fix remove_outlier_replicates to dismiss NaN rows from response colum…#420
Merged
stewarthe6 merged 20 commits into1.8.0from Feb 25, 2026
Merged
fix remove_outlier_replicates to dismiss NaN rows from response colum…#420stewarthe6 merged 20 commits into1.8.0from
stewarthe6 merged 20 commits into1.8.0from
Conversation
…n before removing outliers
There was a problem hiding this comment.
Pull request overview
This PR fixes the remove_outlier_replicates function to handle NaN values in the response column before performing outlier detection. The fix prevents NaN values from affecting median calculations and ensures that only valid numeric values are considered when identifying outlier replicates.
Changes:
- Added NaN filtering logic to remove rows with missing response values before outlier detection
- Added print statement to report the number of rows removed due to missing values
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
|
@paulsonak I've opened a new pull request, #421, to work on those changes. Once the pull request is ready, I'll request review from you. |
remove log statement in preference of print statements like the rest of the module Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: paulsonak <64031328+paulsonak@users.noreply.github.com>
Added an empty value for the last entry in the CSV file to test that remove_outlier_replicates can handle NaN's
update logic to reflect removal of a NaN row
only print statement if rows were removed Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Paulsonak patch 1
Document NaN removal in remove_outlier_replicates docstring
Codecov Report✅ All modified and coverable lines are covered by tests. @@ Coverage Diff @@
## 1.8.0 #420 +/- ##
===========================================
+ Coverage 23.57% 40.51% +16.94%
===========================================
Files 50 50
Lines 13514 13518 +4
===========================================
+ Hits 3186 5477 +2291
+ Misses 10328 8041 -2287
Flags with carried forward coverage won't be shown. Click here to find out more.
... and 27 files with indirect coverage changes 🚀 New features to boost your workflow:
|
Collaborator
Author
|
This solves #419 |
…emove_outlier_replicates. This is done using the capsys feature of pytest. This means that you should no longer call these test functions without pytest and should only test using pytest.
- Replace individual codecov uploads in each test job with artifact saves - Add new coverage-merge job that combines all coverage reports - Upload single merged coverage report to codecov instead of overwriting - Fixes codecov not capturing integrative test coverage (e.g. test_curation_funcs) - Ensures complete coverage picture from both unit and integrative tests Co-authored-by: GitHub Copilot <copilot@github.com>
…structure. This should correct it.
…lp in the future if coverage reports are missing
…ecause they are hidden
Collaborator
|
Ok, this passes all tests and code conv is happy. |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
…n before removing outliers