Merge pull request #208 from malav4994/master

Documentation merge

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/source/changes/index.rst

+Changes
+=======
+
+.. todo:: collect changes from OBS.

docs/source/conf.py

+# -*- coding: utf-8 -*-
+#
+# MOOSE documentation build configuration file, created by
+# sphinx-quickstart on Thu Feb  9 14:56:13 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
+import sphinx_rtd_theme
+# 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']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# 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 = u'MOOSE'
+copyright = u'2017, Upinder S. Bhall, Subhasis Ray, Aditya Gilra, Dilawar Singh, Harsha Rani, Aviral Goel, Malav Shah'
+author = u'Upinder S. Bhall, Subhasis Ray, Aditya Gilra, Dilawar Singh, Harsha Rani, Aviral Goel, Malav Shah'
+
+# 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 = u'3.1'
+# The full version, including alpha/beta/rc tags.
+release = u'ChamCham (3.1.1)'
+
+# 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 = "sphinx_rtd_theme"
+
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+
+# 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 = ['_static']
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+html_logo = 'images/moose_logo.png'
+
+# 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', u'MOOSE Documentation',
+     u'Upinder S. Bhall, Subhasis Ray, Aditya Gilra, Dilawar Singh, Harsha Rani, Aviral Goel, Malav Shah', 'manual'),
+]
+
+
+# -- 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', u'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', u'MOOSE Documentation',
+     author, 'MOOSE', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+

docs/source/conf.py~

+# -*- coding: utf-8 -*-
+#
+# MOOSE documentation build configuration file, created by
+# sphinx-quickstart on Thu Feb  9 14:56:13 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
+import sphinx_rtd_theme
+# 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']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# 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 = u'MOOSE'
+copyright = u'2017, Upinder S. Bhall, Subhasis Ray, Aditya Gilra, Dilawar Singh, Harsha Rani, Aviral Goel, Malav Shah'
+author = u'Upinder S. Bhall, Subhasis Ray, Aditya Gilra, Dilawar Singh, Harsha Rani, Aviral Goel, Malav Shah'
+
+# 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 = u'3.1'
+# The full version, including alpha/beta/rc tags.
+release = u'ChamCham (3.1.1)'
+
+# 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 = "sphinx_rtd_theme"
+
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+
+# 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 ------------------------------------------
+
+html_logo = 'images/moose_logo.png'
+
+# 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', u'MOOSE Documentation',
+     u'Upinder S. Bhall, Subhasis Ray, Aditya Gilra, Dilawar Singh, Harsha Rani, Aviral Goel, Malav Shah', 'manual'),
+]
+
+
+# -- 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', u'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', u'MOOSE Documentation',
+     author, 'MOOSE', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+

docs/source/docs/source/modules.rst

+projectdir
+==========
+
+.. toctree::
+   :maxdepth: 4
+