Change pre-commit to run ruff and ruff-format with fixes

[boxydog]

Pull Request Checklist

Resolves: 3216

• Ensured tests pass and (if applicable) updated functional test output
• Conformed to code style guidelines by running appropriate linting tools

[boxydog]

FYI:

This changes 26 files, while #3239 changes 27. The difference is I didn't port over the log.py change:

__all__ = ["init", "console"]

That change is valid IMO, but isn't part of the ruff fixing. I had just made that change because PyCharm pointed out that the console symbol was being used but not exported.

[justinmayer]

Many thanks for all your work on this, @boxydog! 🌟