delete all commented out code

[morganrivers]

if you want, you can add a conditional like this if you want some options in your code:
CONDITION = True
if Condition:
print("condition is true, run some code")
else:
print("Condition is false, runs some other code")

[jamesmulhall]

This has mostly been addressed, but there are still some cases where code is commented out instead of dealt with properly. I'll leave it open, but unlikely to be addressed unless further work is done with this repo after the paper is out