I would recommend giving Pyramid a try: https://trypyramid.com/

It's a framework that allows you to start with a single file, but also allows you to more logically then split your application up and grow with a huge amount of plug-ability while providing many sane defaults to start off with.

It is not a batteries included framework, so it gives you the flexibility to figure out what is best for your application vs being forced into a certain convention.

Full disclosure: I am a maintainer for the Pylons Project with a focus on: Pyramid, WebOb and waitress.