216 unable to specify negative control name in data preprocessing

[noamteyssier]

No description provided.

[gemini-code-assist]

Summary of Changes

Hello @noamteyssier, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request primarily addresses a limitation in the data preprocessing CLI, enabling users to specify the negative control name. This enhancement ensures that the ntc_name parameter is properly utilized during the data preparation phase, improving the flexibility and correctness of the cell-eval tool for single-cell perturbation predictions.

Highlights

• Version Bump: The project version has been updated from 0.6.7 to 0.6.8 in pyproject.toml.
• Negative Control Name Parameter: The ntc_name argument is now correctly passed to the data_preprocessing function within the run_prep CLI command, addressing the issue of being unable to specify negative control names during data preprocessing.

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[gemini-code-assist]

Code Review

This pull request addresses a bug where the command-line argument for the negative control name (--ntc-name) was being ignored during data preprocessing. The change correctly passes this argument to the strip_anndata function. During the review, I identified a similar issue where the --output-pert-col and --output-celltype-col arguments were also not being passed, causing them to be ignored. I've provided a suggestion to fix this as well, ensuring all relevant CLI arguments are properly handled.