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# 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
from datetime import datetime
sys.path.insert(0, os.path.abspath("../../"))
# -- Project information -----------------------------------------------------
project = "PathML"
copyright = (
f"{datetime.now().year}, Dana-Farber Cancer Institute and Weill Cornell Medicine"
)
author = "Jacob Rosenthal et al."
about = {}
with open("../../pathml/_version.py") as f:
exec(f.read(), about)
version = about["__version__"]
# 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",
"nbsphinx",
"nbsphinx_link",
"sphinx.ext.napoleon",
"sphinx.ext.imgmath",
"IPython.sphinxext.ipython_console_highlighting",
"autoapi.extension",
"sphinx_copybutton",
]
autodoc_default_options = {"members": True, "undoc-members": True}
# 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 = ["../tests/*", "build", "../*.ipynb_checkpoints"]
# using autoapi to generate docs which should use less resources and improve readthedocs builds:
# https://docs.readthedocs.io/en/stable/guides/build-using-too-many-resources.html#document-python-modules-api-statically
autoapi_dirs = ["../../pathml"]
# still use autodoc directives:
# https://sphinx-autoapi.readthedocs.io/en/latest/reference/directives.html#autodoc-style-directives
autoapi_generate_api_docs = False
# -- 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"
# from https://sphinx-rtd-theme.readthedocs.io/en/stable/configuring.html
html_theme_options = {
"logo_only": True,
"display_version": True,
"style_nav_header_background": "grey",
"collapse_navigation": False,
"prev_next_buttons_location": "both",
"style_external_links": True,
}
# link to logo
html_logo = "_static/images/logo.png"
html_show_sphinx = False
# 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", "./examples/static/"]
def setup(app):
app.add_css_file("css/pathml.css")
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