Use ruff for code style checks.

[joaander]

Description

• Use ruff to perform more code style checks in less time with a simpler pre-commit configuration.
• Make changes to the code so that all enabled ruff checks pass.

A future pull request will use ruff for formatting as well. The PRs are separate to separate the review of the fixes for checks separately from the fixes that come from the auto-formatter.

Checklist:

• I have reviewed the Contributor Guidelines.
• I agree with the terms of the HOOMD-blue Contributor Agreement.
• My name is on the list of authors.

[review-notebook-app]

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[melodyyzh]

Everything looks good to me. I have one question regarding the output format in the 04-Custom-Actions-In-Python/04-Custom-Updater.ipynb notebook. When output the KE, PE, and total E, there's a gap between the output values and the top of the cell, I am not sure if that is just a display issue in reviewnb.

[joaander]

Everything looks good to me. I have one question regarding the output format in the 04-Custom-Actions-In-Python/04-Custom-Updater.ipynb notebook. When output the KE, PE, and total E, there's a gap between the output values and the top of the cell, I am not sure if that is just a display issue in reviewnb.

@melodyyzh the output appears correct in Jupyter. ReviewNB is adding the empty line.