Update underlying template to v0.4.2 & linkml to v1.10.0

.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier
-_commit: v0.4.1
+_commit: v0.4.2
 _src_path: https://github.com/linkml/linkml-project-copier
 add_example: true
 copyright_year: '2025'
@@ -9,15 +9,14 @@ gh_action_docs_preview: true
 gh_action_pypi: true
 github_org: nfdi-de
 license: MIT
-project_description: "This metadata schema is an Extension of the DCAT Application\
-    \ Profile for Providing Links to Use-case Specific Context. It allows to provide\
-    \ additional metadata regarding: which kind(s) of entity(s) or activity(s)\
-    \ were evaluated (the dcat:Dataset is about), which kind of activity generated\
-    \ the dcat:Dataset, which kind of instruments were used in the dataset generating\
-    \ activity, in which surrounding (e.g. a laboratory) and according to which\
-    \ plan the dataset generating activity took place, as well as regarding which\
-    \ kind(s) of qualitative and quantitative characteristic were attributed to\
-    \ the evaluated entity or evaluated activity and to the used instruments."
+project_description: 'This metadata schema is an Extension of the DCAT Application
+    Profile for Providing Links to Use-case Specific Context. It allows to provide
+    additional metadata regarding: which kind(s) of entity(s) or activity(s) were
+    evaluated (the dcat:Dataset is about), which kind of activity generated the dcat:Dataset,
+    which kind of instruments were used in the dataset generating activity, in which
+    surrounding (e.g. a laboratory) and according to which plan the dataset generating
+    activity took place, as well as regarding which kind(s) of qualitative and quantitative
+    characteristic were attributed to the evaluated entity or evaluated activity and
+    to the used instruments.'
 project_name: dcat-ap-plus
 project_slug: dcat_ap_plus
-

.github/dependabot.yml

@@ -1,9 +1,14 @@
-# Please see the documentation for all configuration options:
-# https://docs.github.com/en/code-security/dependabot/working-with-dependabot/dependabot-options-reference
+# This configures updates via dependabot only for github actions.
+# All updates are grouped into a single PR.
+# 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:
+          - "*"

.github/workflows/deploy-docs.yaml

@@ -2,7 +2,7 @@
 name: Deploy docs
 on:  # yamllint disable-line rule:truthy
   push:
-    tags:
+    branches: [main]
       - 'v[0-9]+.[0-9]+.[0-9]+'
       - 'v[0-9]+.[0-9]+.[0-9]+rc[0-9]'
     branches:
@@ -18,6 +18,10 @@ jobs:
   build-docs:
     runs-on: ubuntu-latest
 
+    strategy:
+      matrix:
+        pyversion: ["3.13"]
+
     # Grant GITHUB_TOKEN the permissions required to make a gh-pages deployment
     permissions:
       contents: write  # to let mkdocs write the new docs
@@ -42,15 +46,15 @@ jobs:
       - name: Install uv
         uses: astral-sh/[email protected]
         with:
-          python-version: 3.13
+          python-version: ${{ matrix.pyversion }}
           enable-cache: true
           cache-dependency-glob: "uv.lock"
 
       # https://github.com/actions/setup-python
       - name: Set up Python
         uses: actions/[email protected]
         with:
-          python-version: 3.13
+          python-version: ${{ matrix.pyversion }}
 
       - name: Install just
         run: |

.github/workflows/main.yaml

@@ -19,7 +19,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
       fail-fast: false
 
     steps:

.github/workflows/pypi-publish.yaml

@@ -25,6 +25,10 @@ jobs:
     name: Build Python 🐍 distributions 📦 for publishing
     runs-on: ubuntu-latest
 
+    strategy:
+      matrix:
+        pyversion: ["3.13"]
+
     steps:
       # https://github.com/actions/checkout
       - name: Check out repository
@@ -36,14 +40,14 @@ jobs:
       - name: Install uv
         uses: astral-sh/[email protected]
         with:
-          python-version: 3.13
+          python-version: ${{ matrix.pyversion }}
           enable-cache: true
 
       # https://github.com/actions/setup-python
       - name: Set up Python
         uses: actions/[email protected]
         with:
-          python-version: 3.13
+          python-version: ${{ matrix.pyversion }}
 
       - name: Install just
         run: |

.github/workflows/test_pages_build.yaml

@@ -16,7 +16,7 @@ permissions: {}
 
 jobs:
   run:
-    # Don't run for PRs from forks
+    # Don't run for PRs from forks which fails due to lack of permissions.
     if: github.event.pull_request.head.repo.full_name == github.repository
     # Grant GITHUB_TOKEN the permissions required to make a gh-pages deployment
     permissions:
@@ -25,6 +25,11 @@ jobs:
       id-token: write  # allow to generate an OpenID Connect (OIDC) token
       pull-requests: write  # add comment on the PR with the preview URL
     runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        pyversion: ["3.13"]
+
     steps:
       # https://github.com/actions/checkout
       - name: Checkout
@@ -33,16 +38,16 @@ jobs:
           fetch-depth: 0
 
