Cookie-cutter setup

.cruft.json

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+{
+  "template": "[email protected]:amc-corey-cox/monarch-project-template.git",
+  "commit": "7e9480b4c34eef0df4e0494f173b2f859c183d11",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "project_name": "emods",
+      "github_org_name": "monarch-initiative",
+      "__project_slug": "emods",
+      "project_description": "Monarch and Linda Crrnic Center project on phenotype identification",
+      "min_python_version": "3.12",
+      "file_name": "main",
+      "greeting_recipient": "World",
+      "full_name": "Corey Cox",
+      "email": "[email protected]",
+      "__author": "Corey Cox <[email protected]>",
+      "license": "MIT",
+      "github_token_for_doc_deployment": "GH_TOKEN",
+      "github_token_for_pypi_deployment": "PYPI_TOKEN",
+      "_template": "[email protected]:amc-corey-cox/monarch-project-template.git"
+    }
+  },
+  "directory": null
+}

.github/workflows/deploy-docs.yml

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+name: Auto-deployment of Documentation
+on:
+  push:
+    branches: [ main ]
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/[email protected]
+      with:
+        fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+
+    - name: Set up Python 3.
+      uses: actions/setup-python@v3
+      with:
+        python-version: 3.9
+
+    - name: Install Poetry.
+      uses: snok/[email protected]
+
+    - name: Install dependencies.
+      run: |
+        poetry install --with docs
+
+    - name: Build documentation.
+      run: |
+        echo ${{ secrets.GH_TOKEN }} >> src/emods/token.txt
+        mkdir gh-pages
+        touch gh-pages/.nojekyll
+        cd docs/
+        poetry run sphinx-apidoc -o . ../src/emods/ --ext-autodoc -f
+        poetry run sphinx-build -b html . _build
+        cp -r _build/* ../gh-pages/
+
+    - name: Deploy documentation.
+      if: ${{ github.event_name == 'push' }}
+      uses: JamesIves/[email protected]
+      with:
+        branch: gh-pages
+        force: true
+        folder: gh-pages
+        token: ${{ secrets.GH_TOKEN }}

.github/workflows/pypi-publish.yml

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+name: Publish Python Package
+
+on:
+  workflow_dispatch:
+  release:
+    types: [created]
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-latest
+    # needs: [test]
+    environment: release
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.9
+          cache: pip
+          cache-dependency-path: '**/pyproject.toml'
+
+      - name: Install Poetry
+        run: pip install poetry poetry-dynamic-versioning
+
+      - name: Install dependencies
+        run: poetry install --no-interaction
+
+      - name: Build source and wheel archives
+        run: poetry build
+
+      - name: Publish
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/qc.yml

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+name: emods QC
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ "3.8", "3.11" ]
+
+    steps:
+      - uses: actions/[email protected]
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Poetry
+        uses: snok/[email protected]
+      - name: Install dependencies
+        run: poetry install --no-interaction
+
+      - name: Check common spelling errors
+        run: poetry run tox -e codespell
+
+      - name: Check code quality with flake8
+        run: poetry run tox -e lint
+
+      - name: Test with pytest and generate coverage file
+        run: poetry run tox -e py

.gitignore

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+# 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/

.pre-commit-config.yaml

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+default_language_version:
+  python: python3
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+  - id: end-of-file-fixer
+  - id: check-yaml
+  - id: check-toml
+  - id: trailing-whitespace
+- repo: https://github.com/psf/black
+  rev: 23.7.0
+  hooks:
+  - id: black
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.0.278
+  hooks:
+  - id: ruff
+    args: [--fix, --exit-non-zero-on-fix]
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.2.4
+  hooks:
+  - id: codespell
+    additional_dependencies:
+      - tomli

CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+ advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+ address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team representative, [email protected]. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq