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.

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

frequencies: Fix --regions flag #1424

Merged
merged 5 commits into from
Feb 23, 2024
Merged

frequencies: Fix --regions flag #1424

merged 5 commits into from
Feb 23, 2024

Conversation

joverlee521
Copy link
Contributor

@joverlee521 joverlee521 commented Feb 23, 2024

Description of proposed changes

Follow up to #1294 and #1398

Fixes the error raised when using the --regions flag with values other than the default "global" region.
See commits for details.

Related issue(s)

Resolves #1423

Checklist

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

Fixes the use of the `--regions` flag with values other than the default
"global" region by:

1. including the "region" column from the metadata file, similar to how
the weight attribute columns are included in dce0374.
2. annotating the tips with the "region" values from the metadata file,
similar to how the weight attributes are annotated in dde857a.
Copy link

codecov bot commented Feb 23, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 68.65%. Comparing base (f81e6a3) to head (455bcfa).

Additional details and impacted files
@@            Coverage Diff             @@
##           master    #1424      +/-   ##
==========================================
+ Coverage   68.50%   68.65%   +0.14%     
==========================================
  Files          69       69              
  Lines        7537     7544       +7     
  Branches     1846     1849       +3     
==========================================
+ Hits         5163     5179      +16     
+ Misses       2091     2088       -3     
+ Partials      283      277       -6     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

Copy link
Member

@victorlin victorlin left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks! Left a few non-blocking suggestions.

augur/frequencies.py Outdated Show resolved Hide resolved
augur/frequencies.py Show resolved Hide resolved
augur/frequencies.py Outdated Show resolved Hide resolved
The "region" column is only required when specifying regions that are
not the default "global" region.
Update help text to reflect the use of the "region" column and values
from the metadata file.
@joverlee521 joverlee521 merged commit de3071a into master Feb 23, 2024
20 checks passed
@joverlee521 joverlee521 deleted the fix-frequencies-region branch February 23, 2024 21:59
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

frequencies: error with --region flag
2 participants