Doc/cross reference

[timsaucer]

Which issue does this PR close?

No existing issue but a follow on to #750

Rationale for this change

This is almost entirely a documentation update. It allows us to expose all the python APIs on the documentation site. Additionally the cross linking is fixed so that docstrings can link to other functions and classes.

What changes are included in this PR?

Switch from autodoc and autosummary to autoapi.

Change docstring and document rst files to use the generated references.

Are there any user-facing changes?

Updated site documentation, but APIs themselves are not impacted.

Here is a screenshot of documentation site built locally without this PR:

And here is the updated view:

The four points of interest highlighted are:

1. On the navigation bar on the left, now the entire API is exposed. This does come at the cost of no longer pointing out only the most important sections of the interface.
2. Cross linking works from docstrings to the online user documents. That is, you can now cross link from a docstring to a portion of the online manual without a hyperlink required. This helps prevent breaking if the paths change in the online docs.
3. Cross linking now works from one docstring to another class, function, module, etc.
4. The right hand side bar is a little different. I also played around with changing the depth of this but it did get very busy. That might be helpful for easy navigation though.

[Michael-J-Ward]

#795 fixes the missing export tests, right?

Maybe just include that commit in this PR?

Otherwise, LGTM