You don't. Ren'Py only features basic encryption to prevent players from accidentally deleting/modifying files.
As security, game encryption isn't a fight worth picking. You have to decrypt the files to run them and that will always be a weak point to exploit. Anything you put on top is just delaying whoever wants in. You can write your game in binary and it will do exactly squat to someone who really wants to take it apart.
Ren'Py is designed to be mod friendly. Nothing you do will stop someone from dropping a rpyc file into the game directory and hooking into the game. Even if you modify the engine to only read specific files, you won't stop someone who can just insert the functionality back in. All you're really doing is making it more difficult to preserve the game after you're dead.
Nintendo can't stop people from extracting assets from their games. You don't stand a chance. You should hope to be so lucky as to have people interested enough in your game to want to mess around with the assets and code.
If you're talking about a license players need or some sort of login mechanism, you need to implement an online server to validate the credentials they input. There is no secure front-end way to validate credentials.
For all those who are not familiar with ren'py: It's basically python with some modifications. Since the project is coded in python, which can easily be edited by anyone it is not a good idea to include a license validation in the python files.
An executable starts the game, so I thought about wrapping it with a license validation in an .exe (but I honestly don't know how I can take an executable, put some code around and have one executable including the actual one). Maybe there is another way, which is safer than the one I named, suggestions?
How to protect my ren'py project from being copied?