Use only one tool for Python code reformatting

[luizirber]

Currently we use pep8 for checking for PEP 8 errors and autopep8 for automatic formatting. autopep8 is catching more errors than pep8, so sometimes make pep8 doesn't report any errors, but make format will change the code.

We can unify and use only autopep8 by modifying the pep8 Makefile target to:

pep8: $(PYSOURCES) $(wildcard tests/*.py)
    autopep8 --recursive --diff --exclude _version.py --ignore E309 \
                setup.py khmer/*.py scripts/*.py tests/*.py oxli/*.py

but this only shows a diff with the errors, not an explanation of the error like pep8 does.

Initial discussion: https://github.com/dib-lab/khmer/pull/1145#discussion_r33968901

[bocajnotnef]

Is there something preventing us from using the same version of pep8 as autopep8, as @mr-c suggested?

[luizirber]

@bocajnotnef updating pep8 won't solve the issue, since pep8 is not reporting the error anyway.