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Merge pull request #387 from dalito/poetry2-upgrade-contd
Update pyproject.toml & actions to poetry 2.x / PEP 621
2 parents 7d213ee + cda25de commit 2c1cb70

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‎.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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# Activate after migration to uv as package manager
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# - package-ecosystem: "uv"
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# directories:
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# - "/"
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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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# angular:
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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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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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run: |
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pipx install poetry
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pipx inject poetry poetry-dynamic-versioning
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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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uses: actions/checkout@v4.2.2
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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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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5.6.0
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with:
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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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#----------------------------------------------
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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: 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: Regenerating poetry.lock file & install (sync) dependencies
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run: |
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poetry lock --regenerate
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poetry sync
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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: poetry run python -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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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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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: "3.11"
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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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run: pipx install poetry==1.4.0
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run: |
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pipx install poetry
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pipx inject poetry poetry-dynamic-versioning
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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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uses: actions/checkout@v4.2.2
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with:
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fetch-depth: 0
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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uses: actions/setup-python@v5.6.0
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with:
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python-version: ${{ matrix.python-version }}
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cache: 'poetry'
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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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run: |
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poetry install --no-interaction
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#----------------------------------------------
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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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# upload coverage results
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#----------------------------------------------
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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
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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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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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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v4.2.2
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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@v5.6.0
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with:
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python-version: 3.12
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python-version: 3.13
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- name: Install Poetry
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run: pipx install poetry
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- name: Install dependencies
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run: poetry install --no-interaction
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run: |
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pipx install poetry
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pipx inject poetry poetry-dynamic-versioning
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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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- 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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# Next 5 lines prepare for 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@v4.3.0
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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@v1.12
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with:
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password: ${{ secrets.pypi_password }}
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# verbose: true

‎.github/workflows/test-upstream.yaml‎

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# Test linkml-runtime with upstream linkml and run linkml tests
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name: Test with upstream linkml
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on:
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pull_request:
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echo "upstream_repo=${{ inputs.upstream_repo }}" >> "$GITHUB_ENV"
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- name: checkout upstream
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uses: actions/checkout@v4
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uses: actions/checkout@v4.2.2
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with:
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repository: "${{ env.upstream_repo }}"
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path: linkml
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ref: "${{ env.upstream_branch }}"
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fetch-depth: 0
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- name: checkout linkml-runtime
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uses: actions/checkout@v4
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uses: actions/checkout@v4.2.2
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with:
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# don't specify repository like this or else we won't get pull request branches correctly
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# repository: linkml/linkml-runtime
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path: linkml-runtime
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fetch-depth: 0
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git fetch upstream --tags
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- name: set up python
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uses: actions/setup-python@v5
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uses: actions/setup-python@v5.6.0
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install poetry
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run: pipx install poetry==1.*
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- name: Check Poetry version
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run: poetry --version
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- name: Install dynamic versioning plugin
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run: poetry self add "poetry-dynamic-versioning[plugin]"
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run: |
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pipx install poetry
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pipx inject poetry poetry-dynamic-versioning
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- name: Load cached venv
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id: cached-poetry-dependencies
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uses: actions/cache@v3
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uses: actions/cache@v4.2.3
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with:
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path: linkml/.venv
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key: venv-${{ matrix.python-version }}-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
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working-directory: linkml
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run: poetry run python -c 'import linkml_runtime; from importlib.metadata import version; print(linkml_runtime.__file__); print(version("linkml_runtime"))'
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- name: run tests
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- name: run linkml tests
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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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working-directory: linkml
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run: poetry run python -m pytest --with-slow
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