Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Merged
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

Conversation

genehack
Copy link
Contributor

@genehack genehack commented Jul 2, 2024 •
edited
Loading

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

@genehack
Copy link
Contributor Author

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.

@joverlee521
Copy link
Contributor

@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.

@genehack
Copy link
Contributor Author

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
@codecov Codecov
Copy link

codecov bot commented Jul 2, 2024 •
edited
Loading

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.
📢 Have feedback on the report? Share it here.

genehack added 2 commits July 2, 2024 14:50
@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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@joverlee521 joverlee521 joverlee521 approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@genehack @joverlee521