Merge branch 'linkml:main' into main

Author: m00wgli

.github/dependabot.yml

@@ -1,12 +1,17 @@
 # Please see the documentation for all configuration options:
 # https://docs.github.com/en/code-security/dependabot/working-with-dependabot/dependabot-options-reference
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
 
 version: 2
 updates:
   - package-ecosystem: github-actions
     directory: "/"
     schedule:
       interval: monthly
+    groups:
+      github-actions:
+        patterns:
+          - "*"
 
   # Activate after migration to uv as package manager
   # - package-ecosystem: "uv"

.github/scripts/check_links.py

@@ -20,6 +20,9 @@
 # URL pattern to match in docs
 URL_PATTERN = re.compile(r'https?://[^\s<>")\]`\'\,]+')
 
+# Pattern for URLs pointing to files in this repo (verify locally instead of via HTTP)
+REPO_FILE_PATTERN = re.compile(r"https://github\.com/linkml/linkml/(?:tree|blob)/main/(.*)")
+
 # Status classification
 OK_STATUSES = {"200", "201", "202", "203", "204", "301", "302", "303", "307", "308"}
 WARNING_STATUSES = {"403"}  # Bot protection - probably fine, just can't verify
@@ -33,8 +36,6 @@
     "example.net",
     # Example/placeholder domains in docs
     "acme.org",
-    # URL extraction issues - URLs contain special chars that break extraction
-    "yuml.me",
     # Unreliable/slow - frequently timeout or rate limit
     "terminusdb.com",
     "xmlns.com",
@@ -143,6 +144,14 @@ def check_url(url: str, timeout: int = 10) -> tuple[str, str]:
     Returns:
         Tuple of (status_code_or_error, error_message_or_empty)
     """
+    # Self-referencing repo URLs: verify the file exists locally
+    repo_match = REPO_FILE_PATTERN.match(url)
+    if repo_match:
+        path = Path(repo_match.group(1))
+        if path.exists():
+            return "200", ""
+        return "404", f"Local path not found: {path}"
+
     try:
         response = requests.head(
             url,

.github/workflows/check-external-links.yaml

@@ -16,20 +16,20 @@ jobs:
         uses: actions/checkout@v6
 
       - name: Set up Python 3.
-        uses: actions/setup-python@v6.0.0
+        uses: actions/setup-python@v6.2.0
         with:
           python-version: "3.12"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v7.1.6
+        uses: astral-sh/setup-uv@v7.3.1
         with:
           version: ${{ env.UV_VERSION }}
 
       - name: Install dependencies
         run: uv pip install --system requests
 
       - name: Restore link cache
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           path: .github/link-cache.csv
           key: link-cache-${{ github.run_id }}

.github/workflows/doc-pages.yaml

@@ -24,13 +24,13 @@ jobs:
           git fetch upstream --tags
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v7.1.6
+        uses: astral-sh/setup-uv@v7.3.1
         with:
           version: ${{ env.UV_VERSION }}
           enable-cache: true
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v6.0.0
+        uses: actions/setup-python@v6.2.0
         id: setup-python
         with:
           python-version: ${{ matrix.python-version }}
@@ -47,7 +47,7 @@ jobs:
           cp -r _build/* ../gh-pages/
       - name: Deploy documentation.
         if: ${{ github.event_name == 'push' }}
-        uses: JamesIves/github-pages-deploy-action@v4.7.3
+        uses: JamesIves/github-pages-deploy-action@v4.8.0
         with:
           branch: gh-pages
           force: true

.github/workflows/docker-build.yaml

@@ -44,17 +44,17 @@ jobs:
         uses: docker/setup-qemu-action@v3.7.0
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3.11.1
+        uses: docker/setup-buildx-action@v3.12.0
 
       - name: Login to DockerHub
         if: startsWith(github.ref, 'refs/tags/v')
-        uses: docker/login-action@v3.6.0
+        uses: docker/login-action@v3.7.0
         with:
           username: cjmungall
           password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
 
       - name: Build and push
-        uses: docker/build-push-action@v6.18.0
+        uses: docker/build-push-action@v6.19.2
         with:
           context: .
           platforms: linux/amd64,linux/arm64/v8

