# -*- 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 = '3.1' # The full version, including alpha/beta/rc tags. release = '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 = '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': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). #'pointsize': '10pt', # Additional stuff for the LaTeX preamble. #'preamble': '', } # 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 Documentation', u'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 = False # If true, show page references after internal links. latex_show_pagerefs = True # If true, show URL addresses after external links. #latex_show_urls = False # 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 Documentation', [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 = False # -- 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)