From 75b710c3eb024461c73fbfdc533379e908d52933 Mon Sep 17 00:00:00 2001 From: sneakers-the-rat Date: Thu, 7 Sep 2023 19:32:17 -0700 Subject: [PATCH] docs! --- .readthedocs.yaml | 35 + docs/Makefile | 20 + docs/{notes => _notes}/linkml.md | 0 docs/{notes => _notes}/pynwb.md | 0 docs/{notes => _notes}/schema.md | 0 docs/{notes => _notes}/storage.md | 0 docs/{notes => _notes}/todo.md | 0 docs/{notes => _notes}/translation.md | 0 docs/api/index.md | 6 + docs/api/nwb_linkml/adapters/adapter.md | 7 + docs/api/nwb_linkml/adapters/classes.md | 7 + docs/api/nwb_linkml/adapters/dataset.md | 7 + docs/api/nwb_linkml/adapters/group.md | 7 + docs/api/nwb_linkml/adapters/index.md | 10 + docs/api/nwb_linkml/adapters/namespaces.md | 7 + docs/api/nwb_linkml/adapters/schema.md | 7 + docs/api/nwb_linkml/config.md | 1 + docs/api/nwb_linkml/generators/index.md | 5 + docs/api/nwb_linkml/generators/pydantic.md | 7 + docs/api/nwb_linkml/index.md | 14 + docs/api/nwb_linkml/io/git.md | 7 + docs/api/nwb_linkml/io/hdf5.md | 7 + docs/api/nwb_linkml/io/index.md | 7 + docs/api/nwb_linkml/io/schema.md | 7 + docs/api/nwb_linkml/lang_elements.md | 1 + docs/api/nwb_linkml/maps/dtype.md | 7 + docs/api/nwb_linkml/maps/index.md | 8 + docs/api/nwb_linkml/maps/naming.md | 7 + docs/api/nwb_linkml/maps/preload.md | 7 + docs/api/nwb_linkml/maps/quantity.md | 7 + docs/api/nwb_linkml/models/core.md | 8 + docs/api/nwb_linkml/models/hdmf.md | 8 + docs/api/nwb_linkml/models/index.md | 6 + docs/api/nwb_linkml/monkeypatch.md | 1 + docs/api/nwb_linkml/providers/index.md | 9 + docs/api/nwb_linkml/schema/index.md | 3 + docs/api/nwb_schema_language/index.md | 6 + docs/api/nwb_schema_language/models.md | 7 + docs/api/nwb_schema_language/schema.md | 7 + docs/changelog.md | 5 + docs/conf.py | 63 ++ docs/index.md | 21 + docs/make.bat | 35 + nwb_linkml/src/nwb_linkml/translate.py | 2 + poetry.lock | 912 +++++++++++++++++++++ pyproject.toml | 21 + 46 files changed, 1319 insertions(+) create mode 100644 .readthedocs.yaml create mode 100644 docs/Makefile rename docs/{notes => _notes}/linkml.md (100%) rename docs/{notes => _notes}/pynwb.md (100%) rename docs/{notes => _notes}/schema.md (100%) rename docs/{notes => _notes}/storage.md (100%) rename docs/{notes => _notes}/todo.md (100%) rename docs/{notes => _notes}/translation.md (100%) create mode 100644 docs/api/index.md create mode 100644 docs/api/nwb_linkml/adapters/adapter.md create mode 100644 docs/api/nwb_linkml/adapters/classes.md create mode 100644 docs/api/nwb_linkml/adapters/dataset.md create mode 100644 docs/api/nwb_linkml/adapters/group.md create mode 100644 docs/api/nwb_linkml/adapters/index.md create mode 100644 docs/api/nwb_linkml/adapters/namespaces.md create mode 100644 docs/api/nwb_linkml/adapters/schema.md create mode 100644 docs/api/nwb_linkml/config.md create mode 100644 docs/api/nwb_linkml/generators/index.md create mode 100644 docs/api/nwb_linkml/generators/pydantic.md create mode 100644 docs/api/nwb_linkml/index.md create mode 100644 docs/api/nwb_linkml/io/git.md create mode 100644 docs/api/nwb_linkml/io/hdf5.md create mode 100644 docs/api/nwb_linkml/io/index.md create mode 100644 docs/api/nwb_linkml/io/schema.md create mode 100644 docs/api/nwb_linkml/lang_elements.md create mode 100644 docs/api/nwb_linkml/maps/dtype.md create mode 100644 docs/api/nwb_linkml/maps/index.md create mode 100644 docs/api/nwb_linkml/maps/naming.md create mode 100644 docs/api/nwb_linkml/maps/preload.md create mode 100644 docs/api/nwb_linkml/maps/quantity.md