mirror of
https://github.com/p2p-ld/nwb-linkml.git
synced 2024-11-10 00:34:29 +00:00
135 lines
3.9 KiB
Python
135 lines
3.9 KiB
Python
# Configuration file for the Sphinx documentation builder.
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#
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# For the full list of built-in configuration values, see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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import pdb
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# -- Project information -----------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
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project = 'nwb-linkml'
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copyright = '2023, Jonny Saunders'
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author = 'Jonny Saunders'
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release = 'v0.1.0'
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import os
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import sys
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from pathlib import Path
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sys.path.insert(0, str(Path(__file__).parent))
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from directives import AdapterDirective
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from sphinx.util.tags import Tags
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tags: Tags
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# -- General configuration ---------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
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extensions = [
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'sphinx.ext.graphviz',
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'sphinx.ext.napoleon',
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'sphinx.ext.autodoc',
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#'sphinxcontrib.autodoc_pydantic',
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'sphinx.ext.intersphinx',
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'sphinx.ext.doctest',
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"sphinx_design",
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#'myst_parser',
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"myst_nb",
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'sphinx_togglebutton',
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'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']
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if os.environ.get('SPHINX_MINIMAL', None) == 'True':
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exclude_patterns.append('**/models')
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tags.add('minimal')
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else:
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tags.add('full')
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# -- Options for HTML output -------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
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html_theme = 'furo'
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html_static_path = ['_static']
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html_css_files = [
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'css/custom.css'
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]
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intersphinx_mapping = {
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'python': ('https://docs.python.org/3', None),
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'matplotlib': ('https://matplotlib.org/stable/', None),
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'numpy': ('https://numpy.org/doc/stable/', None),
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'pandas': ('https://pandas.pydata.org/docs/', None),
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'pydantic': ('https://docs.pydantic.dev/latest/', None),
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'h5py': ('https://docs.h5py.org/en/stable/', None),
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'dask': ('https://docs.dask.org/en/stable/', None),
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'linkml': ('https://linkml.io/linkml/', None),
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'linkml_runtime': ('https://linkml.io/linkml/', None),
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'linkml-runtime': ('https://linkml.io/linkml/', None)
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}
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# Napoleon settings
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napoleon_google_docstring = True
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napoleon_numpy_docstring = True
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napoleon_include_init_with_doc = False
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napoleon_include_private_with_doc = False
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napoleon_include_special_with_doc = True
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napoleon_use_admonition_for_examples = False
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napoleon_use_admonition_for_notes = False
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napoleon_use_admonition_for_references = False
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napoleon_use_ivar = False
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napoleon_use_param = True
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napoleon_use_rtype = True
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napoleon_preprocess_types = False
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napoleon_type_aliases = None
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napoleon_attr_annotations = True
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# graphviz
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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']
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autodoc_mock_imports = ['curies']
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autoclass_content = "both"
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autodoc_member_order='bysource'
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add_module_names = False
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autodoc_default_options = {
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'exclude-members': 'NDArray,Shape',
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}
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# --------------------------------------------------
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# myst-nb
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nb_render_markdown_format = 'myst'
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nb_append_css = False
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# --------------------------------------------------
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# doctest
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# doctest_global_setup = """
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# from linkml_runtime.linkml_model import ClassDefinition, SlotDefinition, SchemaDefinition
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# from nwb_schema_language import Namespaces, Namespace, Dataset, Group, Schema
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# from linkml_runtime.dumpers import yaml_dumper
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# import yaml
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# from pydantic import BaseModel, Field
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# import numpy as np
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#
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# from nwb_linkml.adapters import BuildResult
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# """
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# --------------------------------------------------
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# Etc one-off settings
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# todo
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todo_include_todos = True
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todo_link_only = True
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def setup(app):
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AdapterDirective.app = app
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app.add_directive('adapter', AdapterDirective)
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return {'parallel_read_safe': True, 'parallel_write_safe': True}
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