BioContextAI Knowledgebase MCP

import os import sys from datetime import datetime from pathlib import Path from typing import List DOCS_DIR = Path(__file__).parent sys.path.insert(0, os.path.abspath("../../src/biocontext_kb")) # Project information project = "BioContextAI KB" author = "BioContextAI Team" copyright = f"{datetime.now():%Y}, {author}." # noqa: A001 # Configuration templates_path = ["_templates"] source_suffix = { ".rst": "restructuredtext", ".md": "markdown", } master_doc = "index" default_role = "literal" extensions = [ "sphinx.ext.autodoc", "sphinx.ext.coverage", "sphinx.ext.doctest", "sphinx.ext.intersphinx", "nbsphinx", "autoapi.extension", "sphinx.ext.napoleon", "sphinx_autodoc_typehints", "IPython.sphinxext.ipython_console_highlighting", "myst_parser", "sphinx.ext.viewcode", ] # Myst parser settings myst_enable_extensions = [ "amsmath", "attrs_inline", "colon_fence", "deflist", "dollarmath", "fieldlist", "html_admonition", "html_image", "replacements", "smartquotes", "strikethrough", "substitution", "tasklist", ] # Mapping for intersphinx extension intersphinx_mapping = { "python": ("https://docs.python.org/3", None), # numpy=("https://numpy.org/doc/stable/", None), # matplotlib=("https://matplotlib.org/stable", None), # pandas=("https://pandas.pydata.org/pandas-docs/stable/", None), # anndata=("https://anndata.readthedocs.io/en/latest/", None), # scipy=("https://docs.scipy.org/doc/scipy", None), # sklearn=("https://scikit-learn.org/stable", None), # flowio=("https://flowio.readthedocs.io/en/latest/", None), } # don't run the notebooks nbsphinx_execute = "never" pygments_style = "sphinx" exclude_trees = ["_build", "dist"] exclude_patterns = [ "_build", "Thumbs.db", ".DS_Store", ] # Generate the API documentation when building autoapi_type = "python" autoapi_add_toctree_entry = False autoapi_ignore: List[str] = ["_*.py"] autoapi_dirs = ["../../src/biocontext_kb"] autoapi_options = [ "members", "undoc-members", "show-inheritance", "show-module-summary", "special-members", "imported-members", ] autoapi_member_order = "alphabetical" autosummary_generate = True autodoc_member_order = "bysource" autodoc_typehints = "description" # Configuration of sphinx.ext.coverage coverage_show_missing_items = True # https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html napoleon_google_docstring = True napoleon_attr_annotations = True # Configurate sphinx rtd theme html_theme = "sphinx_book_theme" html_theme_options = { "repository_url": "https://github.com/biocontext_ai/knowledgebase-mcp", "repository_branch": "main", "use_download_button": True, "use_fullscreen_button": False, "use_repository_button": True, } html_static_path = ["_static"] html_show_sphinx = False html_context = { "display_github": True, "github_user": "biocontext_ai", "github_repo": "server", "github_version": "main", "conf_py_path": "/docs/", "github_button": True, "show_powered_by": False, } html_title = "BioContextAI Knowledgebase MCP" html_css_files = [ "css/custom.css", ]