Switch from flake8 to ruff - and run various linting cleanups

[notatallshaw]

This PR is to switch from flake8 to ruff as the linter, the motivation here is two fold:

• flake8 E704 is not compatible with the black 2024 style - and flake8 maintainers seem uninterested in making this rule compatible with this common style, whereas ruff maintainers seem to be eager to keep in-line with modern black style
• there are many additional rules that come with ruff that can be turned on automatically or easily run manually, and high pace of adding new ones

I may have gone overboard with this PR, let me know if I should make it a minimal transition, but I have split it out hopefully into easily digestible commits.

My biggest concern is 949e612 which moves _patch_criteria into it's own method, rather than an inline function. This personally reads better to me, but I am not a frequent programmer of algorithms that use functional programming. Happy to revert.