Clean up documentation build warnings

Description of your problem

When building docs there is a cascade of warnings, from reference issues to unused files. It would be great to clean these up as the preexisting warnings make it challenging to add docs, as new warnings are lost in a sea of red.

Namely there are some general categories of what needs to be done

Fix formatting issues that are raising warnings

/home/canyon/repos/pymc/docs/source/api.rst:38: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/canyon/repos/pymc/docs/source/api.rst:41: WARNING: Bullet list ends without a blank line; unexpected unindent.

Clear autodoc import issues

WARNING: autodoc: failed to import method 'Chain.init' from module 'transforms'; the following exception was raised: No module named 'transforms' WARNING: autodoc: failed to import method 'Chain.backward' from module 'transforms'; the following exception was raised: No module named 'transforms' WARNING: autodoc: failed to import method 'Chain.forward' from module 'transforms'; the following exception was raised: No module named 'transforms'

Determine what to do with unlinked documents /home/canyon/repos/pymc/docs/source/api/math.rst: WARNING: document isn't included in any toctree /home/canyon/repos/pymc/docs/source/api/shape_utils.rst: WARNING: document isn't included in any toctree

There may be others as well

Dependencies

jupyter-sphinx==0.3.2
pydata-sphinx-theme==0.7.2
sphinx-copybutton==0.4.0
sphinx-design==0.0.13
sphinx-notfound-page==0.8
sphinx-remove-toctrees==0.0.3
sphinx-togglebutton==0.2.3
sphinxcontrib-applehelp==1.0.2
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-htmlhelp==2.0.0
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml==1.1.5