Merge updates from https://github.com/nfdi4cat/voc4cat-template

.github/workflows/ci-pr.yml

@@ -13,6 +13,7 @@ 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
 
 jobs:
@@ -58,23 +59,46 @@ jobs:
           python -m pip install --upgrade pip setuptools wheel
 
           # install tagged version
-          python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@v0.5.1
-
-          # examples for other install options
+          python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@v0.6.2
           # python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@main
-          # from private repo: python -m pip install git+https://anon:${{ SECRETS.READ_PAT_VOC4CAT }}@github.com/dalito/voc4cat-tool.git@main
 
-      - name: Dynamically set RUN_DATE environment variable
-        run: echo "RUN_DATE=$(date +'%Y-%m-%dT%H%M')" >> $GITHUB_ENV
+          # Example for installing from private repo:
+          # python -m pip install git+https://anon:${{ SECRETS.READ_PAT_VOC4CAT }}@github.com/dalito/voc4cat-tool.git@main
+
+      - name: Set dynamic environment variables.
+        run: |
+          echo "RUN_DATE=$(date +'%Y-%m-%dT%H%M')" >> $GITHUB_ENV
 
-      - name: Run voc4cat
+      - name: Run voc4cat (pre-convert checks)
         run: |
           voc4cat --version
-          voc4cat -v --ci-check --config _main_branch/idranges.toml --check --forward --logfile voc4cat.log --docs pylode --output-directory outbox inbox-excel-vocabs/
+          # check inbox file names
+          voc4cat check --config _main_branch/idranges.toml --logfile outbox/voc4cat.log --ci-pre inbox-excel-vocabs/ _main_branch/vocabularies
+          # check xlsx file(s). If the check fails, write annotated file to outbox.
+          voc4cat check --config _main_branch/idranges.toml --logfile outbox/voc4cat.log --outdir outbox inbox-excel-vocabs/
+
+      - name: Run voc4cat (convert)
+        run: |
+          # convert file(s) from xlsx in inbox to turtle in outbox
+          voc4cat convert --config _main_branch/idranges.toml --logfile outbox/voc4cat.log --outdir outbox inbox-excel-vocabs/
+
+      - 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/
+          # 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: Merge changes into vocabulary (in PR branch)
+      - name: Split vocabulary and merge into vocabulary dir (in PR branch)
         run: |
-          merge_vocab --logfile voc4cat.log outbox/ vocabularies/
+          voc4cat transform --split --inplace --logfile outbox/voc4cat.log --outdir outbox_new_voc outbox/
+          merge_vocab --logfile outbox/voc4cat.log  outbox_new_voc/ vocabularies/
+          # copy xlsx to outbox so that the xlsx file is part of the artifact
+          cp $(find inbox-excel-vocabs -name "*.xlsx") outbox/
           git status
 
       - name: Store artifacts

.github/workflows/publish.yml

@@ -1,9 +1,10 @@
 # This action runs when a release is created and on merges to main.
 #
 # Workflow steps:
-# - build docs
+# - create joined vocabulary file in addition to split version
 # - create excel-file from turtle
-# - publish docs and excel-file to gh-pages
+# - build docs
+# - publish docs, vocabulary-turtle files and excel-file to gh-pages
 
 name: Build & Publish
 on:
@@ -18,6 +19,7 @@ env:
   FORCE_COLOR: "1"  # Make tool output pretty.
   PIP_DISABLE_PIP_VERSION_CHECK: "1"
   PIP_PROGRESS_BAR: "off"
+  LOGLEVEL: "DEBUG"
 
 jobs:
   build:
@@ -38,16 +40,28 @@ jobs:
         run: |
           python -VV
           python -m pip install --upgrade pip setuptools wheel
-          python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@v0.5.1
 
-      - name: Run voc4cat to build docs & Excel-files matching turtle files
+          # install tagged version
+          python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@v0.6.2
+          # python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@main
+
+      - name: Run voc4cat (publish joined & split SKOS/turtle)
         run: |
           voc4cat --version
-          voc4cat --docs pylode --output-directory publish vocabularies/
-          voc4cat --output-directory publish vocabularies/ --template templates/voc4cat_template_043.xlsx
+          cp -r vocabularies/ publish/
+          # Build joined turtle
+          voc4cat transform --logfile publish/voc4cat.log --join publish/
+
+      - name: Run voc4cat (build HTML documentation)
+        run: |
+          voc4cat docs --force --logfile publish/voc4cat.log publish/
+
+      - name: Run voc4cat (build current Excel file)
+        run: |
+          voc4cat convert --logfile publish/voc4cat.log --template templates/voc4cat_template_043.xlsx publish/
           ls -l publish/ || echo "publish directory does not exist."
 
-      - name: Deploy documentation
+      - name: Deploy documentation & SKOS/turtle & xlsx
         # Pin third party action (v3.9.3)
         uses: peaceiris/actions-gh-pages@373f7f263a76c20808c831209c920827a82a2847
         if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
@@ -57,14 +71,14 @@ jobs:
           publish_dir: ./publish
           force_orphan: true
 
-      - name: Store xlsx file(s) as artifacts
-        # This step is not required and may be removed.  The xlsx files are
-        # stored in gh-pages and can be linked which makes them easier to find.
+      - name: Store publish dir (=pages) as artifact
+        # This step is not required and may be removed.
+        # It may be helpful for trouble shooting.
         if: ${{ always() }}
         uses: actions/upload-artifact@v3
         with:
-          name: voc4cat-excel-vocab
-          path: publish/*.xlsx
+          name: voc4cat-pages-content
+          path: publish/
 
 # Lit:
 # https://github.com/peaceiris/actions-gh-pages

.gitignore

@@ -101,9 +101,9 @@ cython_debug/
 # setuptools_scm generated version file
 _version.py
 
-# output dir
+# Special directories used in github actions of voc4cat vocabularies
+# which must be ignored to not get committed automatically.
 outbox/
+outbox_new_voc/
 publish/
-
-# Special dir for a clone of main branch in gh-actions
 _main_branch

README.md

@@ -6,7 +6,7 @@
 The vocabulary has been created and maintained as part of the [NFDI4Cat](http://www.nfdi4cat.org) initiative and follows our [Voc4Cat Guidelines](https://doi.org/10.5281/zenodo.7669183).
 
 This repository was created from the template [voc4cat-template](https://github.com/nfdi4cat/voc4cat-template).
-It uses the [voc4cat-tool](https://github.com/nfdi4cat/voc4cat-tool) and GitHub features like gh-actions, pull requests etc. to reduce the maintenance workload for contributors and editors.
+It uses the [voc4cat-tool](https://github.com/nfdi4cat/voc4cat-tool) and GitHub features like pull requests, gh-actions, gh-pages etc. to reduce the maintenance workload for contributors and editors.
 
 ## Basic principles
 
@@ -26,7 +26,7 @@ To discuss about the **voc4cat**-vocabulary maintained here, create an [issue](h
 
 To contribute new concepts or collections or change existing ones, you may either submit your contributions as Excel/xlsx-file or (as an expert) as new/changed turtle file.
 
-> *To try out the workflow with some example data, you may use  [voc4cat-playground](https://github.com/nfdi4cat/voc4cat-playground) which is identical to this repository but will be purged from time to time.*
+> *To try out the workflow with some example data, you may use  [voc4cat-playground](https://github.com/nfdi4cat/voc4cat-playground) which is almost identical to this repository but is not meant to last.