@jensenja The errors on Python extension are from python extension probing the various python installs it finds on your system. You don't need to do anything in particular as long as your flake8 ...
I am running pybuilder from a dedicated python3-only venv. I am not "activating" the venv but rather call <venv>/bin/pyb which is AFAIK a supported approach. strace shows that the system flake8 ...