linkml 1.9.4rc2__tar.gz → 1.9.5rc2__tar.gz

linkml-1.9.5rc2/.github/workflows/check-external-links.yaml

@@ -0,0 +1,35 @@
+name: Check Sphinx external links
+env:
+  UV_VERSION: "0.7.13"
+on:
+  pull_request:
+  schedule:
+    - cron: '0 5 * * 1'  # at 05:00 UTC every Monday
+  workflow_dispatch:
+
+jobs:
+  check-external-links:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5.0.0
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python 3.
+        uses: actions/setup-python@v6.0.0
+        with:
+          python-version: "3.12"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6.6.1
+        with:
+          version: ${{ env.UV_VERSION }}
+
+      - name: Install docs dependencies
+        run: uv sync --group docs
+
+      - name: Build documentation.
+        run: |
+          cd docs/
+          uv run sphinx-build -b linkcheck . _build | grep "broken"

linkml-1.9.5rc2/.github/workflows/doc-pages.yaml

@@ -0,0 +1,54 @@
+name: Sphinx Documentation
+env:
+  UV_VERSION: "0.7.13"
+on:
+  push:
+    branches: [main]
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ "3.12" ]
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v5.0.0
+        with:
+          fetch-depth: 0
+
+      - name: Ensure tags if not run from main repo
+        if: github.repository != 'linkml/linkml'
+        run: |
+          git remote add upstream https://github.com/linkml/linkml
+          git fetch upstream --tags
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6.6.1
+        with:
+          version: ${{ env.UV_VERSION }}
+          enable-cache: true
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6.0.0
+        id: setup-python
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install docs dependencies
+        run: uv sync --group docs
+
+      - name: Build documentation.
+        run: |
+          mkdir gh-pages
+          touch gh-pages/.nojekyll
+          cd docs/
+          uv run sphinx-build -b html . _build
+          cp -r _build/* ../gh-pages/
+      - name: Deploy documentation.
+        if: ${{ github.event_name == 'push' }}
+        uses: JamesIves/github-pages-deploy-action@v4.7.3
+        with:
+          branch: gh-pages
+          force: true
+          folder: gh-pages

linkml-1.9.5rc2/.github/workflows/docker-build.yaml

@@ -0,0 +1,63 @@
+name: Build Docker Image
+
+on:
+  push:
+    branches:
+      - "main"
+    tags:
+      - "v*"
+  pull_request:
+    branches:
+      - "main"
+
+jobs:
+  docker:
+    name: Build and (conditionally) Push Docker Image
+    if: github.repository == 'linkml/linkml'
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5.0.0
+        with:
+          fetch-depth: 0
+
+      - name: Docker metadata
+        id: meta
+        uses: docker/metadata-action@v5.8.0
+        with:
+          images: linkml/linkml
+          tags: |
+            type=ref,event=branch
+            type=ref,event=pr
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+
+      - name: Log Docker tags
+        run: |
+          echo "Docker tags to be used:"
+          echo "${{ steps.meta.outputs.tags }}"
+          echo "Event: ${{ github.event_name }}"
+          echo "Ref: ${{ github.ref }}"
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3.6.0
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3.11.1
+
+      - name: Login to DockerHub
+        if: startsWith(github.ref, 'refs/tags/v')
+        uses: docker/login-action@v3.6.0
+        with:
+          username: cjmungall
+          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+
+      - name: Build and push
+        uses: docker/build-push-action@v6.18.0
+        with:
+          context: .
+          platforms: linux/amd64,linux/arm64/v8
+          push: ${{ startsWith(github.ref, 'refs/tags/v') }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

