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

WIP Elevating skbio.stats.xxx to 1st-level modules #1992

Open
wants to merge 18 commits into
base: main
Choose a base branch
from

Conversation

qiyunzhu
Copy link
Contributor

@qiyunzhu qiyunzhu commented Mar 24, 2024

This PR elevates skbio.stats.xxx to 1st-level modules. Such that a user can do from skbio.composition import ancom. Whereas the original entries are kept for backward compatibility. This PR also standardizes the organization of skbio modules. Now, every module occupies a 1st-level subdirectory, with its own tests directory. This organization makes the codebase more modular. @wasade @mortonjt @mataton This is a proof-of-concept following our email discussion. I will follow up with a more detailed proposal of module organization.

Update: Per @mortonjt 's suggestion, I have reverted evolve, gradient, power and sampling back to stats, and kept only composition, distance, and ordination at the top level -- the three modules that deserve the most user attention.

Please complete the following checklist:

  • I have read the contribution guidelines.

  • I have documented all public-facing changes in the changelog.

  • This pull request includes code, documentation, or other content derived from external source(s). If this is the case, ensure the external source's license is compatible with scikit-bio's license. Include the license in the licenses directory and add a comment in the code giving proper attribution. Ensure any other requirements set forth by the license and/or author are satisfied.

    • It is your responsibility to disclose code, documentation, or other content derived from external source(s). If you have questions about whether something can be included in the project or how to give proper attribution, include those questions in your pull request and a reviewer will assist you.
  • This pull request does not include code, documentation, or other content derived from external source(s).

Note: This document may also be helpful to see some of the things code reviewers will be verifying when reviewing your pull request.

Copy link

codecov bot commented Mar 24, 2024

Codecov Report

Attention: Patch coverage is 98.77800% with 6 lines in your changes are missing coverage. Please review.

Project coverage is 98.63%. Comparing base (4d14ad0) to head (6d7843a).

Files Patch % Lines
skbio/composition/_composition.py 98.49% 6 Missing ⚠️
Additional details and impacted files
@@           Coverage Diff           @@
##             main    #1992   +/-   ##
=======================================
  Coverage   98.63%   98.63%           
=======================================
  Files         179      180    +1     
  Lines       30678    30679    +1     
  Branches     7456     7456           
=======================================
+ Hits        30259    30260    +1     
  Misses        404      404           
  Partials       15       15           

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

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.

None yet

1 participant