From 7ffff42d697059bf938795321bec0833e26ee93a Mon Sep 17 00:00:00 2001
From: malav4994 <malav4994@users.noreply.github.com>
Date: Mon, 19 Jun 2017 14:40:17 +0530
Subject: [PATCH] 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 | 20 +++++++++++++++++++
docs/source/user/py/cookbook/chem_sim_eg.rst | 3 ---
...GraupnerBrunel2012_STDPfromCaPlasticity.py | 15 +++++++-------
moose-examples/snippets/interpol2d.py | 4 +---
moose-examples/snippets/rxdSpineSize.py | 5 +++--
moose-examples/snippets/testRdesigneur.py | 5 +++--
moose-examples/snippets/testWigglySpines.py | 6 +++---
7 files changed, 38 insertions(+), 20 deletions(-)
create mode 100644 docs/Makefile
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 00000000..432ae3c1
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,20 @@
+# 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
diff --git a/docs/source/user/py/cookbook/chem_sim_eg.rst b/docs/source/user/py/cookbook/chem_sim_eg.rst
index 96b19eaf..5eac01de 100644
--- a/docs/source/user/py/cookbook/chem_sim_eg.rst
+++ b/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
-----------------------------
diff --git a/moose-examples/snippets/GraupnerBrunel2012_STDPfromCaPlasticity.py b/moose-examples/snippets/GraupnerBrunel2012_STDPfromCaPlasticity.py
index 556639db..60342817 100644
--- a/moose-examples/snippets/GraupnerBrunel2012_STDPfromCaPlasticity.py
+++ b/moose-examples/snippets/GraupnerBrunel2012_STDPfromCaPlasticity.py
@@ -1,3 +1,10 @@
+"""
+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
diff --git a/moose-examples/snippets/interpol2d.py b/moose-examples/snippets/interpol2d.py
index b4642cae..af234451 100644
--- a/moose-examples/snippets/interpol2d.py
+++ b/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
diff --git a/moose-examples/snippets/rxdSpineSize.py b/moose-examples/snippets/rxdSpineSize.py
index 6e150e2b..b404a34e 100644
--- a/moose-examples/snippets/rxdSpineSize.py
+++ b/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' )
diff --git a/moose-examples/snippets/testRdesigneur.py b/moose-examples/snippets/testRdesigneur.py
index 1de81ad6..4087a3fb 100644
--- a/moose-examples/snippets/testRdesigneur.py
+++ b/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
diff --git a/moose-examples/snippets/testWigglySpines.py b/moose-examples/snippets/testWigglySpines.py
index a85bf1ef..7992e405 100644
--- a/moose-examples/snippets/testWigglySpines.py
+++ b/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' )
--
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