nextstrain / augur

Pipeline components for real-time phylodynamic analysis
https://docs.nextstrain.org/projects/augur/
GNU Affero General Public License v3.0
268 stars 129 forks source link

Remove the requirement for a `database` field in `augur curate parse-genbank-location` [#1511] #1513

Closed genehack closed 3 months ago

genehack commented 3 months ago

Description of proposed changes

Per discussion on #1508 and #1511, the field standardization across records (cf #1510) makes the need to verify a database field less important — essentially, if there's a geo_loc_name field (or a field with the name given in the --location-field argument), parse it. Otherwise, warn that it's not found.

Related issue(s)

Checklist

j23414 commented 3 months ago

The requirement of a database field was a past annoyance of mine. I'm glad to see this change.

codecov[bot] commented 4 days ago

Codecov Report

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

Project coverage is 69.54%. Comparing base (4264701) to head (f1f05da). Report is 226 commits behind head on master.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #1513 +/- ## ========================================== - Coverage 69.57% 69.54% -0.03% ========================================== Files 73 73 Lines 7792 7786 -6 Branches 1906 1904 -2 ========================================== - Hits 5421 5415 -6 Misses 2086 2086 Partials 285 285 ```

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