refactor: update to new pdex

[noamteyssier]

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[gemini-code-assist]

Summary of Changes

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This pull request updates the project's dependency on the pdex library to version 0.2.0, which necessitated a refactoring of existing code to accommodate breaking API changes. The update also raises the minimum required Python version to 3.11. These changes ensure compatibility with the latest pdex features and maintain the project's ability to perform differential expression calculations using the updated library.

Highlights

• Dependency Update: Updated the pdex library dependency from version 0.1.26 to 0.2.0 in pyproject.toml.
• Python Version Bump: Increased the minimum required Python version from >=3.10 to >=3.11.
• pdex API Refactor: Replaced calls to parallel_differential_expression with the new pdex function, adapting parameter names such as groupby_key to groupby and num_workers to threads.
• Parameter Removal: Removed deprecated parameters like metric, batch_size, and de_method from pdex related function calls, aligning with the updated pdex API.
• New pdex Mode: Added mode="ref" to pdex function calls in _baseline.py and _evaluator.py.
• Test Case Adjustment: Modified test cases to reflect the new pdex_kwargs parameters, specifically changing exp_post_agg to geometric_mean and num_workers to threads.

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Changelog

• pyproject.toml
  • Updated pdex dependency to 0.2.0.
  • Increased Python version requirement to >=3.11.
  • Formatted dev dependencies for readability.
• src/cell_eval/_baseline.py
  • Updated pdex import from parallel_differential_expression to pdex.
  • Modified pdex function call parameters to match the new API, including renaming groupby_key to groupby, num_workers to threads, and adding mode="ref".
• src/cell_eval/_evaluator.py
  • Updated pdex import from parallel_differential_expression to pdex.
  • Removed de_method and batch_size parameters from _build_de_comparison and _load_or_build_de.
  • Refactored _build_pdex_kwargs to align with the new pdex API, changing parameter names and removing as_polars.
• tests/test_eval.py
  • Updated pdex_kwargs in test cases, replacing exp_post_agg with geometric_mean and num_workers with threads to match the new pdex API.

Activity

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[gemini-code-assist]

Code Review

This pull request updates the pdex dependency to version 0.2.0 and refactors the code to align with the new API. The changes correctly replace parallel_differential_expression with pdex and update the corresponding arguments. While the core logic is updated, the refactoring appears incomplete. Several functions, including build_base_mean_adata in _baseline.py and _build_de_comparison and MetricsEvaluator.__init__ in _evaluator.py, retain now-unused parameters like de_method and batch_size in their signatures. These should be removed to clean up the code and prevent confusion. I've also added a comment about a potential high-severity issue regarding the removal of an explicit parameter that ensured the differential expression result is a polars DataFrame, which could lead to runtime errors if the new library version's default behavior has changed.

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src/cell_eval/_evaluator.py (285-286)

The removal of as_polars = True could cause runtime errors if the new pdex version doesn't return a polars DataFrame by default, as downstream code expects this type (e.g., for frame.write_csv(...)). The removal of the related comment # always return polars DataFrames makes this change particularly risky if the new default behavior wasn't verified.