Updates to Sphinx 3.2.x

I had to update doc/conf.py since an old flag we were using autodoc_default_flags is not supported anymore. The new one is autodoc_default_options (https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html#confval-autodoc_default_options). After activating it, we observed a few more issues related to double-documentation of attributes in some classes.

@amohammadi: there are some take-aways for Bob projects here as well.