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Port ingest/transform-strain-names to augur curate transform-strain-name [#1486] #1514

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merged 3 commits into from
Jul 2, 2024
Merged

Port ingest/transform-strain-names to augur curate transform-strain-name [#1486] #1514

merged 3 commits into from
Jul 2, 2024

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genehack
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@genehack genehack commented Jul 2, 2024 •
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Description of proposed changes

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

Related issue(s)

#1486
nextstrain/ingest#43

Checklist

  • Checks pass
  • If making user-facing changes, add a message in CHANGES.md summarizing the changes in this PR

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genehack commented Jul 2, 2024

@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.

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@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 #1515.

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genehack commented Jul 2, 2024

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.

@genehack genehack requested a review from a team July 2, 2024 19:55
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codecov bot commented Jul 2, 2024 •
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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).
Report is 224 commits behind head on master.

Files with missing lines Patch % Lines
augur/curate/transform_strain_name.py 96.15% 0 Missing and 1 partial ⚠️
Additional details and impacted files 
@@            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

☔ View full report in Codecov by Sentry.
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@genehack
Port translate-strain-name into augur curate style [#1486]
ff2faf9 
* Convert script over to expected sub-cmd style
* Add type hints throughout
* Add tests
@genehack
Update CHANGES [#1486]
d33556c
@genehack genehack force-pushed the port-xform-strain-name-1486 branch from 455a76b to d33556c Compare July 2, 2024 21:50
@genehack genehack merged commit 9447c66 into master Jul 2, 2024
20 checks passed
@genehack genehack deleted the port-xform-strain-name-1486 branch July 2, 2024 23:45
joverlee521 added a commit that referenced this pull request Jul 3, 2024
@joverlee521
Fix changelog link
6e35dd4 
Follow up to #1514
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