create mode 100644 docs/api/nwb_linkml/models/core.md create mode 100644 docs/api/nwb_linkml/models/hdmf.md create mode 100644 docs/api/nwb_linkml/models/index.md create mode 100644 docs/api/nwb_linkml/monkeypatch.md create mode 100644 docs/api/nwb_linkml/providers/index.md create mode 100644 docs/api/nwb_linkml/schema/index.md create mode 100644 docs/api/nwb_schema_language/index.md create mode 100644 docs/api/nwb_schema_language/models.md create mode 100644 docs/api/nwb_schema_language/schema.md create mode 100644 docs/changelog.md create mode 100644 docs/conf.py create mode 100644 docs/index.md create mode 100644 docs/make.bat create mode 100644 poetry.lock create mode 100644 pyproject.toml diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 0000000..35ed93f --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,35 @@ +# .readthedocs.yaml +# Read the Docs configuration file +# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details + +# Required +version: 2 + +# Build documentation in the "docs/" directory with Sphinx +sphinx: + configuration: docs/conf.py + +build: + os: ubuntu-22.04 + tools: + python: "3.11" + jobs: + post_create_environment: + - pip install poetry + - poetry config virtualenvs.create false + post_install: + - poetry install --no-root + - pip install ./nwb_linkml + - pip install ./nwb_schema_language + +# Optionally build your docs in additional formats such as PDF and ePub +# formats: +# - pdf +# - epub + +# Optional but recommended, declare the Python requirements required +# to build your documentation +# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html +# python: +# install: +# - requirements: docs/requirements.txt \ No newline at end of file diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..d4bb2cb --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = . +BUILDDIR = _build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/notes/linkml.md b/docs/_notes/linkml.md similarity index 100% rename from docs/notes/linkml.md rename to docs/_notes/linkml.md diff --git a/docs/notes/pynwb.md b/docs/_notes/pynwb.md similarity index 100% rename from docs/notes/pynwb.md rename to docs/_notes/pynwb.md diff --git a/docs/notes/schema.md b/docs/_notes/schema.md similarity index 100% rename from docs/notes/schema.md rename to docs/_notes/schema.md diff --git a/docs/notes/storage.md b/docs/_notes/storage.md similarity index 100% rename from docs/notes/storage.md rename to docs/_notes/storage.md diff --git a/docs/notes/todo.md b/docs/_notes/todo.md similarity index 100% rename from docs/notes/todo.md rename to docs/_notes/todo.md diff --git a/docs/notes/translation.md b/docs/_notes/translation.md similarity index 100% rename from docs/notes/translation.md rename to docs/_notes/translation.md diff --git a/docs/api/index.md b/docs/api/index.md new file mode 100644 index 0000000..159046c --- /dev/null +++ b/docs/api/index.md @@ -0,0 +1,6 @@ +# API + +```{toctree} +nwb_linkml/index +nwb_schema_language/index +``` \ No newline at end of file diff --git a/docs/api/nwb_linkml/adapters/adapter.md b/docs/api/nwb_linkml/adapters/adapter.md new file mode 100644 index 0000000..0ecb717 --- /dev/null +++ b/docs/api/nwb_linkml/adapters/adapter.md @@ -0,0 +1,7 @@ +# Adapter + +```{eval-rst} +.. automodule:: nwb_linkml.adapters.adapter + :members: + :undoc-members: +``` \ No newline at end of file diff --git a/docs/api/nwb_linkml/adapters/classes.md b/docs/api/nwb_linkml/adapters/classes.md new