conf.py

# -*- coding: utf-8 -*-
#
# MOOSE documentation build configuration file, created by
# sphinx-quickstart on Tue Jul  1 19:05:47 2014.
# updated on Thr Jan 21 00:30:10 2016
# 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.

#Workaround to fix bug where extensions werent added
from docutils.parsers.rst.directives.admonitions import BaseAdmonition
from sphinx.util import compat
compat.make_admonition = BaseAdmonition

import subprocess
import os
import sys
import sphinx_rtd_theme
import mock

conf_dir_ = os.path.dirname( __file__ )

# 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.
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'))
sys.path.append(os.path.join(conf_dir_, 'Extensions') )

# -- 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',
              'sphinx.ext.mathjax',
              'sphinx.ext.autosummary',
              'sphinx.ext.todo',
              'sphinx.ext.viewcode',
              'hidden_code_block'
		]

todo_include_todos = True

# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']

# The suffix of source filenames.
source_suffix = '.rst'

# The encoding of source files.
#source_encoding = 'utf-8-sig'

# The master toctree document.
master_doc = 'index'

# General information about the project.
project = u'MOOSE'
copyright = u'2018, Upinder Bhalla, Niraj Dudani, Subhasis Ray, ' + \
        'Aditya Gilra,Harsha Rani, Aviral Goel, Dilawar Singh,' + \
        'Malav Shah, Dhruva Gowda Storz'

# 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 = '3.2'
# The full version, including alpha/beta/rc tags.
release = 'chennapoda (3.2.rc)'

# 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 = 'English'

# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
today = ''
# Else, today_fmt is used as the format for a strftime call.
today_fmt = '%B %d, %Y'

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns = ['_build']

# The reST default role (used for this markup: `text`) to use for all documents.
#default_role = None

# If true, '()' will be appended to :func: etc. cross-reference text.
add_function_parentheses = True

# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#add_module_names = True

# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#show_authors = False

# 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 = True

# A list of ignored prefixes for module index sorting.
#modindex_common_prefix = []


# -- 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 = {'stickysidebar': 'true',
#                       'sidebarwidth': '300'}

# Add any paths that contain custom themes here, relative to this directory.
#html_theme_path = []

# The name for this set of Sphinx documents.  If None, it defaults to
# "<project> v<release> documentation".
#html_title = None

# A shorter title for the navigation bar.  Default is the same as html_title.
#html_short_title = None

# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
html_logo = 'images/moose_logo.png'

# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
#html_last_updated_fmt = '%b %d, %Y'

# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#html_use_smartypants = True

# Custom sidebar templates, maps document names to template names.
#html_sidebars = {}

# Additional templates that should be rendered to pages, maps page names to
# template names.
#html_additional_pages = {}

# If false, no module index is generated.
#html_domain_indices = True

# If false, no index is generated.
#html_use_index = True

# If true, the index is split into individual pages for each letter.
#html_split_index = False

# If true, links to the reST sources are added to the pages.
#html_show_sourcelink = True

# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
#html_show_sphinx = True

# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
#html_show_copyright = True

# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it.  The value of this option must be the
# base URL from which the finished HTML is served.
#html_use_opensearch = ''

# This is the file name suffix for HTML files (e.g. ".xhtml").
#html_file_suffix = None

# Output file base name for HTML help builder.
htmlhelp_basename = 'MOOSE'


# -- Options for LaTeX output --------------------------------------------------

latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
'papersize': 'a4paper',

# The font size ('10pt', '11pt' or '12pt').
'pointsize': '11pt',

# Additional stuff for the LaTeX preamble.
'preamble': r'''
\usepackage{libertine} 
\usepackage{mathpazo}
\usepackage{epstopdf}
% Convert GIF to PNG in pdf.
\epstopdfDeclareGraphicsRule{.gif}{png}{.png}{convert gif:#1 png:\OutputFile}
\AppendGraphicsExtensions{.gif}
    '''
}

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
  ('index', 'MOOSE.tex', u'MOOSE User Manual',
   r'Upinder Bhalla, Niraj Dudani, Subhasis Ray \\Aditya Gilra,Harsha Rani, Aviral Goel \\ Dilawar Singh, Malav Shah, Dhruva Gowda Storz' 
   , 'manual'
   ),
]

# The name of an image file (relative to this directory) to place at the top of
# the title page.
latex_logo = 'images/moose_logo.png'

# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
latex_use_parts = True

# If true, show page references after internal links.
latex_show_pagerefs = True

# If true, show URL addresses after external links.
latex_show_urls = True

# Documents to append as an appendix to all manuals.
#latex_appendices = []

# If false, no module index is generated.
latex_domain_indices = True


# -- Options for manual page output --------------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
    ('index', 'moose', u'MOOSE User Manual',
     [u'Upinder Bhalla, Niraj Dudani, Subhasis Ray, Aditya Gilra,Harsha Rani, Aviral Goel, Dilawar Singh, Malav Shah, Dhruva Gowda Storz'], 1)
]

# If true, show URL addresses after external links.
man_show_urls = True


# -- 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 = [
  ('index', 'MOOSE', u'MOOSE Documentation',
   u'Upinder Bhalla, Niraj Dudani, Subhasis Ray, Aditya Gilra,Harsha Rani, Aviral Goel, Dilawar Singh, Malav Shah, Dhruva Gowda Storz'
   , 'MOOSE'
   , 'MOOSE is the Multiscale Object-Oriented Simulation Environment.',
   'Science'),
]

# Documents to append as an appendix to all manuals.
#texinfo_appendices = []

# If false, no module index is generated.
texinfo_domain_indices = True

# How to display URL addresses: 'footnote', 'no', or 'inline'.
#texinfo_show_urls = 'footnote'

#numpydoc option
numpydoc_show_class_members = False

# autodoc options to mock MOOSE module
autodoc_mock_imports = [ 'numpy' , 'moose.sbml' , 'moose.genesis' , 'moose.LIF'
        , 'moogli.extensions.moose' , 'extensions.moose', 'moose' , 'moose.SBML'
        , 'pylab' , 'moose.genesis' , 'datetime' , 'getpass' , 'h5py'
        , 'matplotlib' , 'squid' , 'PyQt4' , 'moogli' , 'moose.utils'
        , 'math' , 'SquidAxon' , '_moogli' , 'XRRRates' , 'neuroml.NeuroML'
        ,'neuroml' , 'rdesigneur' , 'pyplot' , 'gnuplot' , 'cm'
        , 'matplotlib.pyplot' , 'matplotlib.image' , 'matplotlib.cm' , 'shapes'
        , 'chemUtil.add_Delete_ChemicalSolver'
        ]

#include reference files
exclude_patterns = ['/docs/source/user/py/references/*.rst']

#run the doxygen thingy
import subprocess, os
read_the_docs_build = os.environ.get('READTHEDOCS', None) == 'True'

if not read_the_docs_build:
    subprocess.call('cd doxygen; echo HELLO......................; doxygen Doxyfile', shell=True)