Added short hidden section at beginning of cookbook snippet sections explaining how to run the snippets

* Recovered quickstart section in html, added tutorials placeholder and implemented rudimentary integration between doxygen and sphinx (dependecy on breathe sphinx extension)

* removed recursion limit change

* Added section to quickstart, and fixed a few minor typos in the install page

* Updated installation documentation with new mac osx brew install procedure. Made new section for OSX for consistency of format.

* removed some breathe related stuff from conf.py

* fixed minor typo in wildcard.py

* Recovered rdesigneur tutorial. Modified file by adding extended contents, commented out incomplete sections. Modified rdesigneur snippets page title to 'more rdesigneur examples' instead of just 'Rdesigneur'

* Added autorun statement to Compartment_net.py.

removed pyrun1.py documentation as it is exactly the same as pyrun.py.

updated vec information in quickstart to reflect actual ouput.

* uploaded fixed compartment_net.py without all my comments

* minor changes to install page, changes to doxygen readthedocs generation

* forgot to add hyperlink for doxygen page

* Added Chemical Bistables section to tutorials. Rest incoming

* Chemical Oscillators added, minor tweaks to Chemical Bistables to match Oscillators page

* Deleted extension pyc file as requested by dilawar

* Changed few names, reordered tutorials

* Changes to fix all non-references related and non-snippets related 'make html' errors

* Update crossComptNeuroMesh.py

* Added squid demo to tutorials. Removed squid demo from quickstart. Wrote a bit of theory and history about squid demo. removed redundant modules.rst file.

* Undid changes to loadSbmlmodel.py as it might have caused the mac travis to fail

Added squid demo to tutorials. Removed squid demo from quickstart. Wrote a bit of theory and history about squid demo. removed redundant modules.rst file.

removed pyrun1.py documentation as it is exactly the same as pyrun.py.

updated vec information in quickstart to reflect actual ouput.

Recovered rdesigneur tutorial. Modified file by adding extended contents, commented out incomplete sections. Modified rdesigneur snippets page title to 'more rdesigneur examples' instead of just 'Rdesigneur'

Recovered quickstart section in html, added tutorials placeholder and implemented rudimentary integration between doxygen and sphinx (dependecy on breathe sphinx extension)

0c5527e77d Why docs were here?
16ef3f4444 Merge branch 'master' of github.com:BhallaLab/moose-examples
a47d702034 Merge commit '48fc9733'
37d94cb38e Fixed the script. Runs with moose-3.1.2.
fcf47109e5 Merge commit 'edd901da' as 'moose-examples'
423c4759 Removed moose-examples due to screwed up history with https://github.com/BhallaLab/moose-examples.
7b366bcb Merge commit '45f9e9b9'
45f9e9b9 Squashed 'moose-core/' changes from b3b597f41..2ecab963b
4c60725d Merge commit 'af3c29a4'
af3c29a4 Squashed 'moose-core/' changes from ef066f704..b3b597f41
60f3632e Fixes to allow moose module to be installed and imported (#220)
7ffff42d documentation branch merge request (#219)
ec194c8a Documentation final PR (#217)
0318bd7e Added python-lxml in dependencies.
226eb630 Added --git-ignore-branch option.
42cb3feb...

80169bcc5c Resolved a merge error.
d5caa39361 use moose.element over  moose.HHChannel.
26e9aac794 Merge branch 'master' of github.com:BhallaLab/moose-examples
9b83291de6 Merge branch 'master' of github.com:BhallaLab/moose-examples
2f46ad096d Convert u'ABCD' to 'ABCD' to probably fix the python3 issue on travis. Works fine with python3 on ubuntu 16.04/Debian8.
6232b3a888 Send email to malav if build fails.
4a92db239b Merge branch 'master' of github.com:BhallaLab/moose-examples
4800cd62df Adding python-libsbml to dependencies.
c045972c2e Fixed second script as well.
e927a88875 Merge branch 'master' of github.com:BhallaLab/moose-examples
626afb8242 Added a hack to make this script work with both python3 and python2.
24fdc9e1b7 Indentation for python3
e9e5d92828  Using force-yes with -y
3c60a8263a Upi fix the assert error
ca2d4090e7 Upi cleaned up the file
a9ddced2bc Merge branch 'master' of https://github.com/BhallaLab/moose-examples
b4715d09ba F...

* changed files in docs folder for final version of documentation

* changed the README.txt file.

* changed the path to moose-examples in conf.py and formatting in chem_GUI

* removed docs/source/user/py/introduction/index.rst, and /install/index.rst due to redundency

* Changed some moose-example files as online readthedocs was generating some issues, and added Makefile in docs/ directory.

* a couple of more changes..

* changed files in docs folder for final version of documentation

* changed the README.txt file.

* changed the path to moose-examples in conf.py and formatting in chem_GUI

* removed docs/source/user/py/introduction/index.rst, and /install/index.rst due to redundency

7318878 cleanups
9b83291 Merge branch 'master' of github.com:BhallaLab/moose-examples
2f46ad0 Convert u'ABCD' to 'ABCD' to probably fix the python3 issue on travis. Works fine with python3 on ubuntu 16.04/Debian8.
6232b3a Send email to malav if build fails.
4a92db2 Merge branch 'master' of github.com:BhallaLab/moose-examples
4800cd6 Adding python-libsbml to dependencies.
c045972 Fixed second script as well.
e927a88 Merge branch 'master' of github.com:BhallaLab/moose-examples
626afb8 Added a hack to make this script work with both python3 and python2.
24fdc9e Indentation for python3
e9e5d92  Using force-yes with -y
3c60a82 Upi fix the assert error
ca2d409 Upi cleaned up the file
a9ddced Merge branch 'master' of https://github.com/BhallaLab/moose-examples
b4715d0 First commit.
2c4fa33 This is removed b'cos Rdesignuer does the job
4ca1f6d missing closing braces
d120484 small correction for input eval with is str
18990fd enter key replaced to zero, as f...