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v0.4.3 release #68

Merged
merged 19 commits into from
Dec 5, 2023
Merged

v0.4.3 release #68

merged 19 commits into from
Dec 5, 2023

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nebfield
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@nebfield nebfield commented Nov 28, 2023 •
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  • Fix retrying downloads when the EBI servers are sleepy on a Monday morning
  • Give a more helpful error message when there's no valid matches in match_combine
  • Fix numeric sample identifiers breaking ancestry analysis
  • Check chr prefix in samplesheets

smlmbrt and others added 15 commits November 7, 2023 16:22
@smlmbrt
More explicit header expectations (might solve empty row problems)
29f091b 
Signed-off-by: smlmbrt <[email protected]>
@smlmbrt
Ensure sample overlap between datasets (that there should be no data …
d5d8e30 
…loss)

Signed-off-by: smlmbrt <[email protected]>
@smlmbrt
Changes:
2597a49 
- Check probability of the sample coming from any population as a proxy for outlier status via PCs
- Only run the PC-by-PC stratification check if there are over 20 target samples.

These checks will be false positives if the samples are from a population that isn't in the reference.

Signed-off-by: smlmbrt <[email protected]>
@nebfield
handle HTTP connection exceptions
55ae0fb
@nebfield
Merge pull request #66 from PGScatalog/fix_download_reset
9427eb2 
handle HTTP connection exceptions
@nebfield
fix assert which fails when no matches are found
29ff0cc
@nebfield
clarify log message
ab3aa4f
@nebfield
Merge pull request #67 from PGScatalog/fix_combine_assert
e5d6c9d 
remove assert in `match_combine`
@nebfield
bump for patch
d626b60
@nebfield
Merge pull request #64 from PGScatalog/fix_singlesample_ancestry
97f7e76 
Handle single samples in ancestry_analysis
@nebfield
fix numeric IIDs
14b93a1
@nebfield
Merge branch 'dev' into fix_numeric_iids
7da41bd
@nebfield
re-add header=0
4881b44
@nebfield
finish comment
1cc3d96
@nebfield
add link to log
3d41f9c
@nebfield nebfield added this to the v0.4.3 milestone Nov 29, 2023
@nebfield nebfield changed the title patch release v0.4.3 release Nov 29, 2023
@smlmbrt smlmbrt marked this pull request as ready for review December 5, 2023 10:31
@smlmbrt smlmbrt self-requested a review December 5, 2023 10:39
nebfield
nebfield commented Dec 5, 2023
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looks good!

smlmbrt
smlmbrt requested changes Dec 5, 2023
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I think we might need to add that code snippet to the other script too.

pgscatalog_utils/match/combine_matches.py Show resolved Hide resolved
smlmbrt
smlmbrt approved these changes Dec 5, 2023
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My problem is moot - we'll add an issue to make sure that it's consistent in future releases.

@nebfield nebfield merged commit 6da7eb0 into main Dec 5, 2023
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@nebfield nebfield deleted the dev branch December 5, 2023 11:09
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