Doc Strings, Readme, and Drake #2
Description
Doc string ALL THE THINGS!!! It helps with readability. Whether it's a collaborator, coworker, or your future self, having a general description of what the script/class/function is supposed to do go a long way towards implementing the code.
I would recommend moving the stuff that's currently in the Readme to doc strings the respective script. Save the readme for a more detailed explanation of what it is you're trying to accomplish and a high level of how you did it.
Since it sounds like most of this needs to be done sequentially, you might want to check out Drake. It's Make for data let's you chain together various commands. So if C depends on B which depends on A, you can run Drake and it will run A --> B --> C. Also say if you changed B and only B, the next time you run Drake only B and C will be executed.