chore: make setup was run

.cruft.json

@@ -0,0 +1,27 @@
+{
+  "template": "https://github.com/linkml/linkml-project-cookiecutter",
+  "commit": "b2da87eb7835bfec748a76823d098cac85e8363a",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "project_name": "mixs-missing-value-sandbox",
+      "__project_slug": "mixs_missing_value_sandbox",
+      "github_org": "GenomicsStandardsConsortium",
+      "__source_path": "src/mixs_missing_value_sandbox/schema/mixs_missing_value_sandbox.yaml",
+      "project_description": "experimentation with formal representations of missing data",
+      "full_name": "Mark Andrew Miller",
+      "email": "[email protected]",
+      "__author": "Mark Andrew Miller <[email protected]>",
+      "license": "MIT",
+      "main_schema_class": "Person",
+      "create_python_classes": "Yes",
+      "use_schemasheets": "No",
+      "google_sheet_id": "1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ",
+      "google_sheet_tabs": "personinfo enums",
+      "__google_sheet_module": "personinfo_enums",
+      "github_token_for_pypi_deployment": "PYPI_PASSWORD",
+      "_template": "https://github.com/linkml/linkml-project-cookiecutter"
+    }
+  },
+  "directory": null
+}

.env.public

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+# This file is public in git. No sensitive info allowed.
+
+###### schema definition variables, used by makefile
+
+LINKML_SCHEMA_NAME="mixs_missing_value_sandbox"
+LINKML_SCHEMA_AUTHOR="Mark Andrew Miller <[email protected]>"
+LINKML_SCHEMA_DESCRIPTION="experimentation with formal representations of missing data"
+LINKML_SCHEMA_SOURCE_PATH="src/mixs_missing_value_sandbox/schema/mixs_missing_value_sandbox.yaml"
+LINKML_SCHEMA_GOOGLE_SHEET_ID="1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ"
+LINKML_SCHEMA_GOOGLE_SHEET_TABS="personinfo enums"
+
+###### linkml generator variables, used by makefile
+
+## gen-project configuration file
+LINKML_GENERATORS_CONFIG_YAML= --config-file config.yaml
+
+## pass args if gendoc ignores config.yaml (i.e. --no-mergeimports)
+LINKML_GENERATORS_DOC_ARGS=
+
+## pass args to workaround genowl rdfs config bug (linkml#1453)
+##   (i.e. --no-type-objects --no-metaclasses --metadata-profile rdfs)
+LINKML_GENERATORS_OWL_ARGS=
+
+## pass args to trigger experimental java/typescript generation
+LINKML_GENERATORS_JAVA_ARGS=
+LINKML_GENERATORS_TYPESCRIPT_ARGS=
+

.github/workflows/deploy-docs.yaml

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+---
+name: Auto-deployment of mixs_missing_value_sandbox Documentation
+on:
+  push:
+    branches: [main]
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+
+    # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
+    permissions:
+      contents: write  # to let mkdocs write the new docs
+      pages: write     # to deploy to Pages
+      id-token: write  # to verify the deployment originates from an appropriate source
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # otherwise, you will failed to push refs to dest repo
+
+      - name: Set up Python.
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install Poetry.
+        run: pipx install poetry
+
+      - name: Install dependencies.
+        run: poetry install -E docs
+
+      - name: Build documentation.
+        run: |
+          mkdir -p docs
+          touch docs/.nojekyll
+          make gendoc
+          ([ ! -f docs/about.md ] && cp src/docs/about.md docs/) || true
+          make mkd-gh-deploy

.github/workflows/main.yaml

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+# Built from:
+# https://docs.github.com/en/actions/guides/building-and-testing-python
+---
+name: Build and test mixs_missing_value_sandbox
+
+on: [pull_request]
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10"]
+
+    steps:
+
+      - name: Check out repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Poetry
+        run: pipx install poetry
+
+      - name: Install dependencies
+        run: poetry install --no-interaction --no-root
+
+      - name: Install project
+        run: poetry install --no-interaction
+
+      - name: Run test suite
+        run: make test

.github/workflows/pypi-publish.yaml

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+---
+name: Publish Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install Poetry
+        run: |
+          pipx install poetry
+          poetry self add "poetry-dynamic-versioning[plugin]"
+
+      # - name: Install dependencies
+      #   run: poetry install --no-interaction
+
+      - name: Build source and wheel archives
+        run: poetry build
+
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/test_pages_build.yaml

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+name: Preview mixs_missing_value_sandbox documentation build
+
+on:
+  pull_request:
+    types:
+      - opened
+      - reopened
+      - synchronize
+
+concurrency: preview-${{ github.ref }}
+
+jobs:
+  run:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python 3
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install Poetry
+        run: pipx install poetry
+
+      - name: Install dependencies
+        run: poetry install -E docs
+
+      - name: Build documentation
+        run: |
+          mkdir -p site
+          touch site/.nojekyll
+          make gendoc
+          ([ ! -f docs/about.md ] && cp src/docs/about.md docs/) || true
+          poetry run mkdocs build -d site
+
+      - name: Deploy preview
+        uses: rossjrw/pr-preview-action@v1
+        with:
+          source-dir: site/
+          preview-branch: gh-pages

.gitignore

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+/docs/
+/project/docs/
+/tmp/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/