Various flake8 fixes

Fix issues in the Python scripts to fix various issues reported by flake8, some related to PEP 8.

Introduce a .flake8 configuration file, so it is possible to run flake8 safely on the source tree to check for errors in local changes. This configuration has ignores for the current issues, which are mostly related to style, and one legit import situation. Possibly a good idea here would be to reformat the code base using black, to uniform the style also to other projects, and get rid of those issues.