Enable ruff lints and fix them

[berquist]

A follow up and more systematic approach to #1303.

This is, at least initially, a catch-all for cleaning up the codebase.

Deleting this line

cclib/pyproject.toml

Line 18 in 2193e9b

select = []

reverts to the default set of linting rules, which is (https://docs.astral.sh/ruff/configuration/)

select = ["E4", "E7", "E9", "F"]

which enables all rules beginning with the given prefix. Above, this is all rules originating pyflakes and some originating from pycodestyle.

All available rules are at https://docs.astral.sh/ruff/rules/. Beginning with the default rules seems like an ok starting place.