0921 ± 0.0052 s	0.0916 ± 0.0052 s	1.01 ± 0.081
MSA/read/Stockholm	0.0333 ± 0.0025 ms	0.0332 ± 0.0028 ms	1 ± 0.11
MSA/read/Stockholm_annotated	0.0451 ± 0.0084 ms	0.0455 ± 0.0083 ms	0.991 ± 0.26
MSA/read/Stockholm_mapping	0.183 ± 0.015 ms	0.186 ± 0.016 ms	0.986 ± 0.12
MSA/read/Stockholm_mapping_coords	0.0985 ± 0.028 ms	0.0997 ± 0.029 ms	0.988 ± 0.4
MSA/write/FASTA	0.259 ± 0.066 ms	0.257 ± 0.063 ms	1.01 ± 0.36
PDB/_generate_interaction_keys/defaults	29.8 ± 17 μs	30 ± 17 μs	0.994 ± 0.82
PDB/_get_matched_Cαs/hemoglobin	0.0362 ± 0.0085 ms	0.0346 ± 0.008 ms	1.05 ± 0.35
PDB/_pdbresidues_to_mmcifdict/2vqc	0.586 ± 0.018 ms	0.565 ± 0.022 ms	1.04 ± 0.052
PDB/contact/1CBN_20_30_CB	0.2 ± 0.001 μs	0.2 ± 0.001 μs	1 ± 0.0071
PDB/contact/1CBN_20_30_heavy	0.26 ± 0.01 μs	0.241 ± 0.011 μs	1.08 ± 0.064
PDB/count_alanine/1CBN	0.331 ± 0.01 μs	0.33 ± 0.01 μs	1 ± 0.043
PDB/distance/1CBN_20_30	0.14 ± 0.009 μs	0.14 ± 0.001 μs	1 ± 0.065
PDB/read/MMCIFFile	2.92 ± 0.04 ms	2.91 ± 0.045 ms	1 ± 0.021
PDB/squared_distance/1CBN_20_30_CB	0.2 ± 0.01 μs	0.201 ± 0.01 μs	0.995 ± 0.07
PDB/squared_distance/1CBN_20_30_heavy	0.26 ± 0.01 μs	0.251 ± 0.01 μs	1.04 ± 0.057
Pfam/accession mapping/acc2seqnames	0.187 ± 0.009 ms	0.188 ± 0.01 ms	0.993 ± 0.072
SIFTS/ResidueDetails/_get_details	1.64 ± 0.26 μs	1.66 ± 0.29 μs	0.985 ± 0.23
SIFTS/ResidueDetails/_is_missing	1.6 ± 0.31 μs	1.74 ± 0.25 μs	0.919 ± 0.22
SIFTS/SIFTSResidue/18gs	0.1 ± 0 μs	0.1 ± 0.001 μs	1 ± 0.01
SIFTS/siftsmapping/2vqc	2.21 ± 0.043 ms	2.24 ± 0.053 ms	0.989 ± 0.03
Utils/get_n_words/ascii	0.121 ± 0.01 μs	0.13 ± 0.001 μs	0.931 ± 0.077
Utils/get_n_words/utf8	0.111 ± 0.01 μs	0.12 ± 0.009 μs	0.925 ± 0.11
Utils/hascoordinates/invalid	0.09 ± 0.009 μs	0.09 ± 0.001 μs	1 ± 0.1
Utils/hascoordinates/valid	0.13 ± 0.001 μs	0.14 ± 0.001 μs	0.929 ± 0.0097
Utils/list2matrix/upper	0.158 ± 0.041 ms	0.164 ± 0.033 ms	0.962 ± 0.32
Utils/list2matrix/upper_diagonal	0.327 ± 0.13 ms	0.243 ± 0.041 ms	1.35 ± 0.58
Utils/matrix2list/upper	0.0817 ± 0.0096 ms	0.06 ± 0.015 ms	1.36 ± 0.37
Utils/matrix2list/upper_diagonal	0.0714 ± 0.012 ms	0.0665 ± 0.018 ms	1.07 ± 0.34
time_to_load	0.776 ± 0.0015 s	0.776 ± 0.0025 s	1 ± 0.0038

Memory benchmarks

	master	e916df8...	master / e916df8...
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	0.536 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	0.559 k allocs: 0.0413 MB	0.559 k allocs: 0.0412 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: 97.156%. remained the same
when pulling e916df8 on improve_type_annotations
into 04de5ee on master.