old_contents: # -*- coding: utf-8 -*-
  #
  # Configuration file for the Sphinx documentation builder.
  #
  # This file does only contain 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 -----------------------------------------------------
  
  project = 'AskOmics'
  copyright = '2019, Xavier Garnier'
  author = 'Xavier Garnier'
  
  # The short X.Y version
  version = ''
  # The full version, including alpha/beta/rc tags
  release = '19.01.3'
  
  
  # -- 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 = [
      'recommonmark'
  ]
  
  # 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', '.md']
  
  # The master toctree document.
  master_doc = 'index'
  
  # 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 pattern also affects 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'
  
  
  # -- 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 = 'alabaster'
  
  # 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 = {}
  
  # 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.
  #
  # The default sidebars (for documents that don't match any pattern) are
  # defined by theme itself.  Builtin themes are using these templates by
  # default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
  # 'searchbox.html']``.
  #
  # html_sidebars = {}
  
  
  # -- Options for HTMLHelp output ---------------------------------------------
  
  # Output file base name for HTML help builder.
  htmlhelp_basename = 'AskOmicsdoc'
  
  
  # -- 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, 'AskOmics.tex', 'AskOmics Documentation',
       'Xavier Garnier', '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, 'askomics', 'AskOmics 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, 'AskOmics', 'AskOmics Documentation',
       author, 'AskOmics', 'One line description of project.',
       'Miscellaneous'),
  ]
  
new_contents: import os
  import sys
  
  from recommonmark.parser import CommonMarkParser
  
  sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..', 'askomics'))
  
  extensions = ['sphinx.ext.autodoc', 'sphinx.ext.napoleon']
  master_doc = 'index'
  
  # The suffix of source filenames.
  source_suffix = ['.rst', '.md']
  
  source_parsers = {
      '.md': CommonMarkParser,
  }
  
  
  def run_apidoc(_):
      from sphinx.apidoc import main
      parent_folder = os.path.join(os.path.dirname(__file__), '..')
      cur_dir = os.path.abspath(os.path.dirname(__file__))
      sys.path.append(parent_folder)
  
      module = os.path.join(parent_folder, 'askomics')
      output_path = os.path.join(cur_dir, 'api')
      main(['-e', '-f', '-o', output_path, module])
  
  
  def setup(app):
      app.connect('builder-inited', run_apidoc)
  
subject: update conf.py