My recommendation though, it must be kept neat and tidy. 100%. Plus, keep paper notes. It gets complex real fast. Spend your time on good naming conventions and being VERY well organized. Obviously all projects should be that way. But this is one where it's not really a recommendation. It's a flat out must. Don't fall into the trap of "hacking" in something to make it work. Not even once. If something is wrong, fix it completely the moment you notice it. My experience, neural net hacks compound really fast into trouble.
Plus, I had fun with my naming conventions. My hidden layer cell class is called a "centralized understanding neural tracker" with the input cells called "data input command kontroller". As you can tell, I'm not a very mature adult. Pretty sure it wouldn't be appreciated in github.