update docs to python 3

[bobmyhill]

The old sphinx conf.py file does not work with python 3.
This PR

• updates that file,
• updates the master index file, and also
• removes some whitespace and duplicate keywords variables from ref.bib.

[tjhei]

Can you use the authors variable instead?

[bobmyhill]

This still isn't working; a lot of the docs are missing. I'll see if I can fix it tomorrow.

[bobmyhill]

Ok, the autogenerated part of the manual is complete again. I needed to explicitly set the autodoc settings with some or all of the below (depending on case):

  :members:
  :undoc-members:
  :show-inheritance:
  :inherited-members:

[tjhei]

I am not sure, but can you achieve the same by setting https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html instead of adding it to every class?

[bobmyhill]

Ah, thanks @tjhei. The autodoc defaults weren't being obeyed because the object name changed, and is now required to be a dict rather than a list.

The functionality has still changed a bit (it is now more logical), but I've been able to remove most of the new lines.

[tjhei]

Looks good!