old_contents: # Configuration file for the Sphinx documentation builder.
  #
  # This file only contains a selection of the most common options. For a full
  # list see the documentation:
  # https://www.sphinx-doc.org/en/master/usage/configuration.html
  
  # -- Path setup --------------------------------------------------------------
  
  # 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('.'))
  
  
  # -- Project information -----------------------------------------------------
  
  project = 'Auspice'
  copyright = '2020, James Hadfield, Trevor Bedford and Richard Neher'
  author = 'James Hadfield, Trevor Bedford and Richard Neher'
  
  
  # -- General configuration ---------------------------------------------------
  
  # Add any Sphinx extension module names here, as strings. They can be
  # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
  # ones.
  extensions = [
      'recommonmark',
      'sphinx.ext.intersphinx',
      'sphinx_markdown_tables',
      'sphinxarg.ext',
      'sphinx.ext.autodoc'
  ]
  
  # Add any paths that contain templates here, relative to this directory.
  templates_path = ['_templates']
  
  # List of patterns, relative to source directory, that match files and
  # directories to ignore when looking for source files.
  # This pattern also affects html_static_path and html_extra_path.
  exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'README.md']
  
  
  # -- 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 = 'nextstrain-sphinx-theme'
  
  # 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']
  
  html_theme_options = {
      'logo_only': False, # if True, don't display project name at top of the sidebar
      'collapse_navigation': False, # if True, no [+] icons in sidebar
      'titles_only': True, # if True, page subheadings not included in nav
  }
  
  
  # -- Cross-project references ------------------------------------------------
  
  intersphinx_mapping = {
      'docs.nextstrain.org': ('https://docs.nextstrain.org/en/latest/', None),
  }
  
new_contents: # Configuration file for the Sphinx documentation builder.
  #
  # This file only contains a selection of the most common options. For a full
  # list see the documentation:
  # https://www.sphinx-doc.org/en/master/usage/configuration.html
  
  # -- Path setup --------------------------------------------------------------
  
  # 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('.'))
  
  
  # -- Project information -----------------------------------------------------
  
  project = 'Auspice'
  copyright = '2020, James Hadfield, Trevor Bedford and Richard Neher'
  author = 'James Hadfield, Trevor Bedford and Richard Neher'
  
  
  # -- General configuration ---------------------------------------------------
  
  # Add any Sphinx extension module names here, as strings. They can be
  # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
  # ones.
  extensions = [
      'recommonmark',
      'sphinx.ext.intersphinx',
      'sphinx_markdown_tables',
      'sphinxarg.ext',
      'sphinx.ext.autodoc'
  ]
  
  # Add any paths that contain templates here, relative to this directory.
  templates_path = ['_templates']
  
  # List of patterns, relative to source directory, that match files and
  # directories to ignore when looking for source files.
  # This pattern also affects html_static_path and html_extra_path.
  exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'README.md',
      'narratives',
      'contributing',
  ]
  
  
  # -- 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 = 'nextstrain-sphinx-theme'
  
  # 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']
  
  html_theme_options = {
      'logo_only': False, # if True, don't display project name at top of the sidebar
      'collapse_navigation': False, # if True, no [+] icons in sidebar
      'titles_only': True, # if True, page subheadings not included in nav
  }
  
  
  # -- Cross-project references ------------------------------------------------
  
  intersphinx_mapping = {
      'docs.nextstrain.org': ('https://docs.nextstrain.org/en/latest/', None),
  }
  
subject: exclude unused docs from build