made sbml export compartment 3d and size=1
improved font handling in render_species output
fix to make setup.py get_version more robust

Now it only considers a git repo in which setup.py lives at the top level.
This fixed the problem where running setup.py with a relative path from another
directory which happened to be a git repo, or installing the sdist from inside
some other git repo, would make get_version report the version of the *other*
repo.  This was initially encountered in the readthedocs.org build environment,
where the builds seem to be run within the git repo of the RTD source itself.
Modified kappa.py

Added basic documentation to each function. Also made the call to open_file
(to open .gv or .jpg files for contact/influence maps) optional.
Fixed a bug in keyword arg ordering for influence_map
Set influence_map to return influence map filename

I wanted to turn the influence map into a computable networkx
or PyGraphViz object. I thought about creating a new function,
influence_map_as_graph() or something like that, which would
make the influence map and then return the graph built from the
.gv file, but I figured that this would introduce an extra
and completely unnecessary dependence for kappa.py and PySB.

So I left it that influence_map returns the filename, and then
it's trivial to get a Graphviz or networkx object as:

  import pygraphviz as pgv
  import networkx as nx

  graphviz_graph = pgv.AGraph('im_filename.gv')
  nx_graph = nx.Graph(graphviz_graph)
Fixed run_kasim to use new syntax for influence maps

In the previous version, KaSim would generate the influence map if a -im
argument was provided at the command line. In version 3, a %def declaration
is added to the kappa file. I modified the run_kasim function to add
the necessary syntax. I left a placeholder for putting in perturbation
language stuff too, but I haven't really fully implemented that yet.
allow util.write_params to return content
Wrote documentation for run_kasim function

Also changed kappa_filename argument to base_filename.
Changed indentation to 4 spaces from 2
Removed function for generating influence map via Complx
Documentation for all functions in kappa.py
Completed documentation for kappa.py.

Also added a kappa.rst file for kappa.py to be autodoc'ed.
Will do generator.kappa documentation along with documentation for
generator.bng.

Closes issue #51.
refactor odesolve into a class

This makes re-solving the same model over and over with different
parameters (as used in parameter estimation) much faster. It retains the old
odesolve() function, implemented as a call to the new class-based
implementation.
Merge remote-tracking branch 'johnbachman/master'
switch to using external numpydoc package
documentation for integrate
fixed bug in macros.catalyze regarding sites

We were using e_site with product instead of s_site. Since all our models used
the same site 'bf' for e_site and s_site this went unnoticed for a while.
fix to integrate for models with no observables
make catalyze support s_site having a state