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‎.coveragerc‎

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ignore_errors = True
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omit =
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tests/*
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linkml_runtime/linkml_model/*

‎.editorconfig‎

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# Check https://editorconfig.org for more information
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# This is the main config file for this project:
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root = true
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[*]
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charset = utf-8
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end_of_line = lf
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insert_final_newline = true
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indent_style = space
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indent_size = 2
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trim_trailing_whitespace = true
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[*.py]
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indent_style = space
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indent_size = 4
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[*.py.jinja]
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indent_style = space
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indent_size = 4
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[*.md]
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trim_trailing_whitespace = false

‎.github/dependabot.yml‎

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# Please see the documentation for all configuration options:
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# https://docs.github.com/en/code-security/dependabot/working-with-dependabot/dependabot-options-reference
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version: 2
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updates:
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- package-ecosystem: github-actions
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directory: "/"
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schedule:
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interval: monthly
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- package-ecosystem: "uv"
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directory: "/"
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schedule:
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interval: "weekly"
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day: "sunday"
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groups:
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# Individual pull requests for major/minor updates and grouped for patch updates
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dependencies:
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applies-to: version-updates
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patterns:
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- "*"
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update-types:
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- "patch"
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open-pull-requests-limit: 10

‎.github/workflows/check-dependencies.yaml‎

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name: Build and test linkml-runtime with latest dependency versions
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env:
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UV_VERSION: "0.7.13"
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on:
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schedule:
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- cron: '0 5 * * 1' # once per week on Monday at 05:00 UTC
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types: trigger-run-check-dependencies
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jobs:
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quality-checks:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v5.0.0
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- name: Install uv
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uses: astral-sh/setup-uv@v6.8.0
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with:
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version: ${{ env.UV_VERSION }}
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enable-cache: true
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- uses: actions/setup-python@v6.0.0
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with:
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python-version: 3.13
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- name: Install tox
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run: python -m pip install tox
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- name: Run codespell
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run: tox -e codespell
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- name: Run code quality checks
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run: tox -e lint
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test:
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needs:
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- quality-checks
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, windows-latest]
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python-version: ["3.8", "3.9", "3.10"]
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python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
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exclude:
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- os: windows-latest
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python-version: "3.8"
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python-version: "3.10"
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- os: windows-latest
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python-version: "3.11"
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- os: windows-latest
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python-version: "3.12"
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runs-on: ${{ matrix.os }}
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steps:
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#----------------------------------------------
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# install poetry
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#----------------------------------------------
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- name: Install Poetry
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# Pin to 1.3.2 to workaround https://github.com/python-poetry/poetry/issues/7611
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run: pipx install poetry==1.3.2
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#----------------------------------------------
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# check-out repo and set-up python
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#----------------------------------------------
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- name: Check out repository
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uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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- name: Install uv
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uses: astral-sh/setup-uv@v6.8.0
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with:
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enable-cache: true
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version: ${{ env.UV_VERSION }}
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python-version: ${{ matrix.python-version }}
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cache: 'poetry'
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#----------------------------------------------
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# install your root project, if required
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#----------------------------------------------
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- name: Install library
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run: poetry install --no-interaction
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# this step we remove and rebuild the poetry.lock file to ensure that the tests that follow can be run
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# with the latest dependencies
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- name: Check out repository
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uses: actions/checkout@v5.0.0
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with:
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# Fetch all history for all branches and all tags.
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# The tags are required for dynamic versioning.
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fetch-depth: 0
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#----------------------------------------------
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# Remove and Rebuild the poetry.lock File
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#----------------------------------------------
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- name: Remove poetry.lock (Unix)
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if: runner.os != 'Windows'
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run: rm -rf poetry.lock
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- name: Regenerate lock file with latest dependencies
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run: uv lock --upgrade
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- name: Remove poetry.lock (Windows)
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if: runner.os == 'Windows'
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run: Remove-Item poetry.lock -Force
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- name: Install dependencies
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run: uv sync --group dev
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- name: Run tests
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run: poetry run python -m unittest discover
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# Set bash shell to fail correctly on Windows https://github.com/actions/runner-images/issues/6668
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shell: bash
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run: uv run -m pytest --with-slow

‎.github/workflows/main.yaml‎

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# Built from:
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# https://docs.github.com/en/actions/guides/building-and-testing-python
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# https://github.com/actions/checkout/
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# https://github.com/actions/setup-python/
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# https://github.com/codecov/codecov-action
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name: Build and test linkml-runtime
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env:
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UV_VERSION: "0.7.13"
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on:
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push:
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branches:
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- main
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- main
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pull_request:
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workflow_dispatch:
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jobs:
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quality-checks:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v5.0.0
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- name: Install uv
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uses: astral-sh/setup-uv@v6.8.0
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with:
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version: ${{ env.UV_VERSION }}
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enable-cache: true
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- uses: actions/setup-python@v6.0.0
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with:
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python-version: 3.13
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- name: Install tox
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run: python -m pip install tox
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- name: Run codespell
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run: tox -e codespell
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- name: Run code format checks
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run: tox -e format_check
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test:
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needs:
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- quality-checks
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, windows-latest]
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python-version: ["3.9", "3.10", "3.12", "3.13"]
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python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
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# Test on Windows with only the oldest and newest Python versions
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exclude:
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- os: windows-latest
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python-version: "3.10"
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- os: windows-latest
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python-version: "3.12"
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- os: windows-latest
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python-version: "3.10"
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- os: windows-latest
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python-version: "3.11"
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- os: windows-latest
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python-version: "3.12"
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# See https://github.com/snok/install-poetry#running-on-windows
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defaults:
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run:
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shell: bash
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runs-on: ${{ matrix.os }}
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steps:
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- name: Check out repository
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uses: actions/checkout@v5.0.0
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with:
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fetch-depth: 0
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#----------------------------------------------
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# install poetry
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#----------------------------------------------
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- name: Install Poetry
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run: pipx install poetry==1.4.0
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# install uv
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#----------------------------------------------
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# check-out repo and set-up python
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#----------------------------------------------
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- name: Check out repository
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uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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- name: Install uv
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uses: astral-sh/setup-uv@v6.8.0
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with:
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version: ${{ env.UV_VERSION }}
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enable-cache: true
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cache-dependency-glob: "uv.lock"
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python-version: ${{ matrix.python-version }}
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cache: 'poetry'
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#----------------------------------------------
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# install your root project, if required
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#----------------------------------------------
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- name: Install library
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run: poetry install --no-interaction
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# install your root project, if required
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#----------------------------------------------
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- name: Install dependencies
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run: |
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uv sync --group dev
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- name: Verify uv.lock is up-to-date
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run: uv lock --check
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#----------------------------------------------
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# coverage report
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# coverage report
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#----------------------------------------------
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- name: Generate coverage results
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# Set bash shell to fail correctly on Windows https://github.com/actions/runner-images/issues/6668
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# Set bash shell to fail correctly on Windows https://github.com/actions/runner-images/issues/6668
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shell: bash
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run: |
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poetry run coverage run -m pytest
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poetry run coverage xml
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poetry run coverage report -m
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uv run coverage run -m pytest
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uv run coverage xml
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uv run coverage report -m
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#----------------------------------------------
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# upload coverage results
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- name: Upload coverage report
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uses: codecov/codecov-action@v3
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uses: codecov/codecov-action@v5.5.1
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with:
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name: codecov-results-${{ matrix.os }}-${{ matrix.python-version }}
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token: ${{ secrets.CODECOV_TOKEN }}

‎.github/workflows/pypi-publish.yaml‎

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name: Publish Python Package
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# Upload to PyPI is triggered by creating & publishing a release in GitHub UI
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env:
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UV_VERSION: "0.7.13"
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on:
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release:
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# Trigger the workflow only for real releases but not for draft releases
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types: [created]
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jobs:
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build-n-publish:
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name: Build and publish Python 🐍 distributions 📦 to PyPI
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build:
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name: Build Python 🐍 distributions 📦 for publishing to PyPI
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runs-on: ubuntu-latest
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- uses: actions/checkout@v2
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- uses: actions/checkout@v5.0.0
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with:
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# Checkout the code including tags required for dynamic versioning
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fetch-depth: 0
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- name: Set up Python
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uses: actions/setup-python@v2.2.2
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uses: actions/setup-python@v6.0.0
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with:
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python-version: 3.12
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- name: Install Poetry
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run: pipx install poetry
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python-version: 3.13
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- name: Install dependencies
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run: poetry install --no-interaction
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- name: Install uv
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uses: astral-sh/setup-uv@v6.8.0
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with:
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enable-cache: true
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version: ${{ env.UV_VERSION }}
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- name: Build source and wheel archives
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run: |
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poetry version $(git describe --tags --abbrev=0)
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poetry build
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uv build
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- name: Publish distribution 📦 to PyPI
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uses: pypa/gh-action-pypi-publish@v1.2.2
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- name: Store built distribution
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uses: actions/upload-artifact@v4.6.2
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with:
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user: __token__
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password: ${{ secrets.pypi_password }}
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name: distribution-files
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path: dist/
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pypi-publish:
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name: Build and publish Python 🐍 package 📦 to PyPI
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needs: build
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runs-on: ubuntu-latest
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# Uses trusted publishing. https://docs.pypi.org/trusted-publishers/adding-a-publisher/
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environment:
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name: pypi-release
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url: https://pypi.org/p/linkml-runtime
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permissions:
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id-token: write # This permission is mandatory for trusted publishing.
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steps:
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- name: Download built distribution
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uses: actions/download-artifact@v5.0.0
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with:
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name: distribution-files
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path: dist
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- name: Publish package 📦 to PyPI
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if: github.event_name == 'release'
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uses: pypa/gh-action-pypi-publish@v1.13.0
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with:
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verbose: true

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