I've been spending this week figuring out how to run doctests individually for modules in VCS.
To that end, I started using doctest.testmod, which enabled me to make a python script that runs testmod for an individual module. If given the correct commnd-line options, it will also parse a results file for the doctest and create a (simple) .md-formatted log for easy viewing.
I needed to run the tests individually because there is no good way of completely cleaning VCS up without just tearing it down and starting a fresh session. Sphinx's built-in doctest extension didn't allow me to do that. So the process now if for me to run a shell script which runs all the doctests in individual modules, and then logs the relevant results into .md files.