Cleaning up the branch
Cleanup, some work

Removed the cruft (most of it at least) and continued working on the
networkx implementation
Bringing CML back

Getting CML up to speed with the new interface.  Also added some stuff
to testing to make sure I import the new testing programs
Linear paths

- Sidelined CML, it isn't as important
- Linear paths are working
- Added some stuff to how tests are run
Added s

- Json serialization, string support
- Removed cruft
- Fixed CML to work with the updated stuff
- Preparing to merge with the master branch, I'm basically done with
networkx stuff
Merge remote-tracking branch 'origin/Graphing_3'

Merging Graphing_3 and master

Conflicts:
	CheML.py
	Testing/__init__.py
	Testing/test_CML.py
	compound_graphs.py
	periodic_table2.py
Fixed minor bug

I was accidentally still making periodic_table2.py