linkml-1.9.5rc2/.github/workflows/docs-test.yaml

@@ -0,0 +1,53 @@
+name: Build and test documentation
+env:
+  UV_VERSION: "0.7.13"
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  test_docs:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v5.0.0
+        with:
+          fetch-depth: 0
+
+      - name: Ensure tags if not run from main repo
+        if: github.repository != 'linkml/linkml'
+        run: |
+          git remote add upstream https://github.com/linkml/linkml
+          git fetch upstream --tags
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6.6.1
+        with:
+          version: ${{ env.UV_VERSION }}
+          enable-cache: true
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6.0.0
+        id: setup-python
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      #----------------------------------------------
+      # install dependencies
+      #----------------------------------------------
+      - name: Install dependencies
+        run: uv sync --group docs --group lint
+
+      - name: Build docs
+        working-directory: docs
+        env:
+          SPHINXOPTS: "-W --keep-going"
+        run: uv run make html

linkml-1.9.5rc2/.github/workflows/main.yaml

@@ -0,0 +1,168 @@
+# Built from:
+# https://docs.github.com/en/actions/guides/building-and-testing-python
+
+name: Build and test linkml
+env:
+  UV_VERSION: "0.7.13"
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  quality-checks:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5.0.0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6.6.1
+        with:
+          version: ${{ env.UV_VERSION }}
+
+      - uses: actions/setup-python@v6.0.0
+        with:
+          python-version: 3.13
+      - name: Check pyproject.toml and uv.lock
+        run: uv lock --check
+      - name: Install tox
+        run: python -m pip install tox
+      - name: Run pre-commit checks
+        uses: pre-commit/action@v3.0.1
+        with:
+          extra_args: --all-files
+
+  test:
+    needs:
+      - quality-checks
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        # Test on Windows with only the oldest and newest Python versions
+        exclude:
+          - os: windows-latest
+            python-version: "3.10"
+          - os: windows-latest
+            python-version: "3.11"
+          - os: windows-latest
+            python-version: "3.12"
+    # See https://github.com/snok/install-poetry#running-on-windows
+    defaults:
+      run:
+        shell: bash
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v5.0.0
+        with:
+          fetch-depth: 0
+
+      - name: Ensure tags if not run from main repo
+        if: github.repository != 'linkml/linkml'
+        run: |
+          git remote add upstream https://github.com/linkml/linkml
+          git fetch upstream --tags
+
+      - name: Install uv and setup uv caching
+        uses: astral-sh/setup-uv@v6.6.1
+        with:
+          version: ${{ env.UV_VERSION }}
+          enable-cache: true
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6.0.0
+        id: setup-python
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv sync --all-groups
+      - name: Setup Graphviz
+        uses: ts-graphviz/setup-graphviz@v2.0.2
+      - name: Generate coverage results
+        run: |
+          uv run coverage run -m pytest --with-network
+          uv run coverage xml
+          uv run coverage report -m
+        shell: bash
+      - name: Upload coverage report
+        if: github.repository == 'linkml/linkml' && github.actor != 'dependabot[bot]'
+        uses: codecov/codecov-action@v5.5.1
+        with:
+          name: codecov-results-${{ matrix.os }}-${{ matrix.python-version }}
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: coverage.xml
+          fail_ci_if_error: true
+
+  test_slow:
+    name: Slow Tests
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-latest, windows-latest ]
+        python-version: [ "3.9", "3.13" ]
+    needs:
+      - quality-checks
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v5.0.0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6.6.1
+        with:
+          version: ${{ env.UV_VERSION }}
+          enable-cache: true
+
+      - name: Set up Python
+        uses: actions/setup-python@v6.0.0
+        id: setup-python
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: uv sync --all-groups
+      - name: Generate coverage results
+        # Set bash shell to fail correctly on Windows https://github.com/actions/runner-images/issues/6668
+        shell: bash
+        run: |
+          uv run coverage run -m pytest --with-slow --with-biolink -m slow -n auto
+          uv run coverage xml
+          uv run coverage report -m
+      - name: Upload coverage report
+        if: github.repository == 'linkml/linkml' && github.actor != 'dependabot[bot]'
+        uses: codecov/codecov-action@v5.5.1
+        with:
+          name: codecov-results-slow-${{ matrix.os }}-${{ matrix.python-version }}
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: coverage.xml
+          fail_ci_if_error: true
+
+  test_build_package:
+    name: Test Build Package
+    needs:
+      - test
+    runs-on: ubuntu-latest
+    if: github.event_name == 'pull_request'
+    steps:
+      - uses: actions/checkout@v5.0.0
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v6.0.0
+        with:
+          python-version: 3.13
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6.6.1
+        with:
+          version: ${{ env.UV_VERSION }}
+      - name: Build source and wheel archives
+        run: uv build

