text: # 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 = u"aiproteomics"
  copyright = u"2022, Netherlands eScience Center"
  author = u"Robin Richardson"
  
  # 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 = "0.1.0"
  # The full version, including alpha/beta/rc tags.
  release = version
  
  # -- 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 = [
      "sphinx.ext.autodoc",
      "sphinx.ext.coverage",
      "sphinx.ext.doctest",
      "sphinx.ext.intersphinx",
      "sphinx.ext.mathjax",
      "sphinx.ext.napoleon",
      "sphinx.ext.todo",
      "sphinx.ext.viewcode",
      "autoapi.extension",
      "myst_parser",
  ]
  
  # 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 patterns also effect to html_static_path and html_extra_path
  exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
  
  # If true, `todo` and `todoList` produce output, else they produce nothing.
  todo_include_todos = False
  
  # -- Use autoapi.extension to run sphinx-apidoc -------
  
  autoapi_dirs = ['../aiproteomics']
  
  # -- 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"
  
  # 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 = {}
  
  # -- Options for Intersphinx
  
  intersphinx_mapping = {'python': ('https://docs.python.org/3', None),
                         # Commonly used libraries, uncomment when used in package
                         # 'numpy': ('http://docs.scipy.org/doc/numpy/', None),
                         # 'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None),
                         # 'scikit-learn': ('https://scikit-learn.org/stable/', None),
                         # 'matplotlib': ('https://matplotlib.org/stable/', None),
                         # 'pandas': ('http://pandas.pydata.org/docs/', None),
                         }
  