conf.py•3.97 kB
# 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 --------------------------------------------------------------
# import sys
from datetime import datetime
from importlib.metadata import metadata
from pathlib import Path
HERE = Path(__file__).parent
# -- Project information -----------------------------------------------------
# NOTE: If you installed your project in editable mode, this might be stale.
# If this is the case, reinstall it to refresh the metadata
info = metadata("skill-to-mcp")
project_name = info["Name"]
author = info["Author"]
copyright = f"{datetime.now():%Y}, {author}."
version = info["Version"]
urls = dict(pu.split(", ") for pu in info.get_all("Project-URL"))
repository_url = urls["Source"]
# The full version, including alpha/beta/rc tags
release = info["Version"]
# bibtex_bibfiles = ["references.bib"]
templates_path = ["_templates"]
nitpicky = True # Warn about broken links
needs_sphinx = "4.0"
html_context = {
"display_github": True, # Integrate GitHub
"github_user": "biocontext-ai",
"github_repo": project_name,
"github_version": "main",
"conf_py_path": "/docs/",
}
# -- 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 = [
"myst_nb",
"sphinx_copybutton",
"sphinx.ext.intersphinx",
"sphinx.ext.autosummary",
"sphinx.ext.napoleon",
"sphinx_tabs.tabs",
"sphinx.ext.mathjax",
"IPython.sphinxext.ipython_console_highlighting",
"sphinxext.opengraph",
"autoapi.extension",
]
autoapi_dirs = ['../src/skill_to_mcp']
autosummary_generate = True
autodoc_member_order = "groupwise"
default_role = "literal"
napoleon_google_docstring = False
napoleon_numpy_docstring = True
napoleon_include_init_with_doc = False
napoleon_use_rtype = True # having a separate entry generally helps readability
napoleon_use_param = True
myst_heading_anchors = 6 # create anchors for h1-h6
myst_enable_extensions = [
"amsmath",
"colon_fence",
"deflist",
"dollarmath",
"html_image",
"html_admonition",
]
myst_url_schemes = ("http", "https", "mailto")
nb_output_stderr = "remove"
nb_execution_mode = "off"
nb_merge_streams = True
typehints_defaults = "braces"
source_suffix = {
".rst": "restructuredtext",
".ipynb": "myst-nb",
".myst": "myst-nb",
}
intersphinx_mapping = {
"python": ("https://docs.python.org/3", None),
"anndata": ("https://anndata.readthedocs.io/en/stable/", None),
"scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
"numpy": ("https://numpy.org/doc/stable/", None),
"click": ("https://click.palletsprojects.com/en/stable/", 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", "**.ipynb_checkpoints"]
# -- 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_book_theme"
html_static_path = ["_static"]
html_css_files = ["css/custom.css"]
html_title = project_name
html_theme_options = {
"repository_url": repository_url,
"use_repository_button": True,
"path_to_docs": "docs/",
"navigation_with_keys": False,
}
pygments_style = "default"
nitpick_ignore = [
# If building the documentation fails because of a missing link that is outside your control,
# you can add an exception to this list.
# ("py:class", "igraph.Graph"),
]