General code cleanup

[slinderman]

Now that more folks are using pylds, it would be good to go through and clean up the code a bit.

• [ ] Fix or make issues for TODO's
• [ ] Remove commented code
• [ ] Write nice function comments for principal code entry points in models.py
• [ ] Move examples to Jupyter notebooks (easy to see in github)
• [ ] Make sure all the main parameters are easily accessible (A, B, Q, C, D, R)
• [ ] Move experimental features to branches