Clean up the code

[jnfrye]

Before I work on any new features, I want to clean the code up a bunch. I'll use this issue to keep track of what needs cleaning up.

• [ ] Refactor similar code into submodules
• [ ] Examine the code with pylint and coala
• [x] Re-organize file layout

[jnfrye]

Re-organization of the code is taking place in branch reorganizing_files.

[jnfrye]

I've started to address the import problems from reorganizing the code by adding a setup.py file that will let python see this project if you run the script. There might be a better way, though, and I'm not sure this will solve the problems I'm running into.

[jnfrye]

Finished reorganizing files. See commit 820ebaa

[jnfrye]

EDIT: This is now its own issue: #8

Coordination of data output is taking place in branch data_output_configuration.

I am thinking of having a coordinate_data.py file that can be imported by scripts and used to get the appropriate folders for input/output. Also, in the setup.py file, I want to make it so it creates a configuration file or something that specifies where to send data, with the default behavior being a folder located relative to the setup script: ../data/ etc.

[jnfrye]

Refactoring is taking place on branch refactoring_first_pass