.github/workflows/docs-test.yaml

@@ -29,13 +29,13 @@ jobs:
           git fetch upstream --tags
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v7.1.6
+        uses: astral-sh/setup-uv@v7.3.1
         with:
           version: ${{ env.UV_VERSION }}
           enable-cache: true
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v6.0.0
+        uses: actions/setup-python@v6.2.0
         id: setup-python
         with:
           python-version: ${{ matrix.python-version }}

.github/workflows/main.yaml

@@ -17,11 +17,11 @@ jobs:
     steps:
       - uses: actions/checkout@v6
       - name: Install uv
-        uses: astral-sh/setup-uv@v7.1.6
+        uses: astral-sh/setup-uv@v7.3.1
         with:
           version: ${{ env.UV_VERSION }}
 
-      - uses: actions/setup-python@v6.0.0
+      - uses: actions/setup-python@v6.2.0
         with:
           python-version: 3.13
       - name: Check pyproject.toml and uv.lock
@@ -40,7 +40,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
         # Test on Windows with only the oldest and newest Python versions
         exclude:
           - os: windows-latest
@@ -69,13 +69,13 @@ jobs:
           git fetch upstream --tags
 
       - name: Install uv and setup uv caching
-        uses: astral-sh/setup-uv@v7.1.6
+        uses: astral-sh/setup-uv@v7.3.1
         with:
           version: ${{ env.UV_VERSION }}
           enable-cache: true
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v6.0.0
+        uses: actions/setup-python@v6.2.0
         id: setup-python
         with:
           python-version: ${{ matrix.python-version }}
@@ -86,13 +86,13 @@ jobs:
         uses: ts-graphviz/setup-graphviz@v2.0.2
       - name: Test linkml package
         run: |
-          uv run coverage run -m pytest tests/linkml/ --with-network
+          uv run coverage run -m pytest tests/linkml/ --with-network -m "not kroki"
           uv run coverage xml -o coverage-linkml.xml
           uv run coverage report -m
         shell: bash
       - name: Test linkml-runtime package
         run: |
-          uv run coverage run -m pytest tests/linkml_runtime/ --with-network
+          uv run coverage run -m pytest tests/linkml_runtime/ --with-network -m "not kroki"
           uv run coverage xml -o coverage-linkml_runtime.xml
           uv run coverage report -m
         shell: bash
@@ -121,7 +121,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, windows-latest ]
-        python-version: [ "3.9", "3.13" ]
+        python-version: [ "3.10", "3.13" ]
     needs:
       - quality-checks
     runs-on: ${{ matrix.os }}
@@ -132,13 +132,13 @@ jobs:
       - name: Check out repository
         uses: actions/checkout@v6
       - name: Install uv
-        uses: astral-sh/setup-uv@v7.1.6
+        uses: astral-sh/setup-uv@v7.3.1
         with:
           version: ${{ env.UV_VERSION }}
           enable-cache: true
 
       - name: Set up Python
-        uses: actions/setup-python@v6.0.0
+        uses: actions/setup-python@v6.2.0
         id: setup-python
         with:
           python-version: ${{ matrix.python-version }}
@@ -148,7 +148,7 @@ jobs:
         # 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 tests/linkml/ --with-slow --with-biolink -m slow -n auto
+          uv run coverage run -m pytest tests/linkml/ --with-slow --with-biolink -m "slow and not kroki" -n auto
           uv run coverage xml -o coverage-linkml-slow.xml
           uv run coverage report -m
       - name: Upload linkml slow test coverage
@@ -173,12 +173,12 @@ jobs:
           fetch-depth: 0
 
       - name: Set up Python
-        uses: actions/setup-python@v6.0.0
+        uses: actions/setup-python@v6.2.0
         with:
           python-version: 3.13
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v7.1.6
+        uses: astral-sh/setup-uv@v7.3.1
         with:
           version: ${{ env.UV_VERSION }}
       - name: Build source and wheel archives

