WayScience / coSMicQC

Single cell Morphology Quality Control (coSMicQC)
https://wayscience.github.io/coSMicQC/
BSD 3-Clause "New" or "Revised" License
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Add labeled outlier dataframe output capability #16

Closed d33bs closed 4 months ago

d33bs commented 4 months ago

Description

This PR adds capabilities to output a full dataframe with scores and a column indicating whether threshold(s) pass for rows of the provided dataframe. Along the way I found I need to further modularize the work and increase typing / documentation throughout. I also took a chance to increase testing overall with a "basic" / simulated dataset + parquet-based output (which would otherwise be many lines of data within a Python file) to help increase our testing coverage and make changes more visible.

Thanks for any feedback you may have!

Closes #10

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Checklist

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d33bs commented 4 months ago

Thanks @jenna-tomkinson for the review! I've replied to your comments and also applied the suggestion (thanks!). When you're able, could I ask for a revisit on the open comments to ensure everything's good (I'll also re-request review)? Thanks!

d33bs commented 4 months ago

Thanks @jenna-tomkinson ! I made some changes to reflect the default you mentioned and noticed a minor need to reconfigure label_outliers. I also noticed Python 3.8 was included with tests, but not in the minimum version specification so I removed this from tests. Merging this in.

d33bs commented 4 months ago

Another note: Python 3.9 on Ubuntu 22.04 appeared to have issues in GitHub Actions so I cancelled this. All other tests succeeded, and all tests (including 3.9 on Ubuntu 22.04) succeeded in a prior commit. I expect these all to pass on merge to main.