Workflow for Python with Docker + IDE for non-web applications
Actually, I believe that using the Docker interpreter in PyCharm is the way to go. Which version of PyCharm do you have? If you have the 2016 version, it should be set up within seconds. You just have to make sure your docker machine is running and you must have your image built that you would like to use with your project. PyCharm will find the Docker machine in the "add remote interpreter" dialog automatically. Then select your image and you're all set up.
You can run your code as usual then, almost without any delay.
Here's what worked for me: https://www.jetbrains.com/help/pycharm/2016.1/configuring-remote-interpreters-via-docker.html
And make sure to update PyCharm, that solved some issues I had.