Fix some doc warnings and convert to myst

[ascillitoe]

This PR converts the alibi docs to use myst files instead of rst (for consistency with alibi-detect SeldonIO/alibi-detect#325).

This allows for the now deprecated m2r to be removed, and the use of newer sphinx versions going forwards.

TODO:

• A thorough check of the compiled html and latex docs, including api docs. - All looks OK, except for known issue with Bases in api docs.
• Update doc/README.md with a few myst specific details. - Done
• Include xgboost_model_fitting_adult.ipynb in examples, or add orphan tag. - Orphan tag added.

Relevant issues:

• Investigate MyST for doc building #348

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[codecov]

Codecov Report

Merging #482 (965d92c) into master (ef757b9) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master     #482   +/-   ##
=======================================
  Coverage   82.32%   82.32%           
=======================================
  Files          76       76           
  Lines       10315    10315           
=======================================
  Hits         8492     8492           
  Misses       1823     1823           

Impacted Files	Coverage Δ
alibi/explainers/anchor_text.py	86.61% <ø> (ø)
alibi/utils/lang_model.py	96.58% <ø> (ø)

[ascillitoe]

More detailed checks picked up a number of issues in the docs with some (especially amsmath) math environments within Jupyter notebook-derived pages. Standard display math i.e. $$...$$ is fine, but math blocks such as:

\begin{equation}\tag{1}
...
\end{equation}

and

\begin{align}

\end{align}

are not showing up properly in html. alibi-detect is fine for now as we don't have such complex math use cases in the docs. This issue seems to be something to do with myst overriding the mathjax config. Setting myst_update_mathjax=False in conf.py helps sometimes, but not reliably.

These issues seem to all be fixed in sphinx>=4.0 so I think we should wait until we upgrade to sphinx==4.3.0 before moving the alibi docs to myst (related to SeldonIO/alibi-detect#338).

[ascillitoe]

Update: After offline discussion, we have decided to go ahead and merge this in before sphinx 4.3.0 is released. This will break the Bases field in api docs for submodules/subpackages such as https://docs.seldon.io/projects/alibi/en/latest/api/alibi.models.tensorflow.actor_critic.html.

Since this PR will now be merged in, I have opened an issue (#505) as a reminder to update.