Code formatting / changes for pep-8 compliance

This PR gets our codebase up to pep 8 compliance for all but line length considerations, such as when being run via:

```
flake8 --ignore E501 .
```

The first commit deals just with whitespace changes and the subsequent commits deal with code/style changes.
Agree - I don't like the pep8 line limits for comments in general since some comments have to be longer than X characters, but there doesn't seem to be a way to have pep8 differentiate between comments and code.