Securely storing environment variables in GAE with app.yaml

I need to store API keys and other sensitive information in app.yaml as environment variables for deployment on GAE. The issue with this is that if I push app.yaml to GitHub, this information becomes public (not good). I don’t want to store the info in a datastore as it does not suit the project. Rather, I’d like to swap out the values from a file that is listed in .gitignore on each deployment of the app.