       # https://github.com/actions/setup-python
-      - name: Set up Python 3
+      - name: Set up Python
         uses: actions/[email protected]
         with:
-          python-version: 3.13
+          python-version: ${{ matrix.pyversion }}
 
       # https://github.com/astral-sh/setup-uv
       - name: Install uv
         uses: astral-sh/[email protected]
         with:
-          python-version: 3.13
+          python-version: ${{ matrix.pyversion }}
           enable-cache: true
           cache-dependency-glob: "uv.lock"
 

.pre-commit-config.yaml

@@ -7,11 +7,13 @@ repos:
       - id: check-toml
       - id: check-yaml
       - id: end-of-file-fixer
+        exclude: '^(.*\.svg)$'
       - id: trailing-whitespace
+        exclude: '^(.*\.svg)$'
         args: [--markdown-linebreak-ext=md]
 
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.37.1
+    rev: v1.38.0
     hooks:
       - id: yamllint
         args: [-c=.yamllint.yaml]
@@ -24,13 +26,14 @@ repos:
           - tomli
 
   - repo: https://github.com/crate-ci/typos
-    rev: v1.39.2
+    rev: v1.44.0
     hooks:
       - id: typos
+        exclude: '^(.*\.svg)$'
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.14.6
+    rev: v0.15.4
     hooks:
       # Run the linter.
       - id: ruff
@@ -40,6 +43,6 @@ repos:
 
   - repo: https://github.com/astral-sh/uv-pre-commit
     # uv version.
-    rev: 0.9.11
+    rev: 0.10.7
     hooks:
       - id: uv-lock

README.md

@@ -1,18 +1,18 @@
 [![DOI](https://zenodo.org/badge/1080296103.svg)](https://doi.org/10.5281/zenodo.17702369)
 [![PyPI - Version](https://img.shields.io/pypi/v/dcat-ap-plus)](https://pypi.org/project/dcat-ap-plus)
 [![Build and test](https://github.com/nfdi-de/dcat-ap-plus/actions/workflows/main.yaml/badge.svg)](https://github.com/nfdi-de/dcat-ap-plus/actions/workflows/main.yaml)
-[![Copier Badge](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border-teal.json)](https://github.com/linkml/linkml-project-copier) 
+[![Copier Badge](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border-teal.json)](https://github.com/linkml/linkml-project-copier)
 
 # DCAT Application Profile for Providing Links to Use-case Specific Context (DCAT-AP+)
 
 The LinkML schema provided in this repository is an extension of the [DCAT Application Profile](https://semiceu.github.io/DCAT-AP/releases/3.0.0/), which allows to provide additional metadata for a `dcat:Dataset` in a very generic manner, such as:
-* which kind(s) of entity(s) or activity(s) were evaluated, 
-* which kind of activity generated the `dcat:Dataset`, 
-* which kind of instruments were used in the dataset generating activity, 
-* in which surrounding (e.g. a laboratory) and according to which plan the dataset generating activity took place, 
+* which kind(s) of entity(s) or activity(s) were evaluated,
+* which kind of activity generated the `dcat:Dataset`,
+* which kind of instruments were used in the dataset generating activity,
+* in which surrounding (e.g. a laboratory) and according to which plan the dataset generating activity took place,
 * as well as which kind(s) of qualitative and quantitative characteristic(s) were attributed to the evaluated entity or evaluated activity and to the used instruments.
 
-This extension is mainly based on the [Starting Point Terms of the Provenance Ontology (PROV-O)](https://www.w3.org/TR/prov-o/#description-starting-point-terms), 
+This extension is mainly based on the [Starting Point Terms of the Provenance Ontology (PROV-O)](https://www.w3.org/TR/prov-o/#description-starting-point-terms),
 in that it makes the `prov:wasGeneratedBy` property of the `Dataset` class mandatory and specifies necessary properties for its expected range, the `prov:Activity` class.
 
