Draft: Aligning the code with contributing guidelines

[shakedregev]

This is my first pass at the cleanup of the code. It's not ready yet.

1. There's a stylistic choice of inline functions that does not really go with rest of the code. I want to understand the rationale or change it to regular functions.
2. Most functions do not have explanations of their parameters (and are not marked in or out)

[shakedregev]

I further noticed that COO_Matrix is incorrectly defined with an underscore. Is this on purpose?
I put comments in the code, you can search for "SR".