merging in main

linkml · Aug 5, 2024 · 22c44ef · 22c44ef
2 parents ef5f846 + 87f98e1
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diff --git a/.cruft.json b/.cruft.json
@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/linkml/linkml-project-cookiecutter",
-  "commit": "075814464fcb88b2fff34c91d76e8d294b51b3ca",
+  "commit": "b2da87eb7835bfec748a76823d098cac85e8363a",
   "checkout": null,
   "context": {
     "cookiecutter": {

diff --git a/.github/workflows/deploy-docs.yaml b/.github/workflows/deploy-docs.yaml
@@ -1,31 +1,40 @@
+---
 name: Auto-deployment of cmdr Documentation
 on:
   push:
-    branches: [ main ]
+    branches: [main]
 
 jobs:
   build-docs:
     runs-on: ubuntu-latest
+
+    # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
+    permissions:
+      contents: write  # to let mkdocs write the new docs
+      pages: write     # to deploy to Pages
+      id-token: write  # to verify the deployment originates from an appropriate source
+
     steps:
-    - name: Checkout
-      uses: actions/checkout@main
-      with:
-        fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
-
-    - name: Set up Python 3.
-      uses: actions/setup-python@v3
-      with:
-        python-version: 3.9
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # otherwise, you will failed to push refs to dest repo
+
+      - name: Set up Python.
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install Poetry.
+        run: pipx install poetry
 
-    - name: Install Poetry.
-      uses: snok/install-poetry@v1.3
+      - name: Install dependencies.
+        run: poetry install -E docs
 
-    - name: Install dependencies.
-      run: poetry install -E docs
-
-    - name: Build documentation.
-      run: |
-        mkdir -p docs
-        touch docs/.nojekyll
-        poetry run gen-doc -d docs src/cmdr/schema/cmdr.yaml
-        poetry run mkdocs gh-deploy
+      - name: Build documentation.
+        run: |
+          mkdir -p docs
+          touch docs/.nojekyll
+          make gendoc
+          ([ ! -f docs/about.md ] && cp src/docs/about.md docs/) || true
+          make mkd-gh-deploy
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
@@ -1,7 +1,6 @@
 # Built from:
 # https://docs.github.com/en/actions/guides/building-and-testing-python
-# https://github.com/snok/install-poetry#workflows-and-tips
-
+---
 name: Build and test cmdr
 
 on: [pull_request]
@@ -16,38 +15,22 @@ jobs:
 
     steps:
 
-      #----------------------------------------------
-      #       check-out repo and set-up python
-      #----------------------------------------------
       - name: Check out repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - name: Set up Python
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
-      #----------------------------------------------
-      #          install & configure poetry
-      #----------------------------------------------
       - name: Install Poetry
-        uses: snok/install-poetry@v1.3
+        run: pipx install poetry
 
-      #----------------------------------------------
-      # install dependencies if cache does not exist 
-      #----------------------------------------------
       - name: Install dependencies
         run: poetry install --no-interaction --no-root
 
-      #----------------------------------------------
-      #    install your root project, if required 
-      #----------------------------------------------      
-      - name: Install library
+      - name: Install project
         run: poetry install --no-interaction
 
-      #----------------------------------------------
-      #              run test suite   
-      #----------------------------------------------
-      - name: Run tests
+      - name: Run test suite
         run: make test
-
diff --git a/.github/workflows/pypi-publish.yaml b/.github/workflows/pypi-publish.yaml
@@ -1,3 +1,4 @@
+---
 name: Publish Python Package
 