file mode 100644 index 0000000..8d105c0 --- /dev/null +++ b/docs/api/nwb_linkml/adapters/classes.md @@ -0,0 +1,7 @@ +# Classes + +```{eval-rst} +.. automodule:: nwb_linkml.adapters.classes + :members: + :undoc-members: +``` \ No newline at end of file diff --git a/docs/api/nwb_linkml/adapters/dataset.md b/docs/api/nwb_linkml/adapters/dataset.md new file mode 100644 index 0000000..4442056 --- /dev/null +++ b/docs/api/nwb_linkml/adapters/dataset.md @@ -0,0 +1,7 @@ +# Dataset + +```{eval-rst} +.. automodule:: nwb_linkml.adapters.dataset + :members: + :undoc-members: +``` \ No newline at end of file diff --git a/docs/api/nwb_linkml/adapters/group.md b/docs/api/nwb_linkml/adapters/group.md new file mode 100644 index 0000000..8af9140 --- /dev/null +++ b/docs/api/nwb_linkml/adapters/group.md @@ -0,0 +1,7 @@ +# Group + +```{eval-rst} +.. automodule:: nwb_linkml.adapters.group + :members: + :undoc-members: +``` \ No newline at end of file diff --git a/docs/api/nwb_linkml/adapters/index.md b/docs/api/nwb_linkml/adapters/index.md new file mode 100644 index 0000000..c97cf33 --- /dev/null +++ b/docs/api/nwb_linkml/adapters/index.md @@ -0,0 +1,10 @@ +# Adapters + +```{toctree} +adapter +classes +dataset +group +namespaces +schema +``` \ No newline at end of file diff --git a/docs/api/nwb_linkml/adapters/namespaces.md b/docs/api/nwb_linkml/adapters/namespaces.md new file mode 100644 index 0000000..4e5f607 --- /dev/null +++ b/docs/api/nwb_linkml/adapters/namespaces.md @@ -0,0 +1,7 @@ +# Namespaces + +```{eval-rst} +.. automodule:: nwb_linkml.adapters.namespaces + :members: + :undoc-members: +``` \ No newline at end of file diff --git a/docs/api/nwb_linkml/adapters/schema.md b/docs/api/nwb_linkml/adapters/schema.md new file mode 100644 index 0000000..2ccf087 --- /dev/null +++ b/docs/api/nwb_linkml/adapters/schema.md @@ -0,0 +1,7 @@ +# Schema + +```{eval-rst} +.. automodule:: nwb_linkml.adapters.schema + :members: + :undoc-members: +``` \ No newline at end of file diff --git a/docs/api/nwb_linkml/config.md b/docs/api/nwb_linkml/config.md new file mode 100644 index 0000000..46ac1e6 --- /dev/null +++ b/docs/api/nwb_linkml/config.md @@ -0,0 +1 @@ +# Config diff --git a/docs/api/nwb_linkml/generators/index.md b/docs/api/nwb_linkml/generators/index.md new file mode 100644 index 0000000..c8c007a --- /dev/null +++ b/docs/api/nwb_linkml/generators/index.md @@ -0,0 +1,5 @@ +# Generators + +```{toctree} +pydantic +``` \ No newline at end of file diff --git a/docs/api/nwb_linkml/generators/pydantic.md b/docs/api/nwb_linkml/generators/pydantic.md new file mode 100644 index 0000000..22bf8f8 --- /dev/null +++ b/docs/api/nwb_linkml/generators/pydantic.md @@ -0,0 +1,7 @@ +# Pydantic + +```{eval-rst} +.. automodule:: nwb_linkml.generators.pydantic + :members: + :undoc-members: +``` \ No newline at end of file diff --git a/docs/api/nwb_linkml/index.md b/docs/api/nwb_linkml/index.md new file mode 100644 index 0000000..2b418d1 --- /dev/null +++ b/docs/api/nwb_linkml/index.md @@ -0,0 +1,14 @@ +# nwb_linkml + +```{toctree} +adapters/index +generators/index +io/index +maps/index +models/index +providers/index +schema +config +lang_elements +monkeypatch +``` \ No newline at end of file diff --git a/docs/api/nwb_linkml/io/git.md b/docs/api/nwb_linkml/io/git.md new file mode 100644 index 0000000..26486d5 --- /dev/null +++ b/docs/api/nwb_linkml/io/git.md @@ -0,0 +1,7 @@ +# Git + +```{eval-rst} +.. automodule:: nwb_linkml.io.git + :members: + :undoc-members: +``` \ No