Run with PYTHONWARNINGS=d to reveal deprecation warnings, etc.
It would be worthwhile for you to make your tests run with warnings on. flake8 3.2.1 raises a DeprecationWarning on Python 2:
flake8/options/config.py:56: DeprecationWarning: You passed a bytestring as `filenames`. This will not work on Python 3. Use `cp.read_file()` or switch to using Unicode strings across the board. found_files = config.read(files)
It comes from the fact that
read() should take either a list of filenames or a Unicode string.