nextstrain / augur

Pipeline components for real-time phylodynamic analysis
https://docs.nextstrain.org/projects/augur/
GNU Affero General Public License v3.0
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Port `ingest/transform-strain-names` to `augur curate transform-strain-name` [#1486] #1514

Closed genehack closed 5 days ago

genehack commented 6 days ago

Description of proposed changes

Port ingest/transform-strain-names to augur curate transform-strain-name, add tests.

Related issue(s)

1486

https://github.com/nextstrain/ingest/issues/43

Checklist

genehack commented 6 days ago

@joverlee521 I wonder if filter-strain-name would be a better command name? This isn't really transforming anything, it's dropping things that don't match.

joverlee521 commented 6 days ago

@joverlee521 I wonder if filter-strain-name would be a better command name? This isn't really transforming anything, it's dropping things that don't match.

Yeah, I was debating on this when I wrote up the issue. I think eventually the command would be expanded to transform strain names as described in https://github.com/nextstrain/augur/issues/1515.

genehack commented 6 days ago

Yeah, I was debating on this when I wrote up the issue. I think eventually the command would be expanded to transform strain names as described in #1515.

Yeah, okay, fair.

codecov[bot] commented 6 days ago

Codecov Report

Attention: Patch coverage is 96.29630% with 1 line in your changes missing coverage. Please review.

Project coverage is 69.63%. Comparing base (c679fde) to head (d33556c).

Files Patch % Lines
augur/curate/transform_strain_name.py 96.15% 0 Missing and 1 partial :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #1514 +/- ## ========================================== + Coverage 69.54% 69.63% +0.08% ========================================== Files 73 74 +1 Lines 7786 7812 +26 Branches 1904 1910 +6 ========================================== + Hits 5415 5440 +25 Misses 2086 2086 - Partials 285 286 +1 ```

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