Some PEP8 changes

[leotrs]

This is a mostly harmless PR as almost all it does is fix some whitespace/indentation issues that were driving my linter crazy.

The only changes that I would ask to be reviewed carefully are the ones on the last commit. These ones address the "undefined name" errors. There were two files that were using variables without having defined them first.

Addresses #44.

[leotrs]

By the way, this reduces the number of flake8 errors from 546 to 133.