.github/workflows/metamodel-compat.yaml

@@ -0,0 +1,115 @@
+# Weekly compatibility test against the latest linkml-model metamodel
+#
+# This workflow downloads the latest metamodel from linkml-model and runs
+# the compatibility tests to ensure the linkml toolkit can process it.
+# If tests pass and the metamodel has changed, it creates a PR with the update.
+
+name: Metamodel Compatibility
+env:
+  UV_VERSION: "0.7.13"
+on:
+  schedule:
+    # Run every Monday at 9:00 UTC
+    - cron: "0 9 * * 1"
+  workflow_dispatch:
+
+jobs:
+  metamodel-compat:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v6
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7.3.1
+        with:
+          version: ${{ env.UV_VERSION }}
+          enable-cache: true
+
+      - name: Set up Python
+        uses: actions/setup-python@v6.2.0
+        with:
+          python-version: "3.12"
+
+      - name: Install dependencies
+        run: uv sync --all-groups
+
+      - name: Setup Graphviz
+        uses: ts-graphviz/setup-graphviz@v2.0.2
+
+      - name: Download latest metamodel from linkml-model
+        run: make download-metamodel
+
+      - name: Run metamodel compatibility tests
+        id: run_tests
+        run: |
+          mkdir -p temp
+          uv run pytest tests/linkml/test_metamodel_compat/ --with-slow -v 2>&1 | tee temp/test_output.txt
+        continue-on-error: true
+
+      - name: Check for existing issue
+        if: steps.run_tests.outcome == 'failure'
+        id: check_issue
+        run: |
+          EXISTING_ISSUE=$(gh issue list --label "metamodel-compat" --state open --json number --jq '.[0].number // empty')
+          echo "existing_issue=${EXISTING_ISSUE}" >> $GITHUB_OUTPUT
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Create or update issue on failure
+        if: steps.run_tests.outcome == 'failure'
+        run: |
+          ISSUE_TITLE="Metamodel compatibility test failure"
+          ISSUE_BODY=$(cat <<'EOF'
+          ## Metamodel Compatibility Test Failure
+
+          The weekly metamodel compatibility test has failed. This indicates that the
+          current linkml toolkit may not be compatible with the latest linkml-model metamodel.
+
+          **Workflow run:** ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
+
+          ### Test Output (last 100 lines)
+          ```
+          $(tail -n 100 temp/test_output.txt)
+          ```
+
+          ### Next Steps
+          1. Review the test output above
+          2. Check for recent changes in [linkml-model](https://github.com/linkml/linkml-model)
+          3. Update the linkml toolkit to handle any metamodel changes
+          EOF
+          )
+
+          if [ -n "${{ steps.check_issue.outputs.existing_issue }}" ]; then
+            gh issue comment "${{ steps.check_issue.outputs.existing_issue }}" --body "${ISSUE_BODY}"
+          else
+            gh issue create \
+              --title "${ISSUE_TITLE}" \
+              --body "${ISSUE_BODY}" \
+              --label "metamodel-compat"
+          fi
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Fail if tests failed
+        if: steps.run_tests.outcome == 'failure'
+        run: exit 1
+
+      - name: Create PR with updated metamodel
+        if: steps.run_tests.outcome == 'success'
+        uses: peter-evans/create-pull-request@v8
+        with:
+          commit-message: "Update metamodel test fixtures from linkml-model"
+          title: "Update metamodel test fixtures from linkml-model"
+          body: |
+            This PR updates the metamodel test fixtures to the latest version from linkml-model.
+
+            The metamodel compatibility tests have passed with these changes.
+
+            **Workflow run:** ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
+          branch: update-metamodel-fixtures
+          delete-branch: true
+          labels: metamodel-compat

.github/workflows/pypi-publish.yaml

@@ -18,12 +18,12 @@ jobs:
         fetch-depth: 0
 
     - name: Set up Python
-      uses: actions/setup-python@v6.0.0
+      uses: actions/setup-python@v6.2.0
       with:
         python-version: 3.13
 
     - name: Install uv
-      uses: astral-sh/setup-uv@v7.1.6
+      uses: astral-sh/setup-uv@v7.3.1
       with:
         version: ${{ env.UV_VERSION }}
 
@@ -32,7 +32,7 @@ jobs:
         uv build --all-packages
 
     - name: Store built distribution
-      uses: actions/upload-artifact@v6.0.0
+      uses: actions/upload-artifact@v7.0.0
       with:
         name: distribution-files
         path: dist/
@@ -49,7 +49,7 @@ jobs:
       id-token: write  # This permission is mandatory for trusted publishing.
     steps:
       - name: Download built distribution
-        uses: actions/download-artifact@v6.0.0
+        uses: actions/download-artifact@v8.0.0
         with:
           name: distribution-files
           path: dist