Change to multi version schema docs

Author: dalito

.github/workflows/deploy-docs.yaml

@@ -2,7 +2,14 @@
 name: Deploy docs
 on:  # yamllint disable-line rule:truthy
   push:
-    branches: [main]
+    tags:
+      - 'v[0-9]+.[0-9]+.[0-9]+'
+      - 'v[0-9]+.[0-9]+.[0-9]+rc[0-9]'
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
   workflow_dispatch:
 
 permissions: {}
@@ -55,4 +62,28 @@ jobs:
       - name: Generate schema documentation
         run: |
           just gen-doc
-          uv run mkdocs gh-deploy
+
+      # The if-conditions below make sure to select the right step, depending
+      # on the job trigger. Only one of the steps below will run at a time.
+      # The others will be skipped.
+
+      - name: Check docs in pull requests with strict mode
+        if: github.event_name == 'pull_request'
+        run: |
+          # XXX Enable strict mode once docs are clean
+          echo "Strict check of docs disabled."
+          # uv run mkdocs build --strict
+
+      # yamllint disable rule:line-length
+      - name: Build & deploy "dev" docs for a new commit to main
+
+        if: (github.event_name == 'push' && github.ref_type != 'tag') || github.event_name == 'workflow_dispatch'
+        run: |
+          export SHORT_SHA=$(echo "${GITHUB_SHA}" | cut -c1-7)
+          uv run mike deploy --push --update-aliases --title "dev (${SHORT_SHA})" dev
+
+      - name: Build & deploy docs for a new version tag
+        if: github.ref_type == 'tag' && github.event_name == 'push'
+        run: |
+          uv run mike deploy --push --update-aliases ${{ github.ref_name }} latest
+          uv run mike set-default latest --push

.github/workflows/main.yaml

@@ -37,17 +37,17 @@ jobs:
           python-version: ${{ matrix.python-version }}
           enable-cache: true
           cache-dependency-glob: "uv.lock"
+
       # https://github.com/actions/setup-python
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548
+        uses: actions/setup-python@v6.1.0
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Install just
         run: |
           uv tool install rust-just
 
-
       - name: Install project
         run: uv sync --dev
 

.github/workflows/pypi-publish.yaml

@@ -65,36 +65,29 @@ jobs:
     runs-on: ubuntu-latest
     environment:
       name: pypi-release
-      url: https://pypi.org/p/dcat_4c_ap
+      url: https://pypi.org/chem-dcat-ap
     permissions:
       id-token: write  # this permission is mandatory for trusted publishing
     steps:
       # https://github.com/actions/download-artifact
       - name: Download built distribution
-        uses: actions/download-artifact@v4.3.0
+        uses: actions/download-artifact@v6.0.0
         with:
           name: distribution-files
           path: dist
 
       # https://github.com/pypa/gh-action-pypi-publish
       - name: Publish package 📦 to Test PyPI
         if: github.event_name == 'push'
-        uses: pypa/gh-action-pypi-publish@v1.12.4
+        uses: pypa/gh-action-pypi-publish@v1.13.0
         with:
           repository-url: https://test.pypi.org/legacy/
           verbose: true
 
       - name: Publish package 📦 to PyPI
         if: github.event_name == 'release'
-        uses: pypa/gh-action-pypi-publish@v1.12.4
+        uses: pypa/gh-action-pypi-publish@v1.13.0
         with:
           verbose: true
 
 # [1] https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#filter-pattern-cheat-sheet
-# Used actions: (updates managed by dependabot)
-# - https://github.com/actions/checkout
-# - https://github.com/astral-sh/setup-uv
-# - https://github.com/actions/setup-python
-# - https://github.com/actions/upload-artifact
-# - https://github.com/actions/download-artifact
-# - https://github.com/pypa/gh-action-pypi-publish/

.github/workflows/test_pages_build.yaml

@@ -16,6 +16,8 @@ permissions: {}
 
 jobs:
   run:
+    # Don't run for PRs from forks
+    if: github.event.pull_request.head.repo.full_name == github.repository
     # Grant GITHUB_TOKEN the permissions required to make a gh-pages deployment
     permissions:
       contents: write  # to let mkdocs write the new docs
@@ -30,25 +32,30 @@ jobs:
         with:
           fetch-depth: 0
 
+      # https://github.com/actions/setup-python
+      - name: Set up Python 3
+        uses: actions/setup-python@v6.1.0
+        with:
+          python-version: 3.13
+
       # https://github.com/astral-sh/setup-uv
       - name: Install uv
         uses: astral-sh/setup-uv@v7.1.4
         with:
           python-version: 3.13
           enable-cache: true
           cache-dependency-glob: "uv.lock"
-      # https://github.com/actions/setup-python
-      - name: Set up Python 3
-        uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548
-        with:
-          python-version: 3.13
 
