ruff instead of black / isort

[biobootloader]

Pull Request Checklist

• Documentation has been updated, or this change doesn't require that

[mentatbot]

It's a good practice to verify the integrity of the script before executing it. Consider adding a checksum verification step for the install.sh script to ensure its authenticity and integrity.

[mentatbot]

Using uv pip install directly might not be clear to everyone. Consider adding a comment explaining that uv is a tool for managing Python environments and that this command installs dependencies in a virtual environment.

[mentatbot]

Appending to the PATH environment variable directly in the script can lead to unexpected behavior in complex workflows. If possible, consider using environment files or other GitHub Actions features for setting environment variables.

[mentatbot]

The ruff format --check . command is used to check formatting without making changes. If the intent is to also format the code, consider running ruff format without the --check flag in a separate step that only runs on a specific branch or conditionally, to avoid unintended code changes in pull requests.

[mentatbot]

MENTAT CODE REVIEW IN ACTIVE DEVELOPMENT. Only in use on mentat and internal repos.
Please Reply with feedback.

The switch to using ruff for linting and formatting is a significant change. Overall, the implementation looks solid, but there are a few areas where clarity and security could be improved. It's also important to ensure that contributors are aware of this change and understand how to run these checks locally to reduce CI failures.