documentation branch merge request (#219)

* 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..

docs/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = MOOSE
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file

docs/source/user/py/cookbook/chem_sim_eg.rst

@@ -215,9 +215,6 @@ A Turing Model
 .. automodule:: TuringOneDim
    :members:
 
-A Spatial Bistable Model
-------------------------
-
 Reaction Diffusion in Neurons
 -----------------------------
 

moose-examples/snippets/GraupnerBrunel2012_STDPfromCaPlasticity.py

+"""
+Simulate a pseudo-STDP protocol and plot the STDP kernel
+that emerges from Ca plasticity of Graupner and Brunel 2012.
+Author: Aditya Gilra, NCBS, Bangalore, October, 2014.
+
+"""
+
 import moose
 from pylab import *
 
@@ -19,7 +26,7 @@ refrT = 2e-3 # s
 
 ## two neurons: index 0 will be presynaptic, 1 will be postsynaptic
 network = moose.LIF( 'network', 2 );
-moose.le( '/network' )
+moose.le( network )
 network.vec.Em = Vrest
 network.vec.thresh = Vt_base
 network.vec.refractoryPeriod = refrT
@@ -184,12 +191,6 @@ make a neuron spike
     network.vec[nrnidx].inject = 0.
 
 def main():
-    """
-Simulate a pseudo-STDP protocol and plot the STDP kernel
-that emerges from Ca plasticity of Graupner and Brunel 2012.
-Author: Aditya Gilra, NCBS, Bangalore, October, 2014.
-
-    """
     dwlist_neg = []
     ddt = 2e-3 # s
     # since CaPlasticitySynHandler is event based

moose-examples/snippets/interpol2d.py

@@ -44,15 +44,13 @@
 #
 
 # Code:
-"""Example of Interpol object in 2 dimensions."""
-
 import numpy as np
 import sys
 sys.path.append('../../python')
 import moose
 
-
 def interpolation_demo():
+    """Example of Interpol object in 2 dimensions."""
     interpol = moose.Interpol2D('/interpol2D')
     interpol.xmin = 0.0
     interpol.xmax = 1.0

moose-examples/snippets/rxdSpineSize.py

@@ -28,8 +28,6 @@ spineSpacing = 10e-6
 spineSpacingDistrib = 1e-6
 spineSize = 1.0
 spineSizeDistrib = 0.5
-spineAngle= PI / 2.0
-spineAngleDistrib = 0.0
 
 def makeCellProto( name ):
     elec = moose.Neuron( '/library/' + name )
@@ -79,6 +77,9 @@ def makeSpineProto2( name ):
     moose.connect( shaft, 'axial', head, 'raxial' )
 
 def makeModel():
+    spineAngle= PI / 2.0
+    spineAngleDistrib = 0.0
+
     moose.Neutral( '/library' )
     makeCellProto( 'cellProto' )
     makeChemProto( 'cProto' )

moose-examples/snippets/testRdesigneur.py

@@ -22,8 +22,6 @@ spineSpacing = 2.0e-6
 spineSpacingDistrib = 0.0
 spineSize = 1.0
 spineSizeDistrib = 0.2
-spineAngle= 0.0
-spineAngleDistrib = 2*PI
 
 # Here we define a function that is used to make a cell prototype. Normally
 # it would load in a model from a file.
@@ -60,6 +58,9 @@ def makeChemProto( name ):
 
 
 def makeModel():
+    spineAngle= 0.0
+    spineAngleDistrib = 2*PI
+    
     moose.Neutral( '/library' )
     # Here we illustrate building the chem proto directly. This is not
     # good practice as it takes the model definition away from the

moose-examples/snippets/testWigglySpines.py

@@ -26,9 +26,6 @@ spineSpacing = 1.5e-6
 spineSpacingDistrib = 1e-10
 spineSize = 1.0
 spineSizeDistrib = 0
-spineAngle= PI / 2.0
-spineAngleDistrib = 0.0
-
 
 def makeCellProto( name ):
     elec = moose.Neuron( '/library/' + name )
@@ -53,6 +50,9 @@ def makeSpineProto2( name ):
     moose.connect( shaft, 'axial', head, 'raxial' )
 
 def makeModel():
+    spineAngle= PI / 2.0
+    spineAngleDistrib = 0.0
+
     moose.Neutral( '/library' )
     makeCellProto( 'cellProto' )
     makeChemProto( 'cProto' )