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‎.github/CODEOWNERS‎

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* @biocommons/maintainers

‎.github/actions/setup-python-env/action.yml‎

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name: "Setup Python Environment"
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description: "Set up Python environment for the given Python version"
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inputs:
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python-version:
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description: "Python version to use"
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required: true
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default: "3.13"
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uv-version:
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description: "uv version to use"
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required: true
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default: "0.7.14"
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runs:
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using: "composite"
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steps:
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- uses: actions/setup-python@v5
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with:
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python-version: ${{ inputs.python-version }}
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- name: Install uv
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uses: astral-sh/setup-uv@v6
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with:
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version: ${{ inputs.uv-version }}
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enable-cache: 'true'
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cache-suffix: ${{ matrix.python-version }}
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- name: Install Python dependencies
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run: uv sync --frozen
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shell: bash

‎.github/labels.yml‎

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# file must contain an array, which may be empty
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[]

‎.github/workflows/labels.yml‎

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name: Sync labels
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on:
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workflow_dispatch:
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push:
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branches:
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- 'main'
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paths:
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- '.github/labels.yml'
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- '.github/workflows/labels.yml'
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permissions:
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issues: write
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jobs:
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labels:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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sparse-checkout: .github/labels.yml
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- uses: EndBug/label-sync@v2
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with:
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config-file: |
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https://raw.githubusercontent.com/biocommons/.github/main/etc/labels.yml
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.github/labels.yml
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delete-other-labels: false

‎.github/workflows/python-ci-cd.yml‎

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name: Python CI/CD
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permissions:
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contents: write
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id-token: write
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on:
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push:
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branches: ["*"]
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tags: ["*"]
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jobs:
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python-ci-cd:
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name: Python CI/CD
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permissions:
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contents: write
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id-token: write
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uses: biocommons/.github/.github/workflows/python-ci-cd.yml@main
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with:
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publish: ${{ github.event_name == 'push' && startsWith(github.ref, 'refs/tags/') }}
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secrets:
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pypi-token: ${{ secrets.UV_PUBLISH_TOKEN }}

‎.github/workflows/stale.yml‎

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name: 'Close stale issues and PRs'
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on:
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workflow_dispatch:
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schedule:
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- cron: '1 1 * * *'
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jobs:
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stale:
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uses: biocommons/.github/.github/workflows/stale.yml@main

‎.github/workflows/validate-codecov-config.yml‎

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name: Validate Codecov Config
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on:
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pull_request:
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paths: [codecov.yaml]
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push:
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branches: [main]
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jobs:
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validate-codecov-config:
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runs-on: ubuntu-latest
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permissions:
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contents: read
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steps:
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- uses: actions/checkout@v4
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- name: Validate codecov configuration
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run: curl -sSL --fail-with-body --data-binary @codecov.yaml https://codecov.io/validate

‎.gitignore‎

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*$py.class
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*.cover
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*.egg
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*.egg-info/
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*.log
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*.manifest
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*.mo
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*.pot
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*.py.cover
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*.py[codz]
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*.sage.py
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*.so
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*.spec
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*.sqlite3
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*.sqlite3-journal
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*~
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.DS_Store
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.Python
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.abstra/
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.cache
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.coverage
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.coverage.*
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.cursorignore
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.cursorindexingignore
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.dmypy.json
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.eggs/
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.env
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.envrc
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.hypothesis/
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.installed.cfg
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.ipynb_checkpoints
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.mypy_cache/
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.nox/
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.pdm-build/
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.pdm-python
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.pixi
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.pybuilder/
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.pypirc
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.pyre/
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.pytest_cache/
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.pytype/
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.ropeproject
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.ruff_cache/
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.scrapy
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.spyderproject
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.spyproject
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.tox/
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.venv
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.vscode
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.webassets-cache
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/site
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ENV/
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MANIFEST
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__marimo__/
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__pycache__/
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__pypackages__/
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archive
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build/
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celerybeat-schedule
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celerybeat.pid
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cover/
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coverage.xml
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cython_debug/
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develop-eggs/
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dist/
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dmypy.json
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docs/_build/
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docs/source
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downloads/
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eggs/
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env.bak/
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env/
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htmlcov/
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instance/
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ipython_config.py
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lib/
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lib64/
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local_settings.py
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marimo/_lsp/
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marimo/_static/
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nosetests.xml
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parts/
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pip-delete-this-directory.txt
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pip-log.txt
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profile_default/
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sdist/
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share/python-wheels/
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target/
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var/
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venv.bak/
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venv/
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wheels/

‎.mailmap‎

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# I pick the account with the most modified files in git shortlog -sne
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# This is used by Git to consolidate the users who used multiple accounts
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Andreas Prlic <[email protected]> Andreas Prlic <[email protected]>
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Andreas Prlic <[email protected]> Andreas Prlic <[email protected]>
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Caitlin Gong <[email protected]> Caitlin Gong <[email protected]>
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Katie Stahl <[email protected]> katie stahl <[email protected]>
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Manuel Holtgrewe <[email protected]> Manuel Holtgrewe <[email protected]>
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Meng <[email protected]> Meng Wang <[email protected]>
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Reece Hart <[email protected]> Reece Hart <[email protected]>
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Reece Hart <[email protected]> Reece Hart <[email protected]>
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Reece Hart <[email protected]> Reece Hart <[email protected]>
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Reece Hart <[email protected]> Reece Hart <[email protected]>
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Rudy Rico <[email protected]> Rudolph Rico <[email protected]>

‎.pre-commit-config.yaml‎

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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: "v6.0.0"
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hooks:
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- id: check-case-conflict
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- id: check-merge-conflict
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- id: check-json
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exclude: ^.devcontainer/.*devcontainer.json
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- id: check-shebang-scripts-are-executable
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- id: check-symlinks
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- id: check-toml
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- id: check-yaml
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- id: detect-private-key
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- id: end-of-file-fixer
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- id: mixed-line-ending
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args: [ --fix=lf ]
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- id: pretty-format-json
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exclude: ^.devcontainer/.*devcontainer.json
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args: [--autofix, --no-sort-keys]
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- id: trailing-whitespace
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: "v0.12.7"
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hooks:
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- id: ruff-check
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args: [ --fix, --exit-non-zero-on-fix ]
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- id: ruff-format
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- repo: local
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hooks:
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- id: canonicalize-gitignore
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name: Sort unique .gitignore
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entry: sh -c 'LC_ALL=C sort -u -o .gitignore .gitignore'
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language: system
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files: ^\.gitignore$
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- repo: local
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hooks:
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- id: canonicalize-pyproject
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name: Ensure pyproject.toml in canonical order and format
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entry: uvx toml-sort --in-place --all pyproject.toml
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language: system
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files: ^pyproject.toml$

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