initial package structuring and import from nwb_linkml

.github/workflows/tests.yml

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+name: Tests
+
+on:
+  push:
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        python-version: [3.11]
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+
+      - name: Install dependencies
+        run: pip install -e .[tests]
+
+      - name: Run Tests
+        run: pytest
+
+      - name: Report coverage
+        run: "coveralls --service=github"
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: psf/black@stable

.readthedocs.yaml

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+# .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"
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

README.md

@@ -1,2 +1,19 @@
 # numpydantic
+
+[![PyPI - Version](https://img.shields.io/pypi/v/numpydantic)](https://pypi.org/project/numpydantic)
+[![Documentation Status](https://readthedocs.org/projects/numpydantic/badge/?version=latest)](https://numpydantic.readthedocs.io/en/latest/?badge=latest)
+[![Coverage Status](https://coveralls.io/repos/github/p2p-ld/numpydantic/badge.svg)](https://coveralls.io/github/p2p-ld/numpydantic)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
 Type and shape validation and serialization for numpy arrays in pydantic models
+
+This package was picked out of [nwb-linkml](https://github.com/p2p-ld/nwb-linkml/), a 
+translation of the [NWB](https://www.nwb.org/) schema language and data format to
+linkML and pydantic models.
+
+It does two primary things:
+- **Provide types** - Annotations (based on [npytyping](https://github.com/ramonhagenaars/nptyping))
+  for specifying numpy arrays in pydantic models, and
+- **Generate models from LinkML** - extend the LinkML pydantic generator to create models that 
+  that use the [linkml-arrays](https://github.com/linkml/linkml-arrays) syntax
+

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)

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
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'numpydantic'
+copyright = '2024, Jonny Saunders'
+author = 'Jonny Saunders'
+release = 'v0.0.0'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    'sphinx.ext.napoleon',
+    'sphinx.ext.autodoc',
+    'sphinxcontrib.autodoc_pydantic',
+    'sphinx.ext.intersphinx',
+    "sphinx_design",
+    'myst_parser',
+    'sphinx.ext.todo'
+]
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3', None),
+    'numpy': ('https://numpy.org/doc/stable/', None),
+    'pydantic': ('https://docs.pydantic.dev/latest/', None),
+    'linkml': ('https://linkml.io/linkml/', None),
+    'linkml_runtime': ('https://linkml.io/linkml/', None),
+    'linkml-runtime': ('https://linkml.io/linkml/', None)
+}
+
+# -- 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']
+
+# autodoc
+autodoc_pydantic_model_show_json_error_strategy = 'coerce'
+autodoc_pydantic_model_show_json = False
+autodoc_mock_imports = []
+autoclass_content = "both"
+autodoc_member_order='bysource'
+add_module_names = False
+
+# 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
+
+# todo
+todo_include_todos = True
+todo_link_only = True

docs/hooks.md

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+# Hooks
+
+## TODO
+
+- nwb compatibility: allowable precision map in dtype check

docs/index.md

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+# numpydantic
+
+Type and shape validation and serialization for numpy arrays in pydantic models
+
+This package was picked out of [nwb-linkml](https://github.com/p2p-ld/nwb-linkml/), a 
+translation of the [NWB](https://www.nwb.org/) schema language and data format to
+linkML and pydantic models.
+
+It does two primary things:
+- **Provide types** - Annotations (based on [npytyping](https://github.com/ramonhagenaars/nptyping))
+  for specifying numpy arrays in pydantic models, and
+- **Generate models from LinkML** - extend the LinkML pydantic generator to create models that 
+  that use the [linkml-arrays](https://github.com/linkml/linkml-arrays) syntax
+
+```{toctree}
+:maxdepth: 2
+:caption: Contents:
+```
+

docs/make.bat

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+@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

numpydantic/__init__.py

@@ -0,0 +1 @@
+