+      - name: Install just
+        run: |
+          uv tool install rust-just
 
       - name: Install dependencies
         run: uv sync --dev --no-progress
 
       - name: Build documentation
         run: |
+          just gen-doc
           uv run mkdocs build -d site
           touch site/.nojekyll
 

.gitignore

@@ -1,12 +1,23 @@
+docs/local-js-pkgs
+
 # generated part of documentation
-/docs/elements/*.md
+docs/elements/**/*.md
+
+# generated merged schema
+docs/schema/*
+!docs/schema/README.md
 
 # linkml-run-examples output (not useful to have in git in its current form)
 /examples/output/*.yaml
 
 # Derived schemas, generated from the schema.yaml
 tmp/
 
+# generated model representations of generators that ignore config.yaml
+project/java
+project/owl
+project/typescript
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -141,7 +152,3 @@ dmypy.json
 .idea
 # Local vscode editor config
 .vscode
-/docs
-/.idea
-/docs
-/.idea

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # https://pre-commit.com/
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-toml
       - id: check-yaml
@@ -11,7 +11,7 @@ repos:
         args: [--markdown-linebreak-ext=md]
 
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.37.0
+    rev: v1.37.1
     hooks:
       - id: yamllint
         args: [-c=.yamllint.yaml]
@@ -24,13 +24,13 @@ repos:
           - tomli
 
   - repo: https://github.com/crate-ci/typos
-    rev: v1.31.1
+    rev: v1.39.2
     hooks:
       - id: typos
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.11.3
+    rev: v0.14.6
     hooks:
       # Run the linter.
       - id: ruff
@@ -40,6 +40,6 @@ repos:
 
   - repo: https://github.com/astral-sh/uv-pre-commit
     # uv version.
-    rev: 0.6.12
+    rev: 0.9.11
     hooks:
       - id: uv-lock

.zenodo.json

@@ -0,0 +1,43 @@
+{
+  "access_right": "open",
+  "communities": [
+    {"identifier": "nfdi4cat"},
+    {"identifier": "nfdi4chem"}
+  ],
+  "creators": [
+    {
+      "name": "Str\u00f6mert, Philip",
+      "orcid": "0000-0002-1595-3213",
+      "affiliation": "TIB - Leibniz Information Centre for Science and Technology, Germany"
+    },
+    {
+      "name": "Borgelt, Hendrik",
+      "orcid": "0000-0001-5886-7860",
+      "affiliation": "TU Dortmund University, Germany"
+    },
+    {
+      "name": "Doerr, Mark",
+      "orcid": "0000-0003-3270-6895",
+      "affiliation": "University of Greifswald, Germany"
+    },
+    {
+      "name": "Linke, David",
+      "orcid": "0000-0002-5898-1820",
+      "affiliation": "Leibniz Institute for Catalysis, Albert-Einstein-Str. 29 A, 18059 Rostock, Germany"
+    }
+  ],
+  "description": "<p><a href=\"https://nfdi-de.github.io/chem-dcat-ap/\">ChemDCAT-AP</a> is a metadata schema extension for providing chemistry specific metadata for a dataset. It builds upon the domain-agnostic <a href=\"https://nfdi-de.github.io/dcat-ap-plus/\">DCAT-AP-PLUS</a> schema.</p> <p>The metadata schema is developend as <a href=\"https://linkml.io/\">LinkML</a> model which allows to generate various artefacts such as JSON-Schema, SHACL shapes, Python-bindings, and documentation.</p>",
+  "keywords": [
+    "LinkML", "DCAT", "DCAT-AP", "data modelling"
+  ],
+  "license": "MIT",
+  "related_identifiers": [
+    {
+        "identifier": "doi:10.5281/zenodo.5703670",
+        "relation": "requires",
+        "resource_type": "software",
+        "scheme": "doi"
+    }
+  ],
+  "upload_type": "software"
+}

CONTRIBUTING.md

@@ -1,9 +1,9 @@
-# Contributing to dcat-4C-ap
+# Contributing to chem-dcat-ap
 
 :+1: First of all: Thank you for taking the time to contribute!
 
 The following is a set of guidelines for contributing to
-dcat-4C-ap. These guidelines are not strict rules.
+chem-dcat-ap. These guidelines are not strict rules.
 Use your best judgment, and feel free to propose changes to this document
 in a pull request.
 
@@ -22,7 +22,7 @@ in a pull request.
 
 ## Code of Conduct
 
-The dcat-4C-ap team strives to create a
+The chem-dcat-ap team strives to create a
 welcoming environment for editors, users and other contributors.
 Please carefully read our [Code of Conduct](CODE_OF_CONDUCT.md).
 
