Upgrade vocabulary to v1.0 formats (voc4cat-tool 1.0.0 & voc4cat-template 1.0.0)

.github/pull_request_template.md

@@ -0,0 +1,7 @@
+Thank you for opening a Pull Request! Before submitting, please confirm:
+
+- [ ] I have not copied concept definitions from sources with licenses incompatible with voc4cat's CC0 license (e.g., copyleft licenses like CC-BY-SA).
+- [ ] I have cited sources that influenced my definitions (in Influenced by IRIs) or from which definitions were adapted (in Source Vocab IRI). Note: You may cite IUPAC Goldbook as an influence, but not copy its definitions verbatim due to its CC-BY-SA license.
+- [ ] I have created a meaningful PR title and referenced any related issues.
+
+<!--- Explain the why and what of your PR next. --->

.github/workflows/ci-pr.yml

@@ -7,19 +7,25 @@ on:
   # forks. Since the workflow only accesses the xlsx and turtle files, but does
   # not run any code, it is safe to use pull_request_target. More info:
   # https://securitylab.github.com/resources/github-actions-preventing-pwn-requests/
+  # zizmor: ignore[dangerous-triggers] OK as per comment above
   pull_request_target:
     branches:
       - main
     types: [opened, reopened, synchronize]
   workflow_dispatch:
 
 env:
-  FORCE_COLOR: "1"  # Make tool output pretty.
   PIP_DISABLE_PIP_VERSION_CHECK: "1"
   PIP_PROGRESS_BAR: "off"
   LOGLEVEL: "DEBUG"
   RUN_URL: $GITHUB_SERVER_URL/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+permissions: {}
+
 jobs:
   build_vocab:
     name: Merge & build vocabulary
@@ -29,29 +35,31 @@ jobs:
     timeout-minutes: 10
 
     permissions:
-      # Give the default GITHUB_TOKEN write permission to commit to the PR branch.
-      contents: write
+      contents: write  # Give the default GITHUB_TOKEN write permission to commit to the PR branch.
 
     steps:
       - name: Checkout PR branch into cwd
-        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
         with:
           # Checkout the fork/head-repository to push changes to the fork.
           # Without this the base repository will be checked out and committed to.
           repository: ${{ github.event.pull_request.head.repo.full_name }}
-
           # Checkout the branch made in the fork.
           ref: ${{ github.head_ref }}
+          # Be specific about keeping credentials (it is the default)
+          persist-credentials: true
 
       - name: Checkout main branch into directory _main_branch/
-        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
         with:
           ref: main
           path: _main_branch
           # This sparse-checkout includes all toplevel files and everything below vocabularies/
           sparse-checkout: |
             vocabularies/
           fetch-depth: 1
+          # Be specific about keeping credentials (it is the default)
+          persist-credentials: true
 
       - uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548
         with:
@@ -62,19 +70,16 @@ jobs:
           python -VV
           python -m pip install --upgrade pip setuptools wheel
 
-          # install tagged version
-          python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@v0.10.0
+          # Select to install a stable tagged version or main branch (in development)
+          python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@v1.0.0
           # python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@main
 
           # install custom pylode 2.x  (adds sorted collections,
           #    uses URIs as fragment IDs and is git-installable)
           python -m pip install git+https://github.com/dalito/pyLODE.git@nfdi4cat-2.x
 
-          # Example for installing from private repo:
-          # python -m pip install git+https://anon:${{ SECRETS.READ_PAT_VOC4CAT }}@github.com/dalito/voc4cat-tool.git@main
-
       - name: Set dynamic environment variables.
-        run: |
+        run: |  # zizmor: ignore[github-env] safe without user controllable input
           echo "RUN_DATE=$(date +'%Y-%m-%dT%H%M')" >> $GITHUB_ENV
 
       - name: Run voc4cat (pre-convert checks)
@@ -91,34 +96,37 @@ jobs:
           voc4cat convert --config _main_branch/idranges.toml --logfile outbox/voc4cat.log --outdir outbox inbox-excel-vocabs/
           if [ ! -f outbox/*.ttl ]; then
             echo "No ttl file in outbox. Building joined vocabulary ttl-file from individual ttl-files in vocabulary."
-            voc4cat transform --join --logfile outbox/voc4cat.log --outdir outbox/ vocabularies/
+            voc4cat transform --join --config _main_branch/idranges.toml --logfile outbox/voc4cat.log --outdir outbox/ vocabularies/
           fi
 
       - name: Run voc4cat (post-convert checks)
         run: |
           # check all ttl file(s) in outbox
-          voc4cat check --config _main_branch/idranges.toml --logfile outbox/voc4cat.log outbox/
+          voc4cat check --redundant-hierarchies --config _main_branch/idranges.toml --logfile outbox/voc4cat.log outbox/
           # check if vocabulary changes are allowed
           voc4cat check --config _main_branch/idranges.toml --logfile outbox/voc4cat.log --ci-post _main_branch/vocabularies outbox/
 
