Most of our "django projects" are listed as being written in js on GitHub.

A good half of it may just be "we threw jQuery in here instead of making you download it".

How does it calculate the size of the code base for each language? Most people would be using jquery as a minified oneliner. How can that inflate the numbers so much?

GitHub's source code language detection is over there:

https://github.com/github/linguist/tree/master/lib/linguist

It doesn't measure line length, which could be a good way to detect minified JavaScript. It uses file extensions and byte size. There is some exclusion of commonly bundled libraries, but it's a rough heuristic on file paths.

I'd imagine counting by characters would make a lot more sense than counting lines.