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Merge pull request #447 from linkml/migrate-to-uv-clean
Migrate to uv clean
2 parents c62747f + 679af5d commit 7f86016

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‎.github/dependabot.yml‎

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@@ -8,19 +8,17 @@ updates:
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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
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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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runs-on: ubuntu-latest
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steps:
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- uses: actions/[email protected]
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- name: Install Poetry
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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: Install uv
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uses: astral-sh/setup-uv@v6
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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/[email protected]
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with:
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python-version: 3.13
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- name: Check pyproject.toml and poetry.lock
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run: poetry check
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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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runs-on: ${{ matrix.os }}
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steps:
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- name: Install Poetry
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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: Install uv
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uses: astral-sh/setup-uv@v6
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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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- name: Check out repository
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uses: actions/[email protected]
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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/[email protected]
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with:
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python-version: ${{ matrix.python-version }}
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cache: 'poetry'
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- name: Install library
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run: poetry install --no-interaction
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- name: Regenerate lock file with latest dependencies
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run: uv lock --upgrade
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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: Install dependencies
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run: uv sync --group dev
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- name: Run 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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run: poetry run python -m pytest --with-slow
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run: uv run -m pytest --with-slow

‎.github/workflows/main.yaml‎

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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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runs-on: ubuntu-latest
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steps:
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- uses: actions/[email protected]
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- name: Install Poetry
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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: Install uv
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uses: astral-sh/setup-uv@v6
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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/[email protected]
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with:
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python-version: 3.13
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- name: Check pyproject.toml and poetry.lock
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run: poetry check
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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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with:
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fetch-depth: 0
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- name: Install Poetry
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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: Set up Python ${{ matrix.python-version }}
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uses: actions/[email protected]
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#----------------------------------------------
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# install uv
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#----------------------------------------------
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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: ${{ 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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- name: Install library
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#----------------------------------------------
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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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poetry install --no-interaction
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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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#----------------------------------------------
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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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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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#----------------------------------------------
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- name: Upload coverage report
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uses: codecov/codecov-action@v5
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with:

‎.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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with:
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python-version: 3.13
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- name: Install Poetry
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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: Install uv
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uses: astral-sh/setup-uv@v6
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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 build
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uv build
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- name: Store built distribution
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uses: actions/[email protected]

‎.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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env:
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UV_VERSION: "0.7.13"
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on:
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pull_request:
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workflow_dispatch:
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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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env:
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POETRY_VIRTUALENVS_IN_PROJECT: true
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steps:
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- name: Get upstream branch and repo from first lines of PR Body
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git remote add upstream https://github.com/linkml/linkml-runtime
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git fetch upstream --tags
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- name: set up python
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uses: actions/setup-[email protected]
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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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enable-cache: true
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version: ${{ env.UV_VERSION }}
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python-version: ${{ matrix.python-version }}
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- name: Install poetry
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run: |
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pipx install poetry
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pipx inject poetry poetry-dynamic-versioning
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- name: Load cached venv
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id: cached-poetry-dependencies
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uses: actions/[email protected]
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with:
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path: linkml/.venv
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key: venv-${{ matrix.python-version }}-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
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# we are not using linkml-runtime's lockfile, but simulating what will happen
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# when we merge this and update linkml's lockfile
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- name: add linkml-runtime to lockfile
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working-directory: linkml
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run: poetry add ../linkml-runtime
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run: uv add ../linkml-runtime
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# note that we run the installation step always, even if we restore a venv,
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# the cache will restore the old version of linkml-runtime, but the lockfile
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# will only store the directory dependency (and thus will reinstall it)
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# the cache will still speedup the rest of the installation
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- name: install linkml
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working-directory: linkml
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run: poetry sync --no-interaction --all-extras
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run: uv sync --all-groups
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- name: print linkml-runtime version
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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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run: uv 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 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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run: uv run -m pytest --with-slow

‎CONTRIBUTING.md‎

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## Development environment setup
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1. Install [poetry](https://python-poetry.org/docs/#installation).
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2. Install all the dependencies from your project, which are typically specified in a `poetry.lock` file.
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1. Install [uv](https://docs.astral.sh/uv/getting-started/installation/).
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2. Install all the dependencies from your project, which are typically specified in a `uv.lock` file.
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```
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poetry install
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uv sync --all-extras --dev
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```
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3. Run any python scripts or CLI commands by prefixing with `poetry run`.
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3. Run any python scripts or CLI commands by prefixing with `uv run`.
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```
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poetry run python your_script.py # ex of how to run standalone python script
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poetry run pytest # ex of how to invoke CLI tools
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uv run python your_script.py # ex of how to run standalone python script
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uv run pytest # ex of how to invoke CLI tools
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```
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4. Refer to the poetry docs for details on how to use the [add](https://python-poetry.org/docs/cli/#add), [update](https://python-poetry.org/docs/cli/#update) and [remove](https://python-poetry.org/docs/cli/#remove) commands.
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4. Refer to the uv docs for details on how to use the [add](https://docs.astral.sh/uv/concepts/dependencies/), [update](https://docs.astral.sh/uv/concepts/dependencies/#updating-dependencies) and
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[remove](https://docs.astral.sh/uv/concepts/dependencies/#removing-dependencies) commands.
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## Release process
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Once the code has been merged into the `main` branch on this repo, there are a few steps that need to be completed to ensure a release is complete.
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You can run the test suite in the following way:
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```
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poetry run python -m pytest
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uv run python -m pytest
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```
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### Upstream Testing
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To run the upstream `linkml` tests against your branch,
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install `linkml` locally with poetry, and then manually install your
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install `linkml` locally with uv, and then manually install your
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local copy of `linkml-runtime`
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```shell
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git clone https://github.com/linkml/linkml
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cd linkml
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poetry install --all-extras --with tests
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poetry run pip install -e ~/location/of/linkml-runtime
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poetry run pytest
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uv sync --all-extras
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uv add ~/location/of/linkml-runtime
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uv run pytest
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```
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## Code style

‎Makefile‎

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cp -pr $(MODEL_DIR)/* linkml_runtime/linkml_model
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test:
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poetry run pytest
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uv run pytest
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# temporary measure until linkml-model is synced

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