Merge branch 'nfdi4cat:main' into main

nfdi4cat · Feb 20, 2024 · c058b2c · c058b2c
2 parents 9b83f46 + 6d2eebd
commit c058b2c
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Showing 6 changed files with 27 additions and 26 deletions.
diff --git a/.github/workflows/ci-pr.yml b/.github/workflows/ci-pr.yml
@@ -30,7 +30,7 @@ jobs:
 
     steps:
       - name: Checkout PR branch into cwd
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           # Checkout the fork/head-repository to push changes to the fork.
           # Without this the base repository will be checked out and committed to.
@@ -40,7 +40,7 @@ jobs:
           ref: ${{ github.head_ref }}
 
       - name: Checkout main branch into directory _main_branch/
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: main
           path: _main_branch
@@ -49,7 +49,7 @@ jobs:
             vocabularies/
           fetch-depth: 1
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 
@@ -59,7 +59,7 @@ jobs:
           python -m pip install --upgrade pip setuptools wheel
 
           # install tagged version
-          python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@v0.7.8
+          python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@v0.8.1
           # python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@main
 
           # install custom pylode 2.x  (adds sorted collections,
@@ -113,8 +113,8 @@ jobs:
           path: outbox/
 
       - name: Add/stage vocabulary changes
-        # Pin third party action (v4.16.0)
-        uses: stefanzweifel/git-auto-commit-action@3ea6ae190baf489ba007f7c92608f33ce20ef04a
+        # Pinning of action managed by dependabot
+        uses: stefanzweifel/git-auto-commit-action@8756aa072ef5b4a080af5dc8fef36c5d586e521d
         with:
           # glob pattern of files which should be added to the commit
           file_pattern: 'vocabularies/\*.ttl'
@@ -125,8 +125,8 @@ jobs:
           git status
 
       - name: Commit vocabulary changes & xlsx cleanup on behalf of PR-author
-        # Pin third party action (v4.16.0)
-        uses: stefanzweifel/git-auto-commit-action@3ea6ae190baf489ba007f7c92608f33ce20ef04a
+        # Pinning of action managed by dependabot
+        uses: stefanzweifel/git-auto-commit-action@8756aa072ef5b4a080af5dc8fef36c5d586e521d
         with:
           commit_user_name: voc4cat-CI-bot
           commit_message: 'CI: vocabulary update in ${{ GITHUB.SERVER_URL }}/${{ GITHUB.REPOSITORY }}/actions/runs/${{ GITHUB.RUN_ID }}'
diff --git a/.github/workflows/merge.yml b/.github/workflows/merge.yml
@@ -31,19 +31,19 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 10
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           # Using fetch-depth 0 is the only way to get all tags which are needed for building docs.
           fetch-depth: 0
 
       - name: Checkout gh-pages branch to dir publish/
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: gh-pages
           path: publish
           fetch-depth: 1
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 
@@ -53,7 +53,7 @@ jobs:
           python -m pip install --upgrade pip setuptools wheel
 
           # install tagged version
-          python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@v0.7.8
+          python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@v0.8.1
           # python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@main
 
           # install custom pylode 2.x
@@ -89,7 +89,7 @@ jobs:
         # This replaces all prior content in gh-pages branch. But we have
         # checked out the gh-pages branch above so that we keep all prior
         # content and just re-publish the extended version.
-        # Pin third party action (v3.9.3)
+        # Pinning of action managed by dependabot
         uses: peaceiris/actions-gh-pages@373f7f263a76c20808c831209c920827a82a2847
         if: (github.event_name == 'push' || github.event_name == 'workflow_dispatch') && github.ref == 'refs/heads/main'
         with:

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -31,19 +31,19 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 10
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           # Using fetch-depth 0 is the only way to get all tags which are needed for building docs.
           fetch-depth: 0
 
       - name: Checkout gh-pages branch to dir publish/
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: gh-pages
           path: publish
           fetch-depth: 1
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 
@@ -53,7 +53,7 @@ jobs:
           python -m pip install --upgrade pip setuptools wheel
 
