nwb-linkml/docs/conf.py

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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 pdb
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# -- 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'
import os
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import sys
from pathlib import Path
sys.path.insert(0, str(Path(__file__).parent))
from directives import AdapterDirective
from sphinx.util.tags import Tags
tags: Tags
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# -- General configuration ---------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
extensions = [
'sphinx.ext.graphviz',
'sphinx.ext.napoleon',
'sphinx.ext.autodoc',
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#'sphinxcontrib.autodoc_pydantic',
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'sphinx.ext.intersphinx',
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'sphinx.ext.doctest',
"sphinx_design",
#'myst_parser',
"myst_nb",
'sphinx_togglebutton',
'sphinx.ext.todo'
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]
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templates_path = ['_templates']
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exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '.venv']
if os.environ.get('SPHINX_MINIMAL', None) == 'True':
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exclude_patterns.append('**/models')
tags.add('minimal')
else:
tags.add('full')
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# -- 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']
html_css_files = [
'css/custom.css'
]
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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),
'linkml': ('https://linkml.io/linkml/', None),
'linkml_runtime': ('https://linkml.io/linkml/', None),
'linkml-runtime': ('https://linkml.io/linkml/', None)
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}
# 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"
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# autodoc
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autodoc_pydantic_model_show_json_error_strategy = 'coerce'
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autodoc_pydantic_model_show_json = False
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#autodoc_mock_imports = ['pydantic', 'curies', 'pydantic_settings']
autodoc_mock_imports = ['curies']
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autoclass_content = "both"
autodoc_member_order='bysource'
add_module_names = False
autodoc_default_options = {
'exclude-members': 'NDArray,Shape',
}
# --------------------------------------------------
# myst-nb
nb_render_markdown_format = 'myst'
nb_append_css = False
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# --------------------------------------------------
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# doctest
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# doctest_global_setup = """
# from linkml_runtime.linkml_model import ClassDefinition, SlotDefinition, SchemaDefinition
# from nwb_schema_language import Namespaces, Namespace, Dataset, Group, Schema
# from linkml_runtime.dumpers import yaml_dumper
# import yaml
# from pydantic import BaseModel, Field
# import numpy as np
#
# from nwb_linkml.adapters import BuildResult
# """
# --------------------------------------------------
# Etc one-off settings
# todo
todo_include_todos = True
todo_link_only = True
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def setup(app):
AdapterDirective.app = app
app.add_directive('adapter', AdapterDirective)
return {'parallel_read_safe': True, 'parallel_write_safe': True}