Features/improve code style

[ClaraBuettner]

Fixes #445

This branch applies black, isort and flake8 changes to (nearly) all files, with the following exception:

• flake8 tests for "Can not use bare except" are currently excluded. I tried to fix those problems, but since I didn't know the error that could show up for all occurrences, I was not able to fix all of them. We should follow up on this, see Replace bare except statements #669
• the plot.py is not checked yet, since there will be many changes in Feature/#532 update to plotpy #568
• the appl.py is not checked yet, since there are many warnings concerning the overly long comments in the args

I guess none of these things prevent us from merging this branch, I just added the limitations to not forget about them.

[CarlosEpia]

I tested this branch and it is working as expected.