       - name: Run voc4cat (build HTML documentation)
         run: |
           voc4cat docs --logfile outbox/voc4cat.log --force outbox/
 
-      - name: Split vocabulary and merge into vocabulary dir (in PR branch)
+      - name: Split vocabulary, merge into vocabulary dir (in PR branch) and update provenance info
         run: |
-          voc4cat transform --split --inplace --logfile outbox/voc4cat.log --outdir outbox_new_voc outbox/
+          voc4cat transform --split --inplace  --config idranges.toml --logfile outbox/voc4cat.log --outdir outbox_new_voc outbox/
           voc4cat-merge --logfile outbox/voc4cat.log  outbox_new_voc/ vocabularies/
           # copy xlsx to outbox so that the xlsx file is part of the artifact
           find inbox-excel-vocabs -name '*.xlsx' -exec cp {} -t outbox/ \;
           git status
+          # Add/update dct:created and dct:modified base on git history
+          voc4cat transform --prov-from-git --inplace --config idranges.toml --logfile outbox/voc4cat.log vocabularies/
 
       - name: Run voc4cat (re-build updated Excel file and joined turtle vocabulary file)
         # Passing the config is important to make use of the prefixes therein.
         run: |
           mkdir -p outbox/updated-xlsx-ttl
-          voc4cat transform --config idranges.toml --logfile outbox/voc4cat.log -O outbox/updated-xlsx-ttl --join vocabularies/
-          voc4cat convert --config idranges.toml --logfile outbox/voc4cat.log --template templates/voc4cat_template_043.xlsx outbox/updated-xlsx-ttl
+          voc4cat transform --join --config idranges.toml --logfile outbox/voc4cat.log --outdir outbox/updated-xlsx-ttl vocabularies/
+          # Using a template is optional and gives just a warning if missing.
+          voc4cat convert --config idranges.toml --logfile outbox/voc4cat.log --template templates/default_sheets.xlsx outbox/updated-xlsx-ttl
 
       - name: Store artifacts
         if: ${{ always() }}

.github/workflows/merge.yml

@@ -23,31 +23,39 @@ on:
   workflow_dispatch:
 
 env:
-  FORCE_COLOR: "1"  # Make tool output pretty.
   PIP_DISABLE_PIP_VERSION_CHECK: "1"
   PIP_PROGRESS_BAR: "off"
   LOGLEVEL: "DEBUG"
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+permissions: {}
+
 jobs:
   build:
     name: Development build of vocabulary & documentation
     permissions:
-      # Required for peaceiris/actions-gh-pages below
-      contents: write
+      contents: write  # Required for peaceiris/actions-gh-pages below
     runs-on: ubuntu-latest
     timeout-minutes: 10
     steps:
-      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
         with:
           # Using fetch-depth 0 is the only way to get all tags which are needed for building docs.
           fetch-depth: 0
+          # Be specific about keeping credentials (it is the default)
+          persist-credentials: true
 
       - name: Checkout gh-pages branch to dir publish/
-        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
         with:
           ref: gh-pages
           path: publish
           fetch-depth: 1
+          # Be specific about keeping credentials (it is the default)
+          persist-credentials: true
 
       - uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548
         with:
@@ -58,8 +66,8 @@ jobs:
           python -VV
           python -m pip install --upgrade pip setuptools wheel
 
-          # install tagged version
-          python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@v0.10.0
+          # Select to install a stable tagged version or main branch (in development)
+          python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@v1.0.0
           # python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@main
 
           # install custom pylode 2.x
@@ -79,7 +87,7 @@ jobs:
           find publish/dev/ -type f \( -name "*.xlsx" -o -name "*.ttl" -o -name "*.xml" \) -delete
           cp -r vocabularies/. publish/dev/
           # Build joined turtle
-          voc4cat transform --logfile publish/dev/voc4cat.log --join publish/dev/
+          voc4cat transform --join --config idranges.toml --logfile publish/dev/voc4cat.log publish/dev/
 
       - name: Run voc4cat (build pyLODE HTML documentation)
         run: |
@@ -90,7 +98,8 @@ jobs:
       - name: Run voc4cat (build current Excel file)
         # Passing the config is important to make use of the prefixes therein.
         run: |
-          voc4cat convert --config idranges.toml --logfile publish/dev/voc4cat.log --template templates/voc4cat_template_043.xlsx publish/dev/
+          # Using a template is optional and gives just a warning if missing.
+          voc4cat convert --config idranges.toml --logfile publish/dev/voc4cat.log --template templates/default_sheets.xlsx publish/dev/
 
       - name: Run voc4cat (build vocabulary in xml/rdf from Excel file)
         run: |

