In my case I'm using the Dropbox API. Currently I'm storing the key and secret in a JSON file, just so that I can gitignore it and keep it out of the Github repo, but obviously that's no better than having it in the code from a security standpoint. There have been lots of questions about protecting/obfuscating Python before (usually for commercial reasons) and the answer is always "Don't, Python's not meant for that."
Thus, I'm not looking for a way of protecting the code but just a solution that will let me distribute my app without disclosing my API details.