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:
  # http://www.sphinx-doc.org/en/master/config
  
  # -- 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 -----------------------------------------------------
  
  from datetime import date
  import subprocess
  
  def git_authors():
      result = subprocess.run(
          ["git", "shortlog", "--summary", "HEAD"],
          stdout = subprocess.PIPE,
          check  = True)
  
      names = [
          line.strip().split("\t")[1]
              for line in result.stdout.decode("utf-8").splitlines()
      ]
  
      return names
  
  def prose_list(items):
      if not items:
          return ""
      if len(items) == 1:
          return items[0]
      elif len(items) == 2:
          return " and ".join(items)
      else:
          return ", ".join([*items[0:-1], "and " + items[-1]])
  
  project = 'augur'
  copyright = '2014–%d Trevor Bedford and Richard Neher' % (date.today().year)
  author = prose_list(git_authors())
  
  
  # -- 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.autodoc', 'sphinxarg.ext', 'sphinx.ext.napoleon']
  
  # 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']
  
  # A string of reStructuredText that will be included at the end of every source
  # file that is read. This is a possible place to add substitutions that should
  # be available in every file.
  rst_epilog = f"""
  .. |authors| replace:: {author}
  """
  
  
  # -- 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'
  
  # 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']
  
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:
  # http://www.sphinx-doc.org/en/master/config
  
  # -- 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 -----------------------------------------------------
  
  from datetime import date
  import subprocess
  
  def git_authors():
      result = subprocess.run(
          ["git", "shortlog", "--summary", "HEAD"],
          stdout = subprocess.PIPE,
          check  = True)
  
      names = [
          line.strip().split("\t")[1]
              for line in result.stdout.decode("utf-8").splitlines()
      ]
  
      return names
  
  def prose_list(items):
      if not items:
          return ""
      if len(items) == 1:
          return items[0]
      elif len(items) == 2:
          return " and ".join(items)
      else:
          return ", ".join([*items[0:-1], "and " + items[-1]])
  
  project = 'augur'
  copyright = '2014–%d Trevor Bedford and Richard Neher' % (date.today().year)
  author = prose_list(git_authors())
  
  
  # -- 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.autodoc', 'sphinxarg.ext', 'sphinx.ext.napoleon', 'sphinx_markdown_tables']
  
  # 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']
  
  # A string of reStructuredText that will be included at the end of every source
  # file that is read. This is a possible place to add substitutions that should
  # be available in every file.
  rst_epilog = f"""
  .. |authors| replace:: {author}
  """
  
  
  # -- 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'
  
  # 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']
  
subject: add markdown table support for docs