maint: fix code style, check on gha

[dweindl]

Follow-up to #251

• Manual changes for compatibility with selected ruff rules
• run pre-commit hooks on GHA instead of flake8
• run tests on python3.12

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 76.92308% with 6 lines in your changes are missing coverage. Please review.

Project coverage is 76.24%. Comparing base (b7d6130) to head (3fdc57f).

Files	Patch %	Lines
petab/problem.py	78.57%	3 Missing :warning:
petab/core.py	50.00%	1 Missing :warning:
petab/sbml.py	0.00%	1 Missing :warning:
petab/simulate.py	66.66%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## develop #252 +/- ## =========================================== + Coverage 76.20% 76.24% +0.03% =========================================== Files 34 34 Lines 3215 3216 +1 Branches 780 780 =========================================== + Hits 2450 2452 +2 + Misses 561 560 -1 Partials 204 204 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.