 The choice to use LinkML for extending DCAT-AP was based on the need to have different layers that cater to different domain-specific use cases. DCAT-AP+ serves as the basic layer for such extensions and is thus kept very generic. Being the basis of the [ChemDCAT-AP](
@@ -55,7 +55,7 @@ See also the documentation of the template: https://github.com/linkml/linkml-pro
     Note: Environments with private PyPi repository may need extra configuration (example):
 
       export UV_DEFAULT_INDEX=https://nexus.example.com/repository/pypi-all/simple
-* 
+*
 
     Copier
 
@@ -80,7 +80,7 @@ To regenerate the DCAT-AP LinkML representation as well as the PLUS extension ru
 
     uv run python src/dcat_ap_shacl_2_linkml.py
 
-### Test data validation and convertion
+### Test data validation and conversion
 
 Validate and test all: `just test`
 
@@ -106,15 +106,15 @@ To convert the test datasets of each DCAT-AP profile into a TTL graph run:
     ````
 
 ### Build GitHub pages docs locally
-    
+
     uv run mkdocs serve
-    
+
     rm -rf docs/elements/*.md && uv run gen-doc -d docs/elements src/dcat_ap_plus/schema/dcat_ap_plus.yaml
 
 ## Funding
 
-This work was funded by the German Research Foundation (DFG) through the projects: 
-* "[NFDI4Cat](https://nfdi4cat.org/) - NFDI for Catalysis-Related Sciences" (DFG project no. [441926934](https://gepris.dfg.de/gepris/projekt/441926934)) and 
+This work was funded by the German Research Foundation (DFG) through the projects:
+* "[NFDI4Cat](https://nfdi4cat.org/) - NFDI for Catalysis-Related Sciences" (DFG project no. [441926934](https://gepris.dfg.de/gepris/projekt/441926934)) and
 * "[NFDI4Chem](https://nfdi4chem.de) - NFDI for Chemistry" (DFG project no. [441958208](https://gepris.dfg.de/gepris/projekt/441958208))"
 
 within the National Research Data Infrastructure (NFDI) programme of the Joint Science Conference (GWK).

README_pypkg.md

@@ -1,10 +1,10 @@
 # dcat_ap_plus
 
 An extension of the [DCAT Application Profile](https://semiceu.github.io/DCAT-AP/releases/3.0.0/), which allows to provide additional metadata for a `dcat:Dataset` in a very generic manner, such as:
-* which kind(s) of entity(s) or activity(s) were evaluated, 
-* which kind of activity generated the `dcat:Dataset`, 
-* which kind of instruments were used in the dataset generating activity, 
-* in which surrounding (e.g. a laboratory) and according to which plan the dataset generating activity took place, 
+* which kind(s) of entity(s) or activity(s) were evaluated,
+* which kind of activity generated the `dcat:Dataset`,
+* which kind of instruments were used in the dataset generating activity,
+* in which surrounding (e.g. a laboratory) and according to which plan the dataset generating activity took place,
 * as well as which kind(s) of qualitative and quantitative characteristic(s) were attributed to the evaluated entity or evaluated activity and to the used instruments.
 
 This package ships the LinkML-generated Python datamodel for the schema.

config.public.mk

@@ -27,13 +27,10 @@ LINKML_GENERATORS_CONFIG_YAML=config.yaml
 LINKML_GENERATORS_DOC_ARGS="--truncate-descriptions False --hierarchical-class-view --subfolder-type-separation --index-name overview"
 
 ## pass args to workaround genowl rdfs config bug (linkml#1453)
-##   (i.e. --no-type-objects --no-metaclasses --metadata-profile rdfs)
+##   (i.e. --no-type-objects --no-metaclasses --metadata-profile=rdfs)
+# LINKML_GENERATORS_OWL_ARGS="--no-type-objects --no-metaclasses --metadata-profile=rdfs"
 LINKML_GENERATORS_OWL_ARGS=
 
-## pass args to trigger experimental java/typescript generation
-LINKML_GENERATORS_JAVA_ARGS=
-LINKML_GENERATORS_TYPESCRIPT_ARGS=
-
 ## pass args to pydantic generator which isn't supported by gen-project
 ## https://github.com/linkml/linkml/issues/2537
 LINKML_GENERATORS_PYDANTIC_ARGS=

config.yaml

@@ -23,8 +23,10 @@ generator_args:
     mergeimports: true
   owl:
     mergeimports: true
-    metaclasses: true
-    type_objects: true
+    metaclasses: false
+    type_objects: false
+    # add_root_classes: true
+    # mixins_as_expressions: true
     # throws 'Cannot handle metadata profile: rdfs'
     # metadata_profile: rdfs
   markdown:

docs/how-to-extend.md

@@ -15,7 +15,7 @@ DCAT-AP+ is designed to be imported and specialized. [ChemDCAT-AP](https://githu
 ## What you MAY do
 
