adds a new sort utility to order h5ad files for faster cell load

[abhinadduri]

sorts an h5ad file according to a --context-col and a --pert-col, so that cells with the same (context, pert) appear consecutively in the h5ad file

[gemini-code-assist]

Summary of Changes

Hello @abhinadduri, 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 introduces a new command-line utility designed to optimize the loading performance of H5AD files. By allowing users to sort H5AD files based on specific observational columns like context, perturbation, and optionally batch, the utility ensures that related cells are stored contiguously. This structural change is intended to improve data access efficiency for downstream analysis and model training.

Highlights

• New Sort Utility: A new sort subcommand has been added to the CLI, allowing users to reorder H5AD files. This utility sorts cells based on specified context, perturbation, and an optional batch column.
• Performance Optimization: The primary goal of this sorting utility is to group cells with similar characteristics consecutively within the H5AD file, which is expected to lead to faster cell loading times for downstream analysis and model training.
• Dependency Update: The cell-load dependency has been updated to version >=0.9.0, and the project version has been incremented to 0.10.3.

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[gemini-code-assist]

Code Review

This pull request introduces a new sort utility to the command-line interface, designed to reorder cells within an .h5ad file based on specified columns. This is a useful feature for optimizing data loading. The implementation is well-contained in a new module, and it's correctly integrated into the existing CLI structure. My review includes a few suggestions for the new _sort.py module to enhance code style, logging practices, and to simplify some logic.

[gemini-code-assist]

For better code organization and adherence to PEP 8, standard library imports like logging and pathlib should be placed at the top of the file. While it's a good practice to delay importing heavy libraries like anndata inside a function for CLI tools to improve startup time for other subcommands, this doesn't apply to lightweight standard libraries.

[gemini-code-assist]

logging.basicConfig() should ideally be called only once at the application's entry point (e.g., in src/state/__main__.py). Calling it within subcommand functions can lead to unpredictable logging behavior, as it only has an effect the first time it's called. If another part of the application has already configured logging, this call will be ignored. Centralizing logging configuration would make it more robust.

[gemini-code-assist]

The check if output_dir is redundant because Path(output_path).parent always returns a Path object, which is truthy. You can simplify the condition to just check for the directory's existence.

Suggested change

	if output_dir and not output_dir.exists():
	if not output_dir.exists():