newline at end of file diff --git a/docs/api/nwb_linkml/io/hdf5.md b/docs/api/nwb_linkml/io/hdf5.md new file mode 100644 index 0000000..d0e5ebb --- /dev/null +++ b/docs/api/nwb_linkml/io/hdf5.md @@ -0,0 +1,7 @@ +# HDF5 + +```{eval-rst} +.. automodule:: nwb_linkml.io.hdf5 + :members: + :undoc-members: +``` \ No newline at end of file diff --git a/docs/api/nwb_linkml/io/index.md b/docs/api/nwb_linkml/io/index.md new file mode 100644 index 0000000..c51440e --- /dev/null +++ b/docs/api/nwb_linkml/io/index.md @@ -0,0 +1,7 @@ +# I/O + +```{toctree} +git +hdf5 +schema +``` \ No newline at end of file diff --git a/docs/api/nwb_linkml/io/schema.md b/docs/api/nwb_linkml/io/schema.md new file mode 100644 index 0000000..49ef90b --- /dev/null +++ b/docs/api/nwb_linkml/io/schema.md @@ -0,0 +1,7 @@ +# Schema + +```{eval-rst} +.. automodule:: nwb_linkml.io.schema + :members: + :undoc-members: +``` \ No newline at end of file diff --git a/docs/api/nwb_linkml/lang_elements.md b/docs/api/nwb_linkml/lang_elements.md new file mode 100644 index 0000000..a5ae721 --- /dev/null +++ b/docs/api/nwb_linkml/lang_elements.md @@ -0,0 +1 @@ +# Language Elements diff --git a/docs/api/nwb_linkml/maps/dtype.md b/docs/api/nwb_linkml/maps/dtype.md new file mode 100644 index 0000000..00444c8 --- /dev/null +++ b/docs/api/nwb_linkml/maps/dtype.md @@ -0,0 +1,7 @@ +# DType + +```{eval-rst} +.. automodule:: nwb_linkml.maps.dtype + :members: + :undoc-members: +``` diff --git a/docs/api/nwb_linkml/maps/index.md b/docs/api/nwb_linkml/maps/index.md new file mode 100644 index 0000000..45253b6 --- /dev/null +++ b/docs/api/nwb_linkml/maps/index.md @@ -0,0 +1,8 @@ +# Maps + +```{toctree} +dtype +naming +preload +quantity +``` \ No newline at end of file diff --git a/docs/api/nwb_linkml/maps/naming.md b/docs/api/nwb_linkml/maps/naming.md new file mode 100644 index 0000000..8e2018e --- /dev/null +++ b/docs/api/nwb_linkml/maps/naming.md @@ -0,0 +1,7 @@ +# Naming + +```{eval-rst} +.. automodule:: nwb_linkml.maps.naming + :members: + :undoc-members: +``` diff --git a/docs/api/nwb_linkml/maps/preload.md b/docs/api/nwb_linkml/maps/preload.md new file mode 100644 index 0000000..c69d9b1 --- /dev/null +++ b/docs/api/nwb_linkml/maps/preload.md @@ -0,0 +1,7 @@ +# Preload + +```{eval-rst} +.. automodule:: nwb_linkml.maps.preload + :members: + :undoc-members: +``` diff --git a/docs/api/nwb_linkml/maps/quantity.md b/docs/api/nwb_linkml/maps/quantity.md new file mode 100644 index 0000000..cb3b7c4 --- /dev/null +++ b/docs/api/nwb_linkml/maps/quantity.md @@ -0,0 +1,7 @@ +# Quantity + +```{eval-rst} +.. automodule:: nwb_linkml.maps.quantity + :members: + :undoc-members: +``` diff --git a/docs/api/nwb_linkml/models/core.md b/docs/api/nwb_linkml/models/core.md new file mode 100644 index 0000000..9dd154a --- /dev/null +++ b/docs/api/nwb_linkml/models/core.md @@ -0,0 +1,8 @@ +# NWB Core + +```{eval-rst} +.. automodule:: nwb_linkml.models.core + :members: + :undoc-members: + :imported-members: +``` \ No newline at end of file diff --git a/docs/api/nwb_linkml/models/hdmf.md b/docs/api/nwb_linkml/models/hdmf.md new file mode 100644 index 0000000..3a5b1b0 --- /dev/null +++ b/docs/api/nwb_linkml/models/hdmf.md @@ -0,0 +1,8 @@ +# hdmf-common + +```{eval-rst} +.. automodule:: nwb_linkml.models.hdmf_common + :members: + :undoc-members: + :imported-members: +``` \ No newline at end of file diff --git a/docs/api/nwb_linkml/models/index.md b/docs/api/nwb_linkml/models/index.md new file mode 100644 index 0000000..c7e3ac5 --- /dev/null +++ b/docs/api/nwb_linkml/models/index.md @@ -0,0 +1,6 @@ +# Models + +```{toctree} +core +hdmf +``` \ No newline at end of file diff --git a/docs/api/nwb_linkml/monkeypatch.md b/docs/api/nwb_linkml/monkeypatch.md new file mode 100644 index 0000000..f5085ab --- /dev/null +++ b/docs/api/nwb_linkml/monkeypatch.md @@ -0,0 +1 @@ +# Monkeypatches diff --git a/docs/api/nwb_linkml/providers/index.md b/docs/api/nwb_linkml/providers/index.md new file mode 100644 index 0000000..bed90cd --- /dev/null +++ b/docs/api/nwb_linkml/providers/index.md @@ -0,0 +1,9 @@ +# Providers + +## Schema + +```{eval-rst} +.. automodule:: nwb_linkml.providers.schema + :members: + :undoc-members: +``` diff --git a/docs/api/nwb_linkml/schema/index.md b/docs/api/nwb_linkml/schema/index.md new file mode 100644 index 0000000..0e1c687 --- /dev/null +++ b/docs/api/nwb_linkml/schema/index.md @@ -0,0 +1,3 @@ +# Schema + +(i'll include them here l8r) diff --git a/docs/api/nwb_schema_language/index.md b/docs/api/nwb_schema_language/index.md new file mode 100644 index 0000000..8c9efdf --- /dev/null +++ b/docs/api/nwb_schema_language/index.md @@ -0,0 +1,6 @@ +# NWB Schema Language + +```{toctree} +models +schema +``` \ No newline at end of file diff --git a/docs/api/nwb_schema_language/models.md b/docs/api/nwb_schema_language/models.md new file mode 100644 index 0000000..c13b853 --- /dev/null +++ b/docs/api/nwb_schema_language/models.md @@ -0,0 +1,7 @@ +# Models + +```{eval-rst} +.. automodule:: nwb_schema_language.datamodel.nwb_schema_pydantic + :members: + :undoc-members: +``` \ No newline at end of file diff --git a/docs/api/nwb_schema_language/schema.md b/docs/api/nwb_schema_language/schema.md new file mode 100644 index 0000000..e26c925 --- /dev/null +++ b/docs/api/nwb_schema_language/schema.md @@ -0,0 +1,7 @@ +# Schema + +```{literalinclude} ../../../nwb_schema_language/src/nwb_schema_language/schema/nwb_schema_language.yaml +:language: yaml +:linenos: + +``` \ No newline at end of file diff --git a/docs/changelog.md b/docs/changelog.md new file mode 100644 index 0000000..04a29b9 --- /dev/null +++ b/docs/changelog.md @@ -0,0 +1,5 @@ +# Changelog + +## v0.1.0 - Package exists + +thats about as much as can be said \ No newline at end of file diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 0000000..6240f71 --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,63 @@ +# 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' +] + +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), + +} + + +# 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" diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..2b813bb --- /dev/null +++ b/docs/index.md @@ -0,0 +1,21 @@ +.. nwb-linkml documentation master file, created by + sphinx-quickstart on Thu Sep 7 18:57:17 2023. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +# nwb-linkml + +```{toctree} +:caption: Contents: + +api/index +changelog + +``` + + +## Indices and tables + +* {ref}`genindex` +* {ref}`modindex` +* {ref}`search` diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 0000000..954237b --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=. +set BUILDDIR=_build + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.https://www.sphinx-doc.org/ + exit /b 1 +) + +if "%1" == "" goto help + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/nwb_linkml/src/nwb_linkml/translate.py b/nwb_linkml/src/nwb_linkml/translate.py index a6e2fd9..84152de 100644 --- a/nwb_linkml/src/nwb_linkml/translate.py +++ b/nwb_linkml/src/nwb_linkml/translate.py @@ -1,5 +1,7 @@ """ Convenience functions for translating NWB schema + +This module will be deprecated and removed in favor of :mod:`.providers` """ import tempfile from typing import List, Optional, Dict diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..042d007 --- /dev/null +++ b/poetry.lock @@ -0,0 +1,912 @@ +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. + +[[package]] +name = "alabaster" +version = "0.7.13" +description = "A configurable sidebar-enabled Sphinx theme" +optional = false +python-versions = ">=3.6" +files = [ + {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"}, + {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"}, +] + +[[package]] +name = "annotated-types" +version = "0.5.0" +description = "Reusable constraint types to use with typing.Annotated" +optional = false +python-versions = ">=3.7" +files = [ + {file = "annotated_types-0.5.0-py3-none-any.whl", hash = "sha256:58da39888f92c276ad970249761ebea80ba544b77acddaa1a4d6cf78287d45fd"}, + {file = "annotated_types-0.5.0.tar.gz", hash = "sha256:47cdc3490d9ac1506ce92c7aaa76c579dc3509ff11e098fc867e5130ab7be802"}, +] + +[[package]] +name = "autodoc-pydantic" +version = "2.0.1" +description = "Seamlessly integrate pydantic models in your Sphinx documentation." +optional = false +python-versions = ">=3.7.1,<4.0.0" +files = [ + {file = "autodoc_pydantic-2.0.1-py3-none-any.whl", hash = "sha256:d3c302fdb6d37edb5b721f0f540252fa79cea7018bc1a9a85bf70f33a68b0ce4"}, + {file = "autodoc_pydantic-2.0.1.tar.gz", hash = "sha256:7a125a4ff18e4903e27be71e4ddb3269380860eacab4a584d6cc2e212fa96991"}, +] + +[package.dependencies] +pydantic = ">=2.0,<3.0.0" +pydantic-settings = ">=2.0,<3.0.0" +Sphinx = ">=4.0" + +[package.extras] +dev = ["coverage (>=7,<8)", "flake8 (>=3,<4)", "pytest (>=7,<8)", "sphinx-copybutton (>=0.4,<0.5)", "sphinx-rtd-theme (>=1.0,<2.0)", "sphinx-tabs (>=3,<4)", "sphinxcontrib-mermaid (>=0.7,<0.8)", "tox (>=3,<4)"] +docs = ["sphinx-copybutton (>=0.4,<0.5)", "sphinx-rtd-theme (>=1.0,<2.0)", "sphinx-tabs (>=3,<4)", "sphinxcontrib-mermaid (>=0.7,<0.8)"] +erdantic = ["erdantic (>=0.6,<0.7)"] +test = ["coverage (>=7,<8)", "pytest (>=7,<8)"] + +[[package]] +name = "babel" +version = "2.12.1" +description = "Internationalization utilities" +optional = false +python-versions = ">=3.7" +files = [ + {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"}, + {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"}, +] + +[[package]] +name = "beautifulsoup4" +version = "4.12.2" +description = "Screen-scraping library" +optional = false +python-versions = ">=3.6.0" +files = [ + {file = "beautifulsoup4-4.12.2-py3-none-any.whl", hash = "sha256:bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a"}, + {file = "beautifulsoup4-4.12.2.tar.gz", hash = "sha256:492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da"}, +] + +[package.dependencies] +soupsieve = ">1.2" + +[package.extras] +html5lib = ["html5lib"] +lxml = ["lxml"] + +[[package]] +name = "certifi" +version = "2023.7.22" +description = "Python package for providing Mozilla's CA Bundle." +optional = false +python-versions = ">=3.6" +files = [ + {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"}, + {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"}, +] + +[[package]] +name = "charset-normalizer" +version = "3.2.0" +description = "The Real First Universal Charset Detector. 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