(chore): update linting/formatting + pre-commits

[giovp]

starting with adding pre-commits checks from scverse defaults if useful, consider also using https://results.pre-commit.ci/ for CI linting, feel free to close @ilan-gold

For #380

[ilan-gold]

@keller-mark I like the changes ruff made vs. autopep8 / flake and pre-commit runs automatically including backfilling with commits. Feel free to close if you just want to keep things as-is