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

docs/source/index.rst

@@ -35,7 +35,6 @@ MOOSE is a simulation environment, not just a numerical engine: It provides data
 
 .. toctree::
    :maxdepth: 1
-
    :titlesonly:
 
 .. toctree::

docs/source/install/install.rst

@@ -45,7 +45,8 @@ In case your distribution is not listed on `our repository page
 
 First, you need to get the source code. You can use ``git`` (clone the
 repository) or download snapshot of github repo by clicking on `this link
-<https://github.com/BhallaLab/moose/archive/master.zip>`_.::
+<https://github.com/BhallaLab/moose/archive/master.zip>`__.
+::
 
     $ git clone https://github.com/BhallaLab/moose
 
@@ -57,7 +58,7 @@ Or,
     $ unzip master.zip
 
 If you don't want latest snapshot of ``MOOSE``, you can download other released
-versions from `here <`https://github.com/BhallaLab/moose/releases>`_.
+versions from `here <https://github.com/BhallaLab/moose/releases>`__.
 
 Install dependencies
 ^^^^^^^^^^^^^^^^^^^^
@@ -157,8 +158,8 @@ If you have installed the pre-built package, then you already have the GUI.
 You can launch it by runnung `moosegui` command in terminal.
 
 You can get the source of ``moose-gui`` from `here
-<https://github.com/BhallaLab/moose-gui>`_. You can download it either by
-clicking on `this link <https://github.com/BhallaLab/moose-gui/archive/master.zip>`_
+<https://github.com/BhallaLab/moose-gui>`__. You can download it either by
+clicking on `this link <https://github.com/BhallaLab/moose-gui/archive/master.zip>`__
 or by using ``git`` ::
 
     $ git clone https://github.com/BhallaLab/moose-gui
@@ -203,7 +204,7 @@ Building moogli
 ---------------
 
 ``moogli`` is subproject of ``MOOSE`` for visualizing models. More details can
-be found `here <http://moose.ncbs.res.in/moogli>`_.
+be found `here <http://moose.ncbs.res.in/moogli>`__.
 
 `Moogli` is part of `moose` package. Building moogli can be tricky because of
 multiple depednecies it has.
@@ -212,7 +213,7 @@ multiple depednecies it has.
     - OSG (3.2.x) For 3D rendering and simulation of neuronal models
     - Qt4 (4.8.x) For C++ GUI of Moogli
 
-To get the latest source code of ``moogli``, click on `this link <https://github.com/BhallaLab/moogli/archive/master.zip>`_.
+To get the latest source code of ``moogli``, click on `this link <https://github.com/BhallaLab/moogli/archive/master.zip>`__.
 
 Moogli depends on ``OpenSceneGraph`` (version 3.2.0 or higher) which may not
 be easily available for your operating system.

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

@@ -1104,11 +1104,9 @@ the location of the spine. There are three pulses of calcium, the first
 being quite weak.
 
 .. figure:: ../../../../images/rdes10_CaSpread.png
-   :alt: Calcium influx from spine in middle of cylindrical compartment,
-   spreading into the dendrite and then axially in both directions.
+   :alt: Calcium influx from spine in middle of cylindrical compartment, spreading into the dendrite and then axially in both directions.
 
-   Calcium influx from spine in middle of cylindrical compartment,
-   spreading into the dendrite and then axially in both directions.
+   Calcium influx from spine in middle of cylindrical compartment, spreading into the dendrite and then axially in both directions.
 
 Once the simulation completes you'll also see a number of plots, so that
 you can figure out what the calcium influx was doing. Here, we have a

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

@@ -355,6 +355,7 @@ variables can be input from pool object.
 - **New**: **File -> New -> Model name**. This opens a empty widget for model building
 - **Saving models**: **File -> Save Model -> select from dialog**.
 - **Changing numerical methods**: **Preference->Chemical tab** item from Simulation Control. Currently supports:
+
 1. Runge Kutta: This is the Runge-Kutta-Fehlberg implementation from the GNU Scientific Library (GSL). It is a fifth order variable timestep explicit method. Works well for most reaction systems except if they have very stiff reactions.
 2. Gillespie: Optimized Gillespie stochastic systems algorithm, custom implementation. This uses variable timesteps internally. Note that it slows down with increasing numbers of molecules in each pool. It also slows down, but not so badly, if the number of reactions goes up.
 3. Exponential Euler:This methods computes the solution of partial and ordinary differential equations.

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

@@ -53,8 +53,9 @@ Insert Spine heads
 .. automodule:: insertSpinesWithoutRdesigneur
    :members:
 
-Multi compartmental Neuron model
---------------------------------
+.. Multi compartmental Neuron model
+.. --------------------------------
 
-.. automodule:: testHsolve
+.. automodule: testHsolve
    :members:
+   (testHsolve no longer exists in any of the appended paths)

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

@@ -20,5 +20,6 @@ Modeling chemical reactions in neurons
 .. automodule:: gssaRDspiny
    :members:
 
-.. automodule:: rxdSpineSize
+.. automodule: rxdSpineSize
    :members:
+   (rxdSpineSize does not exist in any appended folders -> gives error while building html)

docs/source/user/py/quickstart/classes_demos.rst

@@ -70,6 +70,7 @@ Function
 
 .. automodule:: func
   :members:
+  :noindex:
 
 SymCompartment
 ^^^^^^^^^^^^^^

docs/source/user/py/quickstart/moose_quickstart.rst

@@ -2,10 +2,6 @@
 Getting started with python scripting for MOOSE
 ***********************************************
 
-.. contents:
-   :local:
-   :depth: 1
-
 .. figure:: ../../../images/Gallery_Moose_Multiscale.png
    :alt: **multiple scales in moose**
    :scale: 100%
@@ -30,11 +26,10 @@ MOOSE is a simulation environment, not just a numerical engine: It provides data
 
 Contents:
 
-.. toctree::
-   :maxdepth: 2
-   :numbered:
+.. contents::
+   :local:
+   :depth: 1
 
-   moose_quickstart
 Coding basics and how to use this document
 ==========================================
 
@@ -114,6 +109,7 @@ Alternatively, if you want to see a full list of classes, functions and their fi
 
 * :ref:`genindex`
 * :ref:`modindex`
+
 .. 
    :ref:`search` 
 

moose-examples/snippets/crossComptNeuroMesh.py

@@ -204,7 +204,7 @@ def main():
     files.  Normally one uses standard model formats like
     SBML or kkit to concisely define kinetic and neuronal models.
     This example creates a simple reaction::
-        a <==> b <==> c
+    a <==> b <==> c
     in which **a, b**, and **c** are in the dendrite, spine head, and PSD
     respectively.
     The model is set up to run using the Ksolve for integration. Although

moose-examples/snippets/loadSbmlmodel.py

@@ -46,12 +46,12 @@ from moose.chemUtil.add_Delete_ChemicalSolver import *
 
 def main():
     """
-This example illustrates loading, running of an SBML model defined in XML format.
-Default this  file load's 00001-sbml-l3v1.xml which is taken from l3v1 SBML testcase.
-Plots are setup.
-Model is run for 20sec.
-As a general rule we created model under '/path/model' and plots under '/path/graphs'.
-If someone wants to load anyother file then 
+    This example illustrates loading, running of an SBML model defined in XML format.
+    Default this  file load's 00001-sbml-l3v1.xml which is taken from l3v1 SBML testcase.
+    Plots are setup.
+    Model is run for 20sec.
+    As a general rule we created model under '/path/model' and plots under '/path/graphs'.
+    If someone wants to load anyother file then 
     `python loadSbmlmodel filepath runtime`
     """