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v0.2.0 release #26

Merged
merged 52 commits into from
Oct 11, 2022
Merged

v0.2.0 release #26

merged 52 commits into from
Oct 11, 2022

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nebfield
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@nebfield nebfield commented Oct 11, 2022 •
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  • Decreased memory usage
  • Support Zstandard compressed input data when matching variants
  • Refactor handling multiallelics and flipped matches to be consistent with duplicates / ambiguous matches
  • Handle API / FTP errors
  • Add a user agent to track API statistics

ens-lgil and others added 30 commits September 2, 2022 13:16
@ens-lgil
Fist commit of the 'validate' utils
77098be
@ens-lgil
Python 3.10 compatibility changes and minor updates
08409aa
@ens-lgil
Code updates and add tests for validation
e2fc209
@ens-lgil
Catch ftp download errors
99eb7b1
@nebfield
pin polars to 0.14.9
5fe9fad
@nebfield
bump version for next release
cd7ee78
@ens-lgil
Handle PGS Catalog REST API errors and retries
96896e3
@smlmbrt
Update README.md
50b9e9e
@nebfield
add memory profiler to development dependencies
268e96a
@nebfield
add support for reading zstd compressed targets
012ff6d
@nebfield
remove single match mode, scan_csv not compatible with bytesIO (zstd)
7975951
@nebfield
compress matched scorefiles
b6aa2b0
@nebfield
skeleton aggreggation
92bd91e
@nebfield
Merge pull request #19 from ens-lgil/feature/api_error
db8f63a 
Handle PGS Catalog REST API errors and retries
@nebfield
Merge pull request #16 from ens-lgil/feature/download_error
98f8de7 
Catch ftp download errors
@nebfield
add aggregate_score
da0105e
@ens-lgil
Cleanup the code, ignore some user warnings from pandas_schema and up…
85715dc 
…datepoetry files
@ens-lgil
Attempt to fix poetry error
60e3d9f
@ens-lgil
Fix version discrepancies for numpy
f6d727f
@ens-lgil
Fix path to the 'validate' test data files
13216fe
@ens-lgil
Update the README file
b60b0aa
@nebfield
fix df truthiness
1881c17
@nebfield
fix bumped version
3bf62c3
@nebfield
batch process input to reduce memory usage
f02c58c
@nebfield
read uncompressed data with a bufferedreader
ae8ce14
@nebfield
add lazy evaluation
3bb3e3d
@nebfield
improve RAM usage
a559d76
@nebfield
fix reading bim files
5c15a67
@nebfield
fix tests
0dc745d
@nebfield
fix types
ba793fb
nebfield and others added 22 commits October 4, 2022 12:27
@nebfield
Merge pull request #22 from ens-lgil/feature/scoring_file_validator
7bc290c 
Scoring file validators tool
@nebfield
Merge branch 'dev' into compress
470265d
@nebfield
update poetry lock file
a171e5b
@nebfield
treat lists of files consistently
593757c
@ens-lgil
Setup a user agent for the download_scorefiles utils (REST API calls …
353d8f2 
…to the PGS Catalog)
@ens-lgil
Improve library call
cc41b4f
@nebfield
don't hold scorefiles in memory when combining them
4eec95b
@nebfield
check if input and outputs are empty in combine_scorefiles
03699e2
@smlmbrt
Handle case where we might be removing the missing variants (not defa…
50b1517 
…ult)
@nebfield
add parameter for n_threads, set POLARS_MAX_THREADS with it
0a5dfbe
@nebfield
move dropping multiallelics from preprocessing to labelling
ca1734e
@nebfield
move skipping flips from matching to labelling
8f1f771
@nebfield
is_flipped -> match_flipped, fix uppercase match type
f5b64cf
@nebfield
move label_matches from get_all_matches to match_variants
5b18299
@nebfield
fix setting n_threads when reading
df44d9b
@nebfield
fix tests
be96d14
@nebfield
add sort by match type
d5cfcf0
@nebfield
fix _match_multiple_targets
126f153
@nebfield
oops
6aee170
@nebfield
Merge pull request #20 from PGScatalog/compress
4443ea3 
Compress outputs
@nebfield
Merge pull request #25 from ens-lgil/feature/user_agent
d3da286 
Setup a user agent for the download_scorefiles utils (REST API calls to the PGS Catalog)
@smlmbrt
Update pyproject.toml
4a21393 
Add Laurent
@nebfield nebfield requested a review from smlmbrt October 11, 2022 11:42
@smlmbrt smlmbrt merged commit afd3a53 into main Oct 11, 2022
This was referenced Oct 11, 2022
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@nebfield nebfield deleted the dev branch October 17, 2022 15:03
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@nebfield @smlmbrt @ens-lgil