nwb-linkml/docs/conf.py

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Python

# 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
# -- Project information -----------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
project = 'nwb-linkml'
copyright = '2023, Jonny Saunders'
author = 'Jonny Saunders'
release = 'v0.1.0'
# -- General configuration ---------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
extensions = [
'sphinx.ext.graphviz',
"myst_parser",
'sphinx.ext.napoleon',
'sphinx.ext.autodoc',
'sphinxcontrib.autodoc_pydantic',
'sphinx.ext.intersphinx',
'sphinx.ext.doctest'
]
templates_path = ['_templates']
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
# -- Options for HTML output -------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
html_theme = 'furo'
html_static_path = ['_static']
intersphinx_mapping = {
'python': ('https://docs.python.org/3', None),
'matplotlib': ('https://matplotlib.org/stable/', None),
'numpy': ('https://numpy.org/doc/stable/', None),
'pandas': ('https://pandas.pydata.org/docs/', None),
'pydantic': ('https://docs.pydantic.dev/latest/', None),
'h5py': ('https://docs.h5py.org/en/stable/', None),
'dask': ('https://docs.dask.org/en/stable/', None)
}
# Napoleon settings
napoleon_google_docstring = True
napoleon_numpy_docstring = True
napoleon_include_init_with_doc = False
napoleon_include_private_with_doc = False
napoleon_include_special_with_doc = True
napoleon_use_admonition_for_examples = False
napoleon_use_admonition_for_notes = False
napoleon_use_admonition_for_references = False
napoleon_use_ivar = False
napoleon_use_param = True
napoleon_use_rtype = True
napoleon_preprocess_types = False
napoleon_type_aliases = None
napoleon_attr_annotations = True
# graphviz
graphviz_output_format = "svg"
autodoc_pydantic_model_show_json_error_strategy = 'coerce'
autodoc_pydantic_model_show_json = False
autodoc_mock_imports = ['nptyping']
# doctest
doctest_global_setup = """
from linkml_runtime.linkml_model import ClassDefinition, SlotDefinition, SchemaDefinition
from pydantic import BaseModel, Field
import numpy as np
"""