 - **Subclass DCAT-AP+ classes** using `is_a` to create a new node shape with additional slots or stricter slot constraints. When you do so and also choose to map to a semantically narrower ontology term via `class_uri`, you should make sure to remain aligned with DCAT-AP+ for interoperability. See [Foundational principle: LinkML elements as SHACL shapes](design-patterns.md#foundational-principle-linkml-elements-as-shacl-shapes) for guidance. For example, ChemDCAT-AP defines `SubstanceSample` as `is_a: EvaluatedEntity` with `class_uri: SIO:001378`.
-- **Create sub-slots** using `is_a` on slots for making stricter constraints. When you do so and also choose to map to a semantically narrower ontology term via `slot_uri`, you should make sure to remain aligned with DCAT-AP+ for interoperability. See [Foundational principle: LinkML elements as SHACL shapes](design-patterns.md#foundational-principle-linkml-elements-as-shacl-shapes) for guidance. For example, ChemDCAT-AP defines `used_catalyst` as `is_a: carried_out_by` with `slot_uri: RXNO:0000425`. 
+- **Create sub-slots** using `is_a` on slots for making stricter constraints. When you do so and also choose to map to a semantically narrower ontology term via `slot_uri`, you should make sure to remain aligned with DCAT-AP+ for interoperability. See [Foundational principle: LinkML elements as SHACL shapes](design-patterns.md#foundational-principle-linkml-elements-as-shacl-shapes) for guidance. For example, ChemDCAT-AP defines `used_catalyst` as `is_a: carried_out_by` with `slot_uri: RXNO:0000425`.
 - **Add new slots** to your domain classes.
 - **Constrain ranges** further (narrowing is allowed by DCAT-AP extension rules).
 - **Provide domain-specific enums** to bind `rdf_type` or `type` to specific controlled vocabularies.

docs/index.md

@@ -18,8 +18,8 @@ description: "13C NMR spectral data for acetylsalicylic acid in CDCl3"
 was_generated_by:
   - id: ex:measurement-001
     # an instance of the 13C NMR class from the Chemical Methods Ontology
-    rdf_type:   
-      id: CHMO:0000595       
+    rdf_type:  
+      id: CHMO:0000595  
       title: "carbon-13 nuclear magnetic resonance spectroscopy"
     evaluated_entity:
       - id: ex:sample-001
@@ -37,7 +37,7 @@ was_generated_by:
       - id: ex:spectrometer-001
         # an instance of "JEOL ECX NMR spectrometer" class from OBI
         rdf_type:
-          id: OBI:0000625 
+          id: OBI:0000625
           title: "JEOL ECX NMR spectrometer"
 ```
 

docs/js/extra-loader.js

@@ -0,0 +1,2 @@
+// See https://facelessuser.github.io/pymdown-extensions/extras/mermaid/#custom-loader
+// And https://github.com/facelessuser/pymdown-extensions/blob/main/docs/src/js/material-extra-3rdparty.js

docs/schema/README.md

@@ -1,23 +1,21 @@
 # Merged model
 
 This folder contains the DCAT-AP+ model serialized as:
-* LinkML YAML, 
-* JSON schema, 
-* JSON-LD (including context) 
+* LinkML YAML,
+* JSON schema,
+* JSON-LD (including context)
 * and SHACL shapes.
 
-It also contains the prefix map in YAML and [dcat_ap_linkml.yaml](dcat_ap_linkml.yaml), 
+It also contains the prefix map in YAML and [dcat_ap_linkml.yaml](dcat_ap_linkml.yaml),
 the direct translation of DCAT-AP into LinkML.
 
-These files are auto-generated from the schema in the `src/dcat_ap_plus/schema` folder and version-stamped by 
+These files are auto-generated from the schema in the `src/dcat_ap_plus/schema` folder and version-stamped by
 uv-dynamic-versioning.
-For releases, these files are copied to gh-pages along with the rest of the documentation, 
+For releases, these files are copied to gh-pages along with the rest of the documentation,
 making schema files with version information available on gh-pages. The w3id.org redirects link to these files.
 
-A fully resolved version of the DCAT-AP+ model with imported models merged in is located in the 
+A fully resolved version of the DCAT-AP+ model with imported models merged in is located in the
 subfolder [merged-yaml](merged-yaml).
 
 
 Note, that the generated files are git-ignored.
-
-

justfile

@@ -263,7 +263,7 @@ set allow-duplicate-recipes
 
 # Overriding recipes from the root justfile by adding a recipe with the same
 # name in an imported file is not possible until a known issue in just is fixed,
-# https://github.com/casey/just/issues/2540
+# https://github.com/casey/just/issues/2540 - So we need to override them here.
 
 # Custom recipe for dcat-ap-plus to add project-specific artifacts to the distribution schema path
 _add-artifacts: