feat(gen-shacl): translate presence-implies-value rules to SHACL-SPARQL

.github/scripts/check_links.py

@@ -52,6 +52,8 @@
     "snomed.info",
     # LinkML metamodel - w3id redirects to linkml.io/linkml-model which may have issues
     "w3id.org",
+    # Certificate expired Sep/24/2026
+    "datashapes.org",
 }
 
 

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

@@ -28,7 +28,7 @@ jobs:
           python-version: "3.12"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v10.0.1
+        uses: astral-sh/setup-uv@v10.2.0
         with:
           version: ${{ env.UV_VERSION }}
 

.github/workflows/dependency-audit.yaml

@@ -38,7 +38,7 @@ jobs:
 
       # Pin uv to a known-good, recent release.
       - name: Install uv and setup uv caching
-        uses: astral-sh/setup-uv@v10.0.1
+        uses: astral-sh/setup-uv@v10.2.0
         with:
           version: ${{ env.UV_VERSION }}
           enable-cache: true
@@ -56,7 +56,10 @@ jobs:
       #
       # So gate the audit on whether the change actually altered dependencies,
       # relative to each event's natural base:
-      #   * pull_request -> the PR base
+      #   * pull_request -> the base the checked-out merge commit was built on
+      #     (HEAD^1). Not github.event.pull_request.base.sha: that can be an
+      #     older main commit, so the diff would include main's own uv.lock
+      #     bumps and audit a PR that changed no dependencies.
       #   * push (main)  -> the commit before the push (github.event.before)
       #   * merge_group  -> the queue base
       #   * otherwise (workflow_dispatch, first/force push) -> audit
@@ -78,7 +81,7 @@ jobs:
         run: |
           set -euo pipefail
           case "${{ github.event_name }}" in
-            pull_request) base="${{ github.event.pull_request.base.sha }}" ;;
+            pull_request) base="$(git rev-parse HEAD^1)" ;;
             merge_group)  base="${{ github.event.merge_group.base_sha }}" ;;
             push)         base="${{ github.event.before }}" ;;
             *)            base="" ;;

.github/workflows/doc-pages.yaml

@@ -24,7 +24,7 @@ jobs:
           git fetch upstream --tags
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v10.0.1
+        uses: astral-sh/setup-uv@v10.2.0
         with:
           version: ${{ env.UV_VERSION }}
           enable-cache: true

.github/workflows/docker-build.yaml

@@ -48,10 +48,10 @@ jobs:
           echo "Ref: ${{ github.ref }}"
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v4.2.0
+        uses: docker/setup-qemu-action@v4.4.0
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v4.3.0
+        uses: docker/setup-buildx-action@v4.4.1
 
       - name: Login to DockerHub
         if: startsWith(github.ref, 'refs/tags/v')
@@ -61,7 +61,7 @@ jobs:
           password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
 
       - name: Build and push
-        uses: docker/build-push-action@v7.3.0
+        uses: docker/build-push-action@v7.4.0
         with:
           context: .
           platforms: linux/amd64,linux/arm64/v8

.github/workflows/docs-test.yaml

@@ -36,7 +36,7 @@ jobs:
           git fetch upstream --tags
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v10.0.1
+        uses: astral-sh/setup-uv@v10.2.0
         with:
           version: ${{ env.UV_VERSION }}
           enable-cache: true

.github/workflows/main.yaml

@@ -24,7 +24,7 @@ jobs:
     steps:
       - uses: actions/checkout@v7
       - name: Install uv
-        uses: astral-sh/setup-uv@v10.0.1
+        uses: astral-sh/setup-uv@v10.2.0
         with:
           version: ${{ env.UV_VERSION }}
 