           # install tagged version
-          python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@v0.7.8
+          python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@v0.8.1
           # python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@main
 
           # install custom pylode 2.x
@@ -90,7 +90,7 @@ jobs:
         # This replaces all prior content in gh-pages branch. But we have
         # checked out the gh-pages branch above so that we keep all prior
         # content and just re-publish the extended version.
-        # Pin third party action (v3.9.3)
+        # Pinning of action managed by dependabot
         uses: peaceiris/actions-gh-pages@373f7f263a76c20808c831209c920827a82a2847
         with:
           publish_branch: gh-pages

diff --git a/README.md b/README.md
@@ -9,13 +9,14 @@ The template is maintained as part of the [NFDI4Cat](http://www.nfdi4cat.org) in
 
 ### Trying out the workflow
 
+
 All vocabularies based on this template have the same standard contribution process of
 
 - get and update the vocabulary file (xlsx),
 - submit a pull request with the updated file,
 - collaborate on the pull request with editors or other github users,
 
-After approval your pull request is ready to be merged by the editors. The merge will include your contribution into the SKOS-vocabulary file in the `vocabularies`-folder and it will also be reflected in the documentation that is automatically updated.
+After approval your pull request is ready to be merged by the editors. The merge will include your contribution into the SKOS-vocabulary file in the `vocabularies`-folder. Upon merge the corresponding documentation and a joined turtle file will be automatically built and published to gh-pages.
 
 The Excel/xlsx files submitted as pull request are automatically checked and (if all is good) converted to turtle.
 By using a vocabulary-specific configuration more thorough validation can be activated,
@@ -26,9 +27,9 @@ This allows independent work and avoids using the same ID repeatedly.
 
 The voc4cat-template implements automatic storage of different versions of the vocabularies in gh-pages:
 
- - `dev` - Directory with artifacts built from the most recent commit to the main branch.
- - `latest` - Directory with all files built for the latest release.
- - `vYYYY-MM-DD` (for example `v2023-08-16`) - Directory with all files built for the release with this tag.
+- `dev` - Directory with artifacts built from the most recent commit to the main branch.
+- `latest` - Directory with all files built for the latest release.
+- `vYYYY-MM-DD` (for example `v2023-08-16`) - Directory with all files built for the release with this tag.
 
 For all versions, multiple files are stored (see https://github.com/nfdi4cat/voc4cat-template/issues/11#issuecomment-1680592185 for details). The correct version string is automatically inserted to all build artifacts. For `dev`, the first eight characters of the commit hash are used as version (for example `v_fadfa5f9`).
 
@@ -91,7 +92,7 @@ To discuss about the tool that converts Excel to SKOS in gh-actions of this temp
 
 ### Voc4cat template
 
-- David Linke (ORCID: 0000-0002-5898-1820) - Initial setup of repository and CI/CD pipelines
+- David Linke (ORCID: 0000-0002-5898-1820) - Creator of this repository template and its GitHub workflows.
 
 ## License
 
@@ -101,7 +102,7 @@ All vocabularies in this repository are CC0 licensed, see [LICENSE](LICENSE) for
 
 ### Voc4cat template
 
-The template itself is CC0 licensed, see [LICENSE](LICENSE). Although there is no obligation, we nevertheless appreciate if our work is acknowledged in any derivative work.
+The template itself is CC0-1.0 licensed, see [LICENSE](https://github.com/nfdi4cat/voc4cat-template/blob/main/LICENSE). Although there is no obligation, we nevertheless appreciate if our work is acknowledged in any derivative work.
 
 ## Acknowledgement
 

diff --git a/idranges.toml b/idranges.toml
@@ -66,5 +66,5 @@ v4c-bc = "https://example.org/voc4cat_biocatalysis/"
 first_id = 1
 last_id = 200
 gh_name = "markdoerr"
-orcid = "0000-0001-2345-9999"
-ror_id = "https://ror.org/999"
+orcid = ""
+ror_id = ""
diff --git a/templates/voc4cat_template_043.xlsx b/templates/voc4cat_template_043.xlsx