Merge pull request #7 from argju/master

Code changes, documentation, doctest and examples for sigmoid models.
Use spaces, not tabs.
Fix whitespace, text width, docstrings. Fix typos. A couple of simplifications.

Add missing colon in inheritance_diagram Sphinx directive.
Fix Sphinx issue: install.rst:6: WARNING: Duplicate explicit target name: "r".

This rather cryptic warning occurred because install.rst contained both
    Most dependencies such as [...] `R <http://r-project.org>`_"
and
    * `R <http://www.r-project.org/>`_ , version 2.15.1."

Both of these create a target called "R", causing the "duplicate" warning.
Instead, keep just one target and replace the others with references.

-Most dependencies such as `hdf5 <http://www.hdfgroup.org/HDF5/>`_, `R <http://r-project.org>`_
+Most dependencies such as `hdf5 <http://www.hdfgroup.org/HDF5/>`_, R_

Reference:
http://www.agapow.net/programming/python/rest-and-duplicate-target-names
Rewrap lines. Fix typos.
Fix "Inline interpreted text or phrase reference start-string without end-string".

Automatic rewrapping had added a newline before the last backtick in the lines below, causing a
WARNING: Inline interpreted text or phrase reference start-string without end-string.

Diff:

-<http://www.hdfgroup.org/HDF5/>`_, R_ and various `Python <http://python.org>
-`_ packages are in the Ubuntu repositories an can be installed with apt-get.
+<http://www.hdfgroup.org/HDF5/>`_, R_ and various
+`Python <http://python.org>`_ packages are in the Ubuntu repositories and can
Describe lxml dependency and environment variable adjustments. Simplify installation instructions.
Don't require the R "sensitivity" package to run unit tests.
Note on specifying dependencies in setup.py.
Specify nosetests options in setup.cfg.
Workaround for "__test__ = False" not working for anything called setup().

http://code.google.com/p/python-nose/issues/detail?id=326
Merge branch 'master' of github.com:jonovik/cgptoolbox
Add missing "import matplotlib.pyplot as plt" in splom.py.

Also, drop most explicit imports from pyplot and use the plt namespace instead.
Add exclude-dir=cgp/examples in setup.cfg
Merge branch 'master' of github.com:jonovik/cgptoolbox
Clarify installation instructions.

Generalize section on non-root access.
Remove unneeded option to sundials ./configure.
Clarify section on running unit tests.
Add section on environment variables PATH, CPATH, LD_LIBRARY_PATH and pip options.
Add link to scientific Python distributions.
Clean up coding style in cellmlmodel.py.

Reorder imports as per http://www.python.org/dev/peps/pep-0008/#imports
Use np.recarray instead of separate import.
Removed unnecessary alias for cgp.physmod as cellmlmodels.
Generate _cellml2py in user directory to allow root install of cgptoolbox.

sys.path is extended with $HOME/_cgptoolbox at runtime.
Fix generation of benchmark code in Cellmlmodel.makebench().
Specify customized CellML files as package_data={"cgp.physmod": ["_cellml/*"]}.