Fix COFFEE install instructions.

Fix problems with the current COFFEE instructions:

* Move COFFEE from the section which users are told to skip if they
  don't want GPUs to the compulsory section.
* Tell ordinary users to pip install COFFEE.
* Move the networkx dependency in with all the other required
  dependencies.
Remove explicit networkx dependency.

COFFEE installs this anyway.
Merge pull request #416 from OP2/unbreak_coffee_instructions

Fix COFFEE install instructions.