.github/workflows/pr-checks.yml

@@ -14,14 +14,19 @@ on:
     branches:
       - main
 
-permissions:
-  pull-requests: write
-  contents: read
+permissions: {}
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
 
 jobs:
   check-pr-submission:
     name: Check PR submission best practices
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: write  # to post a message to PR
 
     steps:
       - name: Check if PR is from main branch of fork

.github/workflows/publish.yml

@@ -16,32 +16,40 @@ on:
     types: [published]
 
 env:
-  FORCE_COLOR: "1"  # Make tool output pretty.
   PIP_DISABLE_PIP_VERSION_CHECK: "1"
   PIP_PROGRESS_BAR: "off"
   LOGLEVEL: "DEBUG"
   VOC4CAT_VERSION: ${{github.ref_name}}  # use release tag as version
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+permissions: {}
+
 jobs:
   build:
     name: Release vocabulary & documentation
     permissions:
-      # Required for peaceiris/actions-gh-pages below
-      contents: write
+      contents: write  # Required for peaceiris/actions-gh-pages below
     runs-on: ubuntu-latest
     timeout-minutes: 10
     steps:
-      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
         with:
           # Using fetch-depth 0 is the only way to get all tags which are needed for building docs.
           fetch-depth: 0
+          # Be specific about keeping credentials (it is the default)
+          persist-credentials: true
 
       - name: Checkout gh-pages branch to dir publish/
-        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
         with:
           ref: gh-pages
           path: publish
           fetch-depth: 1
+          # Be specific about keeping credentials (it is the default)
+          persist-credentials: true
 
       - uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548
         with:
@@ -52,8 +60,8 @@ jobs:
           python -VV
           python -m pip install --upgrade pip setuptools wheel
 
-          # install tagged version
-          python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@v0.10.0
+          # Select to install a stable tagged version or main branch (in development)
+          python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@v1.0.0
           # python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@main
 
           # install custom pylode 2.x
@@ -71,7 +79,7 @@ jobs:
           find publish/latest/ -type f \( -name "*.xlsx" -o -name "*.ttl"  -o -name "*.xml" \) -delete
           cp -r vocabularies/. publish/latest/
           # Build joined turtle
-          voc4cat transform --logfile publish/latest/voc4cat.log --join publish/latest/
+          voc4cat transform --join --config idranges.toml --logfile publish/latest/voc4cat.log publish/latest/
 
       - name: Run voc4cat (build pyLODE HTML documentation)
         run: |
@@ -82,7 +90,8 @@ jobs:
       - name: Run voc4cat (build current Excel file)
         # Passing the config is important to make use of the prefixes therein.
         run: |
-          voc4cat convert --config idranges.toml --logfile publish/latest/voc4cat.log --template templates/voc4cat_template_043.xlsx publish/latest/
+          # Using a template is optional and gives just a warning if missing.
+          voc4cat convert --config idranges.toml --logfile publish/latest/voc4cat.log --template templates/default_sheets.xlsx publish/latest/
 
       - name: Run voc4cat (build vocabulary in xml/rdf from Excel file)
         # Passing the config is important to make use of the prefixes therein.
@@ -91,8 +100,8 @@ jobs:
 
       - name: Copy release to release-name directory
         run: |
-          mkdir -p publish/${{ github.ref_name }}
-          cp -r publish/latest/. publish/${{ github.ref_name }}/
+          mkdir -p publish/${GITHUB_REF_NAME}
+          cp -r publish/latest/. publish/${GITHUB_REF_NAME}/
 
       - name: Build Sphinx documentation (website)
         run: |

.zenodo.json

@@ -21,12 +21,12 @@
     {
       "name": "Schumann, Julia",
       "orcid": "0000-0002-4041-0165",
-      "affiliation": "Physics Department and CSMB, Humboldt-Universität zu Berlin, Zum Großen Windkanal 2, 12489 Berlin, Germany"
+      "affiliation": "Physics Department and CSMB, Humboldt-Universität zu Berlin, Zum Großen Windkanal 2, 12489 Berlin, Germany"
     },
     {
-      "name": "Götte, Michael",
+      "name": "Götte, Michael",
       "orcid": "0009-0008-1278-8890",
-      "affiliation": "Helmholtz-Zentrum Berlin für Materialien und Energie, 14109 Berlin, Germany"
+      "affiliation": "Helmholtz-Zentrum Berlin für Materialien und Energie, 14109 Berlin, Germany"
     },
     {
       "name": "Borgelt, Hendrik",
@@ -41,7 +41,7 @@
     {
       "name": "Terboven, Carla",
       "orcid": "0009-0004-3786-0773",
-      "affiliation": "Helmholtz-Zentrum Berlin für Materialien und Energie"
+      "affiliation": "Helmholtz-Zentrum Berlin für Materialien und Energie"
     },
     {
       "name": "Flecken, Franziska",