Squashed 'moose-examples/' changes from 80169bcc5c..0c5527e77d

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...

docs/Makefile

-# Minimal makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
-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/make.bat

-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-set SPHINXPROJ=MOOSE
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.http://sphinx-doc.org/
-	exit /b 1
-)
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-
-:end
-popd

docs/source/conf.py

-# -*- coding: utf-8 -*-
-#
-# MOOSE documentation build configuration file, created by
-# sphinx-quickstart on Tue Jan 31 14:57:39 2017.
-#
-# This file is execfile()d with the current directory set to its
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-import os
-import sys
-# sys.path.insert(0, os.path.abspath('.'))
-sys.path.insert(0, os.path.abspath('../python'))
-sys.path.append(os.path.abspath('../../../moose-examples/snippets'))
-sys.path.append(os.path.abspath('../../../moose-examples/tutorials/ChemicalOscillators'))
-sys.path.append(os.path.abspath('../../../moose-examples/tutorials/ChemicalBistables'))
-sys.path.append(os.path.abspath('../../../moose-examples/tutorials/ExcInhNet'))
-sys.path.append(os.path.abspath('../../../moose-examples/neuroml/lobster_pyloric'))
-sys.path.append(os.path.abspath('../../../moose-examples/tutorials/ExcInhNetCaPlasticity'))
-
-
-# -- General configuration ------------------------------------------------
-
-# If your documentation needs a minimal Sphinx version, state it here.
-#
-# needs_sphinx = '1.0'
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
-extensions = ['sphinx.ext.autodoc']
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.napoleon']
-#extensions = ['numpydoc']
-#extensions = ['sphinx.ext.autodoc', 'numpydoc']
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['ntemplates']
-
-# The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-#
-# source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
-
-# The master toctree document.
-master_doc = 'index'
-
-# General information about the project.
-project = 'MOOSE'
-copyright = '(c) 2017, Malav Shah <malavs@ncbs.res.in>'
-author = 'Malav Shah <malavs@ncbs.res.in>'
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-# The short X.Y version.
-version = '3.1.1'
-# The full version, including alpha/beta/rc tags.
-release = 'Chamcham'
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
-# This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
-language = None
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = []
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
-
-# If true, `todo` and `todoList` produce output, else they produce nothing.
-todo_include_todos = False
-
-
-# -- Options for HTML output ----------------------------------------------
-
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-#
-html_theme = 'alabaster'
-
-# Theme options are theme-specific and customize the look and feel of a theme
-# further.  For a list of options available for each theme, see the
-# documentation.
-#
-# html_theme_options = {}
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['nstatic']
-
-
-# -- Options for HTMLHelp output ------------------------------------------
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'MOOSEdoc'
-
-
-# -- Options for LaTeX output ---------------------------------------------
-
-latex_elements = {
-    # The paper size ('letterpaper' or 'a4paper').
-    #
-    # 'papersize': 'letterpaper',
-
-    # The font size ('10pt', '11pt' or '12pt').
-    #
-    # 'pointsize': '10pt',
-
-    # Additional stuff for the LaTeX preamble.
-    #
-    # 'preamble': '',
-
-    # Latex figure (float) alignment
-    #
-    # 'figure_align': 'htbp',
-}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title,
-#  author, documentclass [howto, manual, or own class]).
-latex_documents = [
-    (master_doc, 'MOOSE.tex', 'MOOSE Documentation',
-     'Malav Shah', 'manual'),
-]
-
-#  -----NumpyDoc----------------
-numpydoc_show_class_members = False
-#numpydoc_use_plots: True
-#numpydoc_show_class_members: True
-#numpydoc_show_inherited_class_members: True
-#numpydoc_class_members_toctree: True
-#numpydoc_edit_link: True
-
-# -- Options for manual page output ---------------------------------------
-
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'moose', 'MOOSE Documentation',
-     [author], 1)
-]
-
-
-# -- Options for Texinfo output -------------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-#  dir menu entry, description, category)
-texinfo_documents = [
-    (master_doc, 'MOOSE', 'MOOSE Documentation',
-     author, 'MOOSE', 'One line description of project.',
-     'Miscellaneous'),
-]
-
-
-

docs/source/docs/source/modules.rst

-projectdir
-==========
-
-.. toctree::
-   :maxdepth: 4
-