Apply black and flake8 + add to ci

Common flake8 warnings

• type(var) == int is replaced isinstance(var, int) and equivalent occurences
• Bare excepts except: are replaced by except Exception: because they capture SystemExit or CTRL-C (BaseException) and sometimes absorb it
• Multi-lime imports are split. For example import os, sys, unittest
• Variable is assigned but never used. For example unused = myfunc(...) becomes _ = myfunc(...) or remove the call in case there are no side effects and it is not intended as a validation.
• Module level import not at top of file.
• Module imported but unused.
• not a in b becomes a not in b
• A function def run(beamline, **kwargs): which does not use kwargs can be defined as def run(beamline, **_):
• unicode is str but when used in combination with str (which used to be bytes) you need to take care of str and bytes