@@ -76,7 +76,7 @@ jobs:
           git fetch upstream --tags
 
       - name: Install uv and setup uv caching
-        uses: astral-sh/setup-uv@v10.0.1
+        uses: astral-sh/setup-uv@v10.2.0
         with:
           version: ${{ env.UV_VERSION }}
           enable-cache: true
@@ -105,7 +105,7 @@ jobs:
         shell: bash
       - name: Upload linkml coverage report
         if: github.repository == 'linkml/linkml' && github.actor != 'dependabot[bot]'
-        uses: codecov/codecov-action@v7.0.0
+        uses: codecov/codecov-action@v7.1.1
         with:
           name: codecov-linkml-${{ matrix.os }}-${{ matrix.python-version }}
           token: ${{ secrets.CODECOV_TOKEN }}
@@ -114,7 +114,7 @@ jobs:
           fail_ci_if_error: true
       - name: Upload runtime coverage report
         if: github.repository == 'linkml/linkml' && github.actor != 'dependabot[bot]'
-        uses: codecov/codecov-action@v7.0.0
+        uses: codecov/codecov-action@v7.1.1
         with:
           name: codecov-runtime-${{ matrix.os }}-${{ matrix.python-version }}
           token: ${{ secrets.CODECOV_TOKEN }}
@@ -139,7 +139,7 @@ jobs:
       - name: Check out repository
         uses: actions/checkout@v7
       - name: Install uv
-        uses: astral-sh/setup-uv@v10.0.1
+        uses: astral-sh/setup-uv@v10.2.0
         with:
           version: ${{ env.UV_VERSION }}
           enable-cache: true
@@ -160,7 +160,7 @@ jobs:
           uv run coverage report -m
       - name: Upload linkml slow test coverage
         if: github.repository == 'linkml/linkml' && github.actor != 'dependabot[bot]'
-        uses: codecov/codecov-action@v7.0.0
+        uses: codecov/codecov-action@v7.1.1
         with:
           name: codecov-linkml-slow-${{ matrix.os }}-${{ matrix.python-version }}
           token: ${{ secrets.CODECOV_TOKEN }}
@@ -189,7 +189,7 @@ jobs:
       - name: Check out repository
         uses: actions/checkout@v7
       - name: Install uv
-        uses: astral-sh/setup-uv@v10.0.1
+        uses: astral-sh/setup-uv@v10.2.0
         with:
           version: ${{ env.UV_VERSION }}
           enable-cache: true
@@ -207,7 +207,7 @@ jobs:
           uv run pytest tests/linkml/test_notebooks/ -m "not kroki" --cov --cov-report xml:coverage-notebooks.xml --cov-report term-missing
       - name: Upload notebook coverage
         if: github.repository == 'linkml/linkml' && github.actor != 'dependabot[bot]'
-        uses: codecov/codecov-action@v7.0.0
+        uses: codecov/codecov-action@v7.1.1
         with:
           name: codecov-notebooks-${{ matrix.os }}-${{ matrix.python-version }}
           token: ${{ secrets.CODECOV_TOKEN }}
@@ -232,7 +232,7 @@ jobs:
           python-version: 3.13
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v10.0.1
+        uses: astral-sh/setup-uv@v10.2.0
         with:
           version: ${{ env.UV_VERSION }}
       - name: Build source and wheel archives

.github/workflows/metamodel-compat.yaml

@@ -27,7 +27,7 @@ jobs:
         uses: actions/checkout@v7
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v10.0.1
+        uses: astral-sh/setup-uv@v10.2.0
         with:
           version: ${{ env.UV_VERSION }}
           enable-cache: true

.github/workflows/pypi-publish.yaml

@@ -23,7 +23,7 @@ jobs:
         python-version: 3.13
 
     - name: Install uv
-      uses: astral-sh/setup-uv@v10.0.1
+      uses: astral-sh/setup-uv@v10.2.0
       with:
         version: ${{ env.UV_VERSION }}
 

.github/workflows/rustgen.yaml

@@ -34,7 +34,7 @@ jobs:
           git fetch upstream --tags
 
       - name: Install uv and setup uv caching
-        uses: astral-sh/setup-uv@v10.0.1
+        uses: astral-sh/setup-uv@v10.2.0
         with:
           version: ${{ env.UV_VERSION }}
           enable-cache: true
@@ -63,7 +63,7 @@ jobs:
 
       - name: Upload coverage report
         if: github.repository == 'linkml/linkml' && github.actor != 'dependabot[bot]'
-        uses: codecov/codecov-action@v7.0.0
+        uses: codecov/codecov-action@v7.1.1
         with:
           name: codecov-results-rustgen
           token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/typedb-integration.yaml

@@ -31,7 +31,7 @@ jobs:
           --health-start-period 30s
     steps:
       - uses: actions/checkout@v7
-      - uses: astral-sh/setup-uv@v10.0.1
+      - uses: astral-sh/setup-uv@v10.2.0
       - uses: actions/setup-python@v7.0.0
         with:
           python-version: "3.12"

.github/workflows/update-feature-dashboard.yaml

@@ -32,7 +32,7 @@ jobs:
           git fetch upstream --tags
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v10.0.1
+        uses: astral-sh/setup-uv@v10.2.0
         with:
           version: ${{ env.UV_VERSION }}
           enable-cache: true

docs/generators/openapi.rst

@@ -2,8 +2,9 @@ OpenAPI
 =======
 
 `OpenAPI <https://www.openapis.org/>`_ is a specification for describing
-RESTful HTTP APIs. The OpenAPI generator produces an OpenAPI v3.0.3
-specification in YAML from a LinkML schema.
+RESTful HTTP APIs. The OpenAPI generator produces an OpenAPI
+specification in YAML from a LinkML schema. As of now it supports OpenAPI
+specification versions v3.0.3 and v3.1.0.
 
