improve documentation in main loops

[amoodie]

some docs effort. Nothing important.

[elbeejay]

Few minor things but overall it is a pretty straightforward one.

Realized I need to look into my local sphinx setup as well as the stratigraphy stuff (#43, some of which you created a framework for documenting here)

[elbeejay]

I guess a follow-up note was that I re-built an environment to try to sort out the docs locally and still didn't get the full API documentation and method links. Checking the hosted documentation reveals that we have the same issue with the 'live' version (e.g. here). I don't have a clue as to why it isn't working (especially given that it appeared to be fine on your local version).

[amoodie]

thanks for checking it out @elbeejay, and for catching that the builds on travis were JUNK! I've pinned the sphinx version to 2.0.1 (so you should downgrade your environment version) and I've opened an issue to remind myself to revisit this down the road.