#!/usr/bin/env python3 # -*- coding: utf-8 -*- # # loompy documentation build configuration file, created by # sphinx-quickstart on Tue Oct 3 00:11:17 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_bootstrap_theme sys.path.insert(0, os.path.abspath('..')) sys.path.insert(0, os.path.abspath('.')) sys.path.insert(0, os.path.abspath('_ext')) # -- 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.viewcode', 'sphinx.ext.githubpages', 'sphinx.ext.napoleon', 'sphinx.ext.intersphinx', 'edit_on_github'] intersphinx_mapping = { 'urllib3': ('http://urllib3.readthedocs.org/en/latest', None), 'python': ('http://docs.python.org/3', None), 'numpy': ('http://docs.scipy.org/doc/numpy/', None), 'scipy': ('http://docs.scipy.org/doc/scipy/reference', None), 'matplotlib': ('http://matplotlib.org', None), 'h5py': ('http://docs.h5py.org/en/latest/', None) } # 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 = 'loompy' copyright = '2017, LinnarssonLab' author = 'Linnarsson lab members' # 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. # __version__ = "0.0.0" exec(open('../loompy/_version.py').read()) # The short X.Y version. version = ".".join(__version__.split(".")[:-1]) # The full version, including alpha/beta/rc tags. release = __version__ # 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 = ['_build', 'Thumbs.db', '.DS_Store'] # 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 = 'bootstrap' html_theme_path = sphinx_bootstrap_theme.get_html_theme_path() # (Optional) Logo. Should be small enough to fit the navbar (ideally 24x24). # Path should be relative to the ``_static`` files directory. html_logo = "Loom_icon.png" # Theme options are theme-specific and customize the look and feel of a # theme further. html_theme_options = { # Navigation bar title. (Default: ``project`` value) 'navbar_title': "Loom", # Tab name for entire site. (Default: "Site") 'navbar_site_name': "Contents", # A list of tuples containing pages or urls to link to. # Valid tuples should be in the following forms: # (name, page) # a link to a page # (name, "/aa/bb", 1) # a link to an arbitrary relative url # (name, "http://example.com", True) # arbitrary absolute url # Note the "1" or "True" value above as the third argument to indicate # an arbitrary url. 'navbar_links': [ ("loompy.org", "http://loompy.org", True), ("GitHub", "https://github.com/linnarsson-lab/loompy", True), ], # Render the next and previous page links in navbar. (Default: true) 'navbar_sidebarrel': False, # Render the current pages TOC in the navbar. (Default: true) 'navbar_pagenav': False, # Tab name for the current pages TOC. (Default: "Page") 'navbar_pagenav_name': "Page", # Global TOC depth for "site" navbar tab. (Default: 1) # Switching to -1 shows all levels. 'globaltoc_depth': 2, # Include hidden TOCs in Site navbar? # # Note: If this is "false", you cannot have mixed ``:hidden:`` and # non-hidden ``toctree`` directives in the same page, or else the build # will break. # # Values: "true" (default) or "false" 'globaltoc_includehidden': "true", # HTML navbar class (Default: "navbar") to attach to
element. # For black navbar, do "navbar navbar-inverse" 'navbar_class': "navbar navbar-light", # Fix navigation bar to top of page? # Values: "true" (default) or "false" 'navbar_fixed_top': "true", # Location of link to source. # Options are "nav" (default), "footer" or anything else to exclude. 'source_link_position': "", # Bootswatch (http://bootswatch.com/) theme. # # Options are nothing (default) or the name of a valid theme # such as "cosmo" or "sandstone". # # The set of valid themes depend on the version of Bootstrap # that's used (the next config option). # # Currently, the supported themes are: # - Bootstrap 2: https://bootswatch.com/2 # - Bootstrap 3: https://bootswatch.com/3 'bootswatch_theme': "simplex", # Choose Bootstrap version. # Values: "3" (default) or "2" (in quotes) 'bootstrap_version': "3", } # 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'] # Custom sidebar templates, must be a dictionary that maps document names # to template names. # # This is required for the alabaster theme # refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars html_sidebars = { '**': ['localtoc.html'] } # -- Options for HTMLHelp output ------------------------------------------ # Output file base name for HTML help builder. htmlhelp_basename = 'loompydoc' # -- 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, 'loompy.tex', 'loompy Documentation', 'LinnarssonLab', '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, 'loompy', 'loompy 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, 'loompy', 'loompy Documentation', author, 'loompy', 'One line description of project.', 'Miscellaneous'), ] # -- Options for Epub output ---------------------------------------------- # Bibliographic Dublin Core info. epub_title = project epub_author = author epub_publisher = author epub_copyright = copyright # The unique identifier of the text. This can be a ISBN number # or the project homepage. # # epub_identifier = '' # A unique identification for the text. # # epub_uid = '' # A list of files that should not be packed into the epub file. epub_exclude_files = ['search.html'] # --- Options for "Edit on GitHub" --- edit_on_github_project = 'linnarsson-lab/loompy' edit_on_github_branch = 'master/doc' # --- Sort the autodocs by source (currently not workin not sure why) autodoc_member_order = 'bysource' html_scaled_image_link = False