Simplifying the test suite

[alexrd]

Simply installing pytest and running pytest in the main wepy directory will run meaningful tests that cover a large range of the practical wepy functionality.

Other changes:

• deleting older tests
• removing mdtraj from required packages
• removing topology as a required argument for HDF5Reporters and WepyHDF5s (now it is only recommended)
• updating geomm dependence (to include the minimum_distance function)

Because of the latter, this should not be merged until the geomm 0.2.1 version is up.

[salotz]

I'd recommend merging the commits I made before making more changes so the PR is smaller. There are 240 files changed currently so I can't see what changed easily.