Improve documentation and output of documentation

[dccote]

Move to Sphynx and sphynx-style documentation because the current format looks like garbage.

1. This requires looking through the different formats for Python documentation here: https://realpython.com/documenting-python-code/ and here: https://www.sphinx-doc.org/en/master/
2. Using a simple test file such as rays.py, see what the output format looks like once it is formatted properly.
3. Modify all source files to adopt the documentation format
4. Create scripts to fully document and update when needed.