Flake8 fixes

[timvaillancourt]

This PR moves the code to adhering to flake8 with these ignored/exception codes (for now):

1. E221 multiple spaces before operator = because we align equals-signs and dict colons (=/:) in the code.
2. E241 multiple spaces after ':' = same thing as E221.
3. E501 line too long = this is valid and should be fixed but one step at a time.

NOTE: "# NOQA" tags are added to our dynamic imports that cause flake8 issues. Due to the way we dynamically load our modules I don't think this can be avoided. "# NOQA" causes flake8 to ignore the problem in these cases.

The fixes in this PR were mostly:

1. Functions/modules imported but not used.
2. Variables set but not used.
3. Whitespace issues.
4. In a few cases Error-types used but not imported.
5. 'if !=' to 'if not' style fixes.

After this is done we can do flake8 checks in travis-ci (after #197 is reviewed/merged)