 on:
@@ -10,30 +11,26 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-
-    - name: Set up Python
-      uses: actions/setup-python@v2.2.2
-      with:
-        python-version: 3.9
-
-    - name: Install Poetry
-      run: |
-        pip install poetry
-        poetry self add "poetry-dynamic-versioning[plugin]"
-      # uses: snok/install-poetry@v1.1.6
-      # with:
-      #   virtualenvs-create: true
-      #   virtualenvs-in-project: true
-
-    # - name: Install dependencies
-    #   run: poetry install --no-interaction
-
-    - name: Build source and wheel archives
-      run: poetry build
-
-    - name: Publish distribution 📦 to PyPI
-      uses: pypa/gh-action-pypi-publish@v1.2.2
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_PASSWORD }}
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install Poetry
+        run: |
+          pipx install poetry
+          poetry self add "poetry-dynamic-versioning[plugin]"
+
+      # - name: Install dependencies
+      #   run: poetry install --no-interaction
+
+      - name: Build source and wheel archives
+        run: poetry build
+
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@v1.2.2
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}
diff --git a/.github/workflows/test_pages_build.yaml b/.github/workflows/test_pages_build.yaml
@@ -0,0 +1,44 @@
+name: Preview cmdr documentation build
+
+on:
+  pull_request:
+    types:
+      - opened
+      - reopened
+      - synchronize
+
+concurrency: preview-${{ github.ref }}
+
+jobs:
+  run:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python 3
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install Poetry
+        run: pipx install poetry
+
+      - name: Install dependencies
+        run: poetry install -E docs
+
+      - name: Build documentation
+        run: |
+          mkdir -p site
+          touch site/.nojekyll
+          make gendoc
+          ([ ! -f docs/about.md ] && cp src/docs/about.md docs/) || true
+          poetry run mkdocs build -d site
+
+      - name: Deploy preview
+        uses: rossjrw/pr-preview-action@v1
+        with:
+          source-dir: site/
+          preview-branch: gh-pages
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -2,11 +2,17 @@
 
 ## Our Pledge
 
-In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to make participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to make participation in our project and
+our community a harassment-free experience for everyone, regardless of age,
+body size, disability, ethnicity, gender identity and expression, level of
+experience, nationality, personal appearance, race, religion, or sexual
+identity and orientation.
 
 ## Our Standards
 
-Examples of behavior that contributes to creating a positive environment include:
+Examples of behavior that contributes to creating a positive environment
+include:
 
 * Using welcoming and inclusive language
 * Being respectful of differing viewpoints and experiences
@@ -16,31 +22,55 @@ Examples of behavior that contributes to creating a positive environment include
 
 Examples of unacceptable behavior by participants include:
 
-* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
 * Trolling, insulting/derogatory comments, and personal or political attacks
 * Public or private harassment
-* Publishing others' private information, such as a physical or electronic address, without explicit permission
-* Other conduct which could reasonably be considered inappropriate in a professional setting
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
 
 ## Our Responsibilities
 
-Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
 
-Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
 
 ## Scope
 
-This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an
+appointed representative at an online or offline event. Representation of a
+project may be further defined and clarified by project maintainers.
 
 ## Enforcement
 
-Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by [contacting the project team](contact.md). All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by [contacting the project team](contact.md). All complaints will be
+reviewed and investigated and will result in a response that is deemed
+necessary and appropriate to the circumstances. The project team is obligated
+to maintain confidentiality with regard to the reporter of an incident. Further
+details of specific enforcement policies may be posted separately.
 
-Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
 
 ## Attribution
 
-This code of conduct has been derived from the excellent code of conduct of the [ATOM project](https://github.com/atom/atom/blob/master/CODE_OF_CONDUCT.md) which in turn is adapted from the [Contributor Covenant][homepage], version 1.4, available at [https://contributor-covenant.org/version/1/4][version]
+This code of conduct has been derived from the excellent code of conduct of the
+[ATOM project](https://github.com/atom/atom/blob/master/CODE_OF_CONDUCT.md)
+which in turn is adapted from the [Contributor Covenant][homepage], version
+1.4, available at [https://contributor-covenant.org/version/1/4][version]
 
 [homepage]: https://contributor-covenant.org
 [version]: https://contributor-covenant.org/version/1/4/