Update docs to be sphinx 3+ compatible

[lilyminium]

Is your feature request related to a problem?

Sphinx is pinned to 1.8.5 which is a pretty old version. I think it has something to do with #2667.

Describe the solution you'd like

Update the documentation so we don't have to pin sphinx to such an old version. However, we likely do have to pin it to mesh well with the RTD theme -- the user guide recently pinned its versions to sphinx==3.4.2 and sphinx_rtd_theme==0.5.1 to fix a search problem. MDAnalysis/UserGuide#141

Describe alternatives you've considered

Don't and hope for the best.

Additional context

[orbeckst]

This is going to be a fair amount of busy-work fixing docs. Perhaps we start a PR and then anyone who wants some good karma can contribute by fixing errors in a few files.

[orbeckst]

Now our CI doc build build_docs is failing, e.g. https://github.com/MDAnalysis/mdanalysis/pull/3421/checks?check_run_id=3690514153

running build_sphinx
Running Sphinx v1.8.5
/usr/share/miniconda/envs/test/lib/python3.7/site-packages/setuptools/dist.py:487: UserWarning: Normalizing '2.1.0-dev0' to '2.1.0.dev0'
  warnings.warn(tmpl.format(**locals()))

Warning, treated as error:
Sphinx 1.x is deprecated with sphinx_rtd_theme, update to Sphinx 2.x or greater
Error: Process completed with exit code 1.