converted to markdown, with corrections

[jwestw]

Pull Request submission

I have created the markdown version of https://docs.google.com/document/d/1WZUjNgiQwbN0AOrqpznFUNeYeo_XncuIzyAFFOm4LOA/edit?usp=sharing

I have not rebuilt the Sphinx pages as we are currently looking into alternatives.

Closes or fixes

Fixes #175

Documentation

• [x] Updated Documentation: Working doc has been updated and a new ticket to update the master documentation has been created.

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Peer Review Section

• [ ] All requirements install from (updated) requirements.txt
• [ ] Documentation has been created and is clear - check the google Doc
• [ ] Doctrings (Google format) have been created and accurately describe the function's functionality
• [ ] Unit tests pass, or if not present a new ticket to create tests has been created
• [ ] Code runs The code runs on reviewer's machine

Final approval (post-review)

The author has responded to my review and made changes to my satisfaction.

• [ ] I recommend merging this request.

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Review comments

Insert detailed comments here!

These might include, but not exclusively:

• bugs that need fixing (does it work as expected? and does it work with other code that it is likely to interact with?)
• alternative methods (could it be written more efficiently or with more clarity?)
• documentation improvements (does the documentation reflect how the code actually works?)
• additional tests that should be implemented (do the tests effectively assure that it works correctly?)
• code style improvements (could the code be written more clearly?)

Your suggestions should be tailored to the code that you are reviewing. Be critical and clear, but not mean. Ask questions and set actions.