Add some helpers

Accessing the database and the like is a very common activity so I'm adding
helpers for that stuff. The database help allows one to do things like:

    with self.session() as session:
        code

making it easier to have a session per step and the like. It will handle rolling
back on exceptions and has some generic logging for such things. It also has
some simple code for storing data.

I've also added a cif file finder helper. This shows up in a couple places so
I've added code for it. Simple code, nothing special but useful. There are tests
for it as well.
Minor reogranization
Add row2dict function
Add useful grouper function
First chain break loader class

This is a first pass at making something which can load chain breaks from a PDB
file.
Update chain break storage

This now uses a new table and thus a new model. Also, I store pdb, model and
chain as well.