Feature/python scipts formatting linting

Fixes #1050 (closed)

TODO

• Make all the linters happy (pylint is the most difficult but has good suggestions)
• Make sure the scripts are still working (some changes are at least somewhat non-trivial)
  • bin/testing (can be decently tested by running CI with some fake change)
  • bin/postprocessing -> manual testing (partially tested)
  • extract_module -> manual testing
  • create_docker -> manual testing (partially tested)