Various Python 3 support updates

[aliask]

Sorry for the massive pull request.

At a high level, this PR:

• Consolidates Python 3 as the only supported version
• Fixes a number of issues relating to this transition, however I make no promises about full compatibility. More tests are needed.
• Add a Dockerfile to get a quick working environment
• Update README with updated installation instructions (including Docker) and updated usage output
• Begins to split the main file out to more manageable chunks
• Adds a couple of new tests

Still needed:

• More tests. I have no idea if half this stuff still works.
• Delete unused code.
• MacOS and Windows installation instructions should be updated
• More tests.

Appears to address #25 , #30 , #38 , #39 , #40 , #41