More coherent dependency handling

[bwohlberg]

The current dependency specification approach should be revisited. In particular:

• Coherent choice of required vs optional dependencies
• Specification of dependencies in a way that supports installation of astra via conda
• Specification in setup.py vs requirements.txt files
• Support for optional dependencies in setup.py

See also discussion for #139.

[Michael-T-McCann]

Adding on a couple problems I faced when remaking my conda environment to try to build the docs:

• pip-installed pandoc isn't working for me (need the command-line version), need to install pandoc with conda
• pip isn't able to install pygraphviz without graphviz installed on the system
• ipython is a requirement to get syntax highlighting in examples, but is not in any requirements file