Cleanup Sphinx documentation

[lundybernard]

The documentation needs to be reviewed and cleaned up. Feel free to take on smaller tasks and open new Issues to track them.

Some things that need improvement:

• Auto-generated API documentation
• Add a detailed User Guide
• Enable make docs from the project's root directory, so we don't need to cd into docs/

[lundybernard]

• Add versions to the sphinx documentation on readthedocs.io, ensure 'latest' points to the latest released version.