linkml-1.9.5rc2/.github/workflows/pypi-publish.yaml

@@ -0,0 +1,61 @@
+name: Publish Python Package
+# Upload to PyPI is triggered by creating & publishing a release in GitHub UI
+env:
+  UV_VERSION: "0.7.13"
+on:
+  release:
+    # Trigger the workflow only for real releases but not for draft releases
+    types: [created]
+
+jobs:
+  build:
+    name: Build Python 🐍 distributions 📦 for publishing to PyPI
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v5.0.0
+      with:
+        # Checkout the code including tags required for dynamic versioning
+        fetch-depth: 0
+
+    - name: Set up Python
+      uses: actions/setup-python@v6.0.0
+      with:
+        python-version: 3.13
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6.6.1
+      with:
+        version: ${{ env.UV_VERSION }}
+
+    - name: Build source and wheel archives
+      run: |
+        uv build
+
+    - name: Store built distribution
+      uses: actions/upload-artifact@v4.6.2
+      with:
+        name: distribution-files
+        path: dist/
+
+  pypi-publish:
+    name: Build and publish Python 🐍 package 📦 to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    # Uses trusted publishing. https://docs.pypi.org/trusted-publishers/adding-a-publisher/
+    environment:
+      name: pypi-release
+      url: https://pypi.org/p/linkml
+    permissions:
+      id-token: write  # This permission is mandatory for trusted publishing.
+    steps:
+      - name: Download built distribution
+        uses: actions/download-artifact@v5.0.0
+        with:
+          name: distribution-files
+          path: dist
+
+      - name: Publish package 📦 to PyPI
+        if: github.event_name == 'release'
+        uses: pypa/gh-action-pypi-publish@v1.13.0
+        with:
+          verbose: true

linkml-1.9.5rc2/.github/workflows/rustgen.yaml

@@ -0,0 +1,64 @@
+name: Build and test linkml (rustgen)
+
+env:
+  UV_VERSION: "0.7.13"
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  test-rustgen:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
+
+      - name: Ensure tags if not run from main repo
+        if: github.repository != 'linkml/linkml'
+        run: |
+          git remote add upstream https://github.com/linkml/linkml
+          git fetch upstream --tags
+
+      - name: Install uv and setup uv caching
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: ${{ env.UV_VERSION }}
+          enable-cache: true
+
+      - name: Set up Python
+        uses: actions/setup-python@v6.0.0
+        with:
+          python-version: '3.12'
+
+      - name: Install Rust toolchain
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Show rust/cargo version
+        run: |
+          rustc -V
+          cargo -V
+
+      - name: Install Python deps (rustgen tests)
+        run: uv sync --group dev --group tests-rustgen --group tests-extra
+
+      - name: Run rustgen tests with coverage
+        run: |
+          uv run --group dev --group tests-rustgen coverage run -m pytest -m rustgen --with-rustgen
+          uv run coverage xml
+          uv run coverage report -m
+
+      - name: Upload coverage report
+        if: github.repository == 'linkml/linkml' && github.actor != 'dependabot[bot]'
+        uses: codecov/codecov-action@v5.5.1
+        with:
+          name: codecov-results-rustgen
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: coverage.xml
+          fail_ci_if_error: true

