Ruff formatting and style fixes

[Yannicked]

Automated formatting and linting fixes obtained by running:

ruff format
ruff check src tests --fix
ruff check src tests --fix --unsafe-fixes

[olivhoenen]

Ok. Would be good (next PR in the pipeline maybe?) to add an action workflow for linting, and add a small item in https://github.com/iterorganization/SimDB/blob/develop/docs/developer_guide.md to show contributors what is expected and how to check it themselves.