Fix all stylistic and docstring issues reported by flake8

[Midnighter]

So far, we have been using pep8 for style checks. This has been deprecated for ages and I finally replaced it with flake8 in #969. However, flake8 checks are much more extensive and pedantic so there are many issues to fix. Currently, flake8 is ignored during continuous testing which should be remedied as soon as possible.

This is a big clean up effort and will touch almost every module.