@@ -73,7 +73,7 @@ Please submit a [Pull Request][pulls] to submit a new term for consideration.
     - Never work on the main branch, always work on an issue/feature branch
     - Core developers can work on branches off origin rather than forks
     - Always create a PR on a branch to maximize transparency of what you are doing
-    - PRs should be reviewed and merged in a timely fashion by the dcat-4C-ap technical leads
+    - PRs should be reviewed and merged in a timely fashion by the chem-dcat-ap technical leads
     - PRs that do not pass GitHub actions should never be merged
     - In the case of git conflicts, the contributor should try and resolve the conflict
     - If a PR fails a GitHub action check, the contributor should try and resolve the issue in a timely fashion
@@ -102,20 +102,20 @@ Core developers should read the material on the [LinkML site](https://linkml.io/
 - Include examples and counter-examples (intentionally invalid examples)
     - Rationale: these serve as documentation and unit tests
     - These will be used by the automated test suite
-    - All elements of the nmdc-schema must be illustrated with valid and invalid data examples in src/data. New schema elements will not be merged into the main branch until examples are provided
+    - All elements of the schema must be illustrated with valid and invalid data examples in src/data. New schema elements will not be merged into the main branch until examples are provided
     - Invalid example data files should be invalid for one single reason, which should be reflected in the filename. It should be possible to render the invalid example files valid by addressing that single fault.
 - Use enums for categorical values
     - Rationale: Open-ended string ranges encourage multiple values to represent the same entity, like “water”, “H2O” and “HOH”
     - Any slot whose values could be constrained to a finite set should use an Enum
     - Non-categorical values, e.g. descriptive fields like `name` or `description` fall outside of this.
 - Reuse
     - Existing scheme elements should be reused where appropriate, rather than making duplicative elements
-    - More specific classes can be created by refinining classes using inheritance (`is_a`)
+    - More specific classes can be created by refining classes using inheritance (`is_a`)
 
 [about-branches]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-branches
 [about-issues]: https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues
 [about-pulls]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests
-[issues]: https://github.com/StroemPhi/dcat-4C-ap/issues/
-[pulls]: https://github.com/StroemPhi/dcat-4C-ap/pulls/
+[issues]: https://github.com/nfdi-de/chem-dcat-ap/issues/
+[pulls]: https://github.com/nfdi-de/chem-dcat-ap/pulls/
 
 We recommend also reading [GitHub Pull Requests: 10 Tips to Know](https://blog.mergify.com/github-pull-requests-10-tips-to-know/)

README.md

@@ -1,3 +1,8 @@
+[![DOI](https://zenodo.org/badge/1080296103.svg)](https://doi.org/10.5281/zenodo.17702369)
+[![PyPI - Version](https://img.shields.io/pypi/v/chem-dcat-ap)](https://pypi.org/project/chem-dcat-ap)
+[![Build and test](https://github.com/nfdi-de/chem-dcat-ap/actions/workflows/main.yaml/badge.svg)](https://github.com/nfdi-de/chem-dcat-ap/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) 
+
 # Chem-DCAT-AP
 
 This is an extension of the DCAT Application Profile v3.0 in LinkML. It is intended to be used by NFDI4Chem & NFDI4Cat

README_pypkg.md

@@ -0,0 +1,56 @@
+# Chem-DCAT-AP
+
+Extension of the DCAT Application Profile (DCAT-AP) tailored for chemistry-related data.  
+It adds links to use-case specific context and enables describing:
+
+- chemical datasets (e.g. spectra, chromatograms, assay results)
+- related samples, substances and instruments
+- provenance, experimental conditions and other domain-specific metadata
+
+From the LinkML schemas in `src/chem_dcat_ap/schema/*.yaml`, two Python datamodel variants are generated:
+
+- A variant based on Python `dataclasses`
+- A variant based on Pydantic models
+
+## Installation
+
+```powershell
+pip install chem-dcat-ap
+```
+
+Requires Python >= 3.9, < 4.0.
+
+## Quick start
+
+The package exposes the generated classes that correspond to the entities defined in the
+`src/chem_dcat_ap/schema/*.yaml` LinkML schemas.
+
+```python
+import chem_dcat_ap
+from chem_dcat_ap.datamodel.chem_dcat_ap import Dataset, DataGeneratingActivity
+
+print(chem_dcat_ap.__version__)
+
+dataset = Dataset(
+    id="https://example.org/dataset/chem-001",
+    title="Example chemical dataset",
+    description="Minimal example dataset following the Chem-DCAT-AP schema.",
+    was_generated_by=DataGeneratingActivity(
+        id="https://example.org/activity/chem-001"
+    ),
+)
+
+print(dataset)
+```
+
+For details about all available classes and fields, inspect the schema YAML files in
+`src/chem_dcat_ap/schema/` and the generated module `chem_dcat_ap.datamodel.chem_dcat_ap`.
+
+## Documentation
+
+- Project docs and schema reference: <https://nfdi-de.github.io/dcat-ap-plus>
+- Source code: <https://github.com/nfdi-de/chem-dcat-ap>
+
+## License
+
+MIT License. See the bundled `LICENSE` file for details.