Update deps to latest supported & minor cleanup

[BelleNottelling]

This pull request updates all of the python dependencies to the latest supported by Python 2.7 & removes some unneeded deps to reduce unneeded image sizing.

I did try to perform a full upgrade to python 3, but I ended up running into issues that weren't very obvious to me. I'll likely look into those at a later date, but this at least gets the docker image a little bit closer to being up-to-date.