linkml-1.9.5rc2/.github/workflows/test-with-unreleased-runtime.yaml

@@ -0,0 +1,134 @@
+name: Test with unreleased linkml-runtime
+env:
+  UV_VERSION: "0.7.13"
+on:
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+    inputs:
+      upstream_repo:
+        description: "Upstream linkml-runtime repository to test with."
+        required: true
+        default: "linkml/linkml-runtime"
+      upstream_branch:
+        description: "Upstream linkml-runtime branch to test with."
+        required: true
+        default: "main"
+
+jobs:
+  test:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-latest, windows-latest ]
+        python-version: [ "3.9", "3.13" ]
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - name: Get upstream branch and repo from first lines of PR Body
+        if: github.event_name == 'pull_request'
+        shell: bash
+        env:
+          PR_BODY: ${{ github.event.pull_request.body }}
+        run: |
+          set +e
+          set +o pipefail
+
+          UPSTREAM_BRANCH=$( \
+            echo "$PR_BODY" | \
+            head -2 | \
+            grep upstream_branch | \
+            cut -d ":" -f 2 | \
+            awk '{$1=$1};1' \
+          )
+          echo "Got upstream branch:"
+          echo $UPSTREAM_BRANCH
+
+          if [[ -z "$UPSTREAM_BRANCH" ]]; then
+            echo "Using main as default"
+            UPSTREAM_BRANCH="main"
+          fi
+
+          UPSTREAM_REPO=$( \
+            echo "$PR_BODY" | \
+            head -2 | \
+            grep upstream_repo | \
+            cut -d ":" -f 2 | \
+            awk '{$1=$1};1' \
+          )
+          echo "Got upstream repo:"
+          echo $UPSTREAM_REPO
+
+          if [[ -z "$UPSTREAM_REPO" ]]; then
+            echo "Using linkml/linkml-runtime as default"
+            UPSTREAM_REPO="linkml/linkml-runtime"
+          fi
+
+          echo "upstream_branch=$UPSTREAM_BRANCH" >> "$GITHUB_ENV"
+          echo "upstream_repo=$UPSTREAM_REPO" >> "$GITHUB_ENV"
+
+      - name: Get upstream branch from workflow dispatch
+        if: github.event_name == 'workflow_dispatch'
+        shell: bash
+        run: |
+          echo "upstream_branch=${{ inputs.upstream_branch }}" >> "$GITHUB_ENV"
+          echo "upstream_repo=${{ inputs.upstream_repo }}" >> "$GITHUB_ENV"
+
+      - name: checkout upstream linkml-runtime
+        uses: actions/checkout@v5.0.0
+        with:
+          repository: "${{ env.upstream_repo }}"
+          path: linkml-runtime
+          ref: "${{ env.upstream_branch }}"
+          fetch-depth: 0
+
+      - name: checkout linkml
+        uses: actions/checkout@v5.0.0
+        with:
+          # don't specify repository like this or else we won't get pull request branches correctly
+          # repository: linkml/linkml
+          path: linkml
+          fetch-depth: 0
+
+      - name: Ensure tags for linkml-runtime upstream if a different one than linkml/linkml-runtime is specified
+        if: "${{ env.upstream_repo != 'linkml/linkml-runtime' }}"
+        working-directory: linkml-runtime
+        run: |
+          git remote add upstream https://github.com/linkml/linkml-runtime
+          git fetch upstream --tags
+
+      - name: Ensure tags for linkml if not run from main repo
+        if: github.repository != 'linkml/linkml'
+        working-directory: linkml
+        run: |
+          git remote add upstream https://github.com/linkml/linkml
+          git fetch upstream --tags
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6.6.1
+        with:
+          version: ${{ env.UV_VERSION }}
+          enable-cache: true
+
+      - name: Set up python
+        uses: actions/setup-python@v6.0.0
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      # note that we run the installation step always, even if we restore a venv,
+      # the cache will restore the old version of linkml, but the lockfile
+      # will only store the directory dependency (and thus will reinstall it)
+      # the cache will still speedup the rest of the installation
+      - name: Add checked-out linkml-runtime
+        working-directory: linkml
+        run: uv add ../linkml-runtime
+      - name: Update environment according to lockfile
+        working-directory: linkml
+        run: uv sync --all-groups
+      - name: print linkml-runtime version
+        working-directory: linkml
+        run: uv run python -c 'from importlib.metadata import version; print(version("linkml-runtime"))'
+      - name: run tests
+        working-directory: linkml
+        run: uv run -m pytest --with-slow