Fix linting

[hechth]

Currently many linter warnings are suppressed - this should be addressed and actually fixed rather than suppressed.

[florian-huber]

@hechth good point!

So here is a better place the the current PR for my suggestion:

I would switch from pylint to ruff as we did for MS2DeepScore.

The workflow would need something like this:

      - name: Check style against standards using Ruff
        run: ruff check .

And we could add a config file ruff.toml or .ruff.toml, e.g. like this ruff.toml. In principle this should also work with something like tool.ruff in the existing toml-file.