Run Black, flake8, and isort via tox.ini (#294)

We add three commonly used linters and code formatters; Black, flake8, 
and isort. Together they make sure all Python code is consistently
formatted and has a reasonably consistent style in other aspects. All
code has been adjusted to satisfy these programs.

Of the flake8 corrections made, one was a rather subtle shadowing of
the json module import in a loop variable. The variable was renamed
to better describe what it contains.