Switch to use `ruff`

This pull request has the project switch to using ruff instead of pyflakes and handles the slight differences it has. I was considering moving this into another pull request to follow this one, but I also switched to using ruff's integrated version of isort as well. They have a quite compelling advertisement of sorts of why you should use their system in [their readme](https://github.com/astral-sh/ruff#readme), but in the end I am suggesting to switch to ruff because it's got nearly all the warnings flake8 does but also has autofix support, and it's way faster. https://github.com/astral-sh/ruff/issues/970 is tracking pyflakes re-implementation progress, and using ruff opens the door to enabling even more checks in the future with almost no performance loss for doing so.