 .. note:: This generator produces a complete OpenAPI spec by combining a
           user-provided *template* (containing the API header, endpoints, and
@@ -15,15 +16,16 @@ Overview
 
 The generator works in two stages:
 
-1. The user provides an **OpenAPI template** — a valid OpenAPI v3.0.3 YAML
+1. The user provides an **OpenAPI template** — a valid OpenAPI YAML
    file that defines the API metadata (title, version, servers), paths
-   (endpoints), and security schemes.
+   (endpoints), and security schemes. It also specifies the version of
+   the OpenAPI specification in its top-level attribute `openapi`.
 2. The generator fills the ``components/schemas`` section with JSON Schema
    definitions generated from the LinkML schema, keeping only those classes
    that are transitively reachable from the endpoints.
 
 Both the input template and the final output are automatically validated
-against the OpenAPI 3.0.3 specification using
+against the corresponding OpenAPI specification version using
 `openapi-spec-validator <https://github.com/p1c2u/openapi-spec-validator>`_.
 
 To run:
@@ -32,6 +34,9 @@ To run:
 
    gen-openapi personinfo.yaml --template api-template.yaml > personinfo.openapi.yaml
 
+The **template's top-level attribute `openapi` MUST specify the supported OpenAPI
+version**.
+
 The ``--template`` / ``-t`` option is required when generating a concrete
 specification. If omitted, the generator prints a generic template that can
 be used as a starting point:
@@ -47,14 +52,8 @@ The generator validates both the input template and the final output against
 the OpenAPI specification using
 `openapi-spec-validator <https://github.com/p1c2u/openapi-spec-validator>`_.
 
-The ``openapi`` field in the template is checked against the expected
-version for the chosen output format (currently ``openapi303`` →
-``3.0.3``). If the versions do not match, the generator raises a
-``ValueError``.
-
-Additionally, the template's ``components/schemas`` section must declare each
-resource that is referenced by an endpoint, using two custom extension
-fields:
+The template's ``components/schemas`` section must declare each resource
+that is referenced by an endpoint, using two custom extension fields:
 
 ``x-linkml-schema``
    The ``id`` of the LinkML schema being used. Must match exactly.

examples/tutorial/tutorial01/personinfo.json

@@ -1,7 +1,7 @@
 {
     "$defs": {
         "Person": {
-            "additionalProperties": true,
+            "additionalProperties": false,
             "description": "",
             "properties": {
                 "age": {

packages/linkml/pyproject.toml

@@ -59,13 +59,13 @@ dependencies = [ # Specifier syntax: https://peps.python.org/pep-0631/
     "pyyaml",
     "rdflib>=7.6.0",
     "requests >= 2.22",
-    "sqlalchemy>=2.0.53",
+    "sqlalchemy>=2.0.54",
     "watchdog >= 0.9.0",
     "typing-extensions >= 4.6.0; python_version < '3.12'",
     "sphinx-click (>=6.0.0)",
     "openapi-spec-validator >= 0.8.4",
     "pydantic-settings>=2.15.0",
-    "platformdirs>=4.11.8",
+    "platformdirs>=4.11.12",
 ]
 
 [dependency-groups]
@@ -97,7 +97,7 @@ dev = [
   "nbconvert",
   "nbformat",
   "coverage>=7.16.0",
-  "tox>=4.61.2",
+  "tox>=4.64.1",
   "tox-uv",
   "myst-nb>=1.4.0; python_version >= '3.10'",
   "sphinx-design >= 0.5.0",
@@ -114,7 +114,7 @@ tests-rustgen = [
   "maturin>=1.15.0"
 ]
 typedb = [
-  "typedb-driver>=3.12.3,<4.0",
+  "typedb-driver>=3.13.6,<4.0",
 ]
 bigquery = [
   "sqlalchemy-bigquery >= 1.9.0",