Remove pydocstyle and configure ruff check for D rules

[eracah]

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Pydocstyle is now deprecated, so we remove it and configure ruff to do what it did.

Our pydocstyle did the following:

• used "google" style, which enforces all D rules except D203, D204, D213, D215, D400, D401, D404, D406, D407, D408, D409 and D413
• ignores (adds to the the "google" style ignore list) D102, D105, D107, D401
• selects (aka removes from the "google" style ignore list) D400, D404

To enable the above functionality in ruff, we:

• select all D rules
• ignore: D102, D105, D107, D203, D204, D213, D215, D401, D406, D407, D408, D409, D413
• ignore 103 and 417 since those resulted in fresh errors when we disabled pydocstyle (so that means we didn't enforce them?)

Also:

• a couple files got minor fixes with the new setup