Thanks, I will work on incorporating these changes. In my defense it was my first project and I was solely focused on getting the results and didn't focus much on making the code "accessible"

This is a good summary of a large portion of code written in academia. "Didn't know how to program," "wrote it for myself," and "just trying to get a result." I've heard that a billion times. Not such a big deal if it's just for yourself and not shared with the world. Unfortunately in larger academic collaborations these mentalities end up slowing down research more than enabling it. (And if you intend on making your research public, the "collaboration" should be seen as anyone who views your github.)

Academics are great at finding "local optima," but rarely do they see beyond their next result, and then others have the onerous task of trying to verify the previous results or worse still using the previous work to build towards "larger" results.