My biggest takeaway from the article is that you "want something simple", and most people would agree with you. What you don't talk about, or dodge along the lines of is saying "X is how we should do it".

Personally I like node's way of using package.json and cargo's Cargo.toml. If someone made that for python that'd be awesome.

The other thing node has specifically is the "node_modules" folder, which recursively has all the dependencies and their node_modules folders. While it might not be super space efficient it's really stupid simple.