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
  
  import sphinx.ext.apidoc
  
  sys.path.append(os.path.join(os.path.dirname(__name__), "../src"))
  
  
  # -- Project information -----------------------------------------------------
  
  project = "ASLSENS"
  copyright = "2020, Gold Standard Phantoms"
  author = "Aaron Oliver-Taylor"
  
  
  # -- 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.mathjax"]
  
  # This value contains a list of modules to be mocked up.
  # This is useful when some external dependencies are not met at build time
  # and break the building process. You may only specify the root package of
  # the dependencies themselves and omit the sub-modules:
  autodoc_mock_imports = ["numpy", "nibabel", "pandas", "jsonschema"]
  
  # Add any paths that contain templates here, relative to this directory.
  templates_path = ["_templates"]
  
  
  language = "en"
  
  # 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"]
  
  # -- 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"]
  
  todo_include_todos = True
  
  
  def run_apidoc(_):
      """A hook to run on documentation building which will
      first generate the API stubs for the Sphinx build"""
  
      sys.path.append(os.path.join(os.path.dirname(__file__)))
      current_dir = os.path.abspath(os.path.dirname(__file__))
      output_dir = os.path.join(current_dir, "_api")
      source_dir = os.path.join(current_dir, "..", "src")
      exclude_pattern = "../src/**/test_*.py"
      sphinx.ext.apidoc.main(["-f", "-o", output_dir, source_dir, exclude_pattern])
  
  
  def setup(app):
      """ Hook the apidoc generation on build """
      app.connect("builder-inited", run_apidoc)
  