Paper branch

[conorheins]

• JOSS manuscript now in paper folder
• initial changes based on reviews from @seankmartin (added Summary section to paper, added documentation for Agent API)
• other minor tweaks (some minor variable renaming in the internals of Agent)

[conorheins]

The new Agent API autodocumentation was in response to #67 by @seankmartin (see also https://github.com/openjournals/joss-reviews/issues/4098#issuecomment-1049772353). That new documentation can be found on the RTD page specifically for the paper_branch, which can be found here: https://pymdp-rtd.readthedocs.io/en/paper_branch/agent.html

I am not going to close #67 because we still need to add API documentation for the Env base class to the RTD website to fully address @seankmartin's comments..

[conorheins]

In response to #67 and https://github.com/openjournals/joss-reviews/issues/4098#issuecomment-1049772353, we have now added a specific sub-section in the APIs documentation section that documents the Env base class and the sub-class implementations. That can be found here: https://pymdp-rtd.readthedocs.io/en/paper_branch/env.html

I think this now fully addresses #67