search

nextstrain / augur

Pipeline components for real-time phylodynamic analysis
https://docs.nextstrain.org/projects/augur/
GNU Affero General Public License v3.0
268 stars 128 forks source link

Port `transform-field-names` to `augur curate rename` #1506

Open jameshadfield opened 1 week ago

jameshadfield commented 1 week ago

See commit messages for details, and especially the added tests which describe the expected behaviour - most of which is slightly different from the previous transform-field-names script.

This assumes that NDJSON records have the same fields, so it's probably blocking on #1510, although I can add a simple check for that within the rename code in the name of expediency if desired.

Closes #1484

jameshadfield commented 4 days ago

@joverlee521 I think this is good to go now. I added 650bd56 which allows you to drop columns via --field-map X= as well.

codecov[bot] commented 4 days ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 69.90%. Comparing base (b69444a) to head (c7091ce).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #1506 +/- ## ========================================== + Coverage 69.69% 69.90% +0.21% ========================================== Files 74 75 +1 Lines 7827 7882 +55 Branches 1914 1933 +19 ========================================== + Hits 5455 5510 +55 Misses 2086 2086 Partials 286 286 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.