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

♻️ Refactor organism handling in curators #2415

Merged
merged 4 commits into from
Feb 2, 2025
Merged

Conversation

falexwolf
Copy link
Member

@falexwolf falexwolf commented Feb 1, 2025

Is part of a sequence of PRs that refactors the curators:


Replace self._kwargs with explicit organism passing; remove ability to pass an organism ad-hoc in .validate() etc.

  • goal is to define an organism as part of a feature dtype in cases in which it is needed -- e.g., Gene.ensembl_gene_id does not need it, whereas Gene.symbol needs it
  • there should and can't be no need to pass an organism at any later stages of the workflow; it both opens up the door for integrity errors and makes the code complicated

Copy link

codecov bot commented Feb 2, 2025

Codecov Report

Attention: Patch coverage is 96.42857% with 1 line in your changes missing coverage. Please review.

Project coverage is 91.48%. Comparing base (d503387) to head (57bd94f).
Report is 34 commits behind head on main.

Files with missing lines Patch % Lines
lamindb/curators/__init__.py 96.42% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #2415      +/-   ##
==========================================
- Coverage   91.71%   91.48%   -0.24%     
==========================================
  Files          62       62              
  Lines        9138     9601     +463     
==========================================
+ Hits         8381     8783     +402     
- Misses        757      818      +61     

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

Copy link

github-actions bot commented Feb 2, 2025

@github-actions github-actions bot temporarily deployed to pull request February 2, 2025 03:14 Inactive
@falexwolf falexwolf changed the title ♻️ Replace self._kwargs with explicit organism passing ♻️ Refactor organism handling in curators Feb 2, 2025
@falexwolf falexwolf merged commit 9113cb8 into main Feb 2, 2025
17 of 18 checks passed
@falexwolf falexwolf deleted the refactorcatcurators branch February 2, 2025 05:11
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.

1 participant