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# Configuration file for the Sphinx documentation builder.
#
# For the full list of built-in configuration values, see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
import pathlib
import re
import sys
from sphinx.ext import autodoc
sys.path.insert(0, pathlib.Path(__file__).parents[2].resolve().as_posix())
# -- Project information -----------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
project = "geneformer"
copyright = "2024, Christina Theodoris"
author = "Christina Theodoris"
release = "0.1.0"
repository_url = "https://huggingface.co/ctheodoris/Geneformer"
# -- General configuration ---------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
extensions = [
"sphinx.ext.autodoc",
"sphinx.ext.autosummary",
"nbsphinx",
"sphinx.ext.viewcode",
"sphinx.ext.doctest",
]
templates_path = ["_templates"]
exclude_patterns = [
"**.ipynb_checkpoints",
]
autoclass_content = "both"
class MockedClassDocumenter(autodoc.ClassDocumenter):
def add_line(self, line: str, source: str, *lineno: int) -> None:
if line == " Bases: :py:class:`object`":
return
super().add_line(line, source, *lineno)
autodoc.ClassDocumenter = MockedClassDocumenter
add_module_names = False
def process_signature(app, what, name, obj, options, signature, return_annotation):
# loop through each line in the docstring and replace path with
# the generic path text
signature = re.sub(r"PosixPath\(.*?\)", "FILEPATH", signature)
return (signature, None)
def setup(app):
app.connect("autodoc-process-signature", process_signature)
# -- Options for HTML output -------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
html_theme = "sphinx_rtd_theme"
html_show_sphinx = False
html_static_path = ["_static"]
html_logo = "_static/gf_logo.png"
html_theme_options = {
"collapse_navigation": False,
"sticky_navigation": True,
"navigation_depth": 3,
"logo_only": True,
}
html_css_files = [
"css/custom.css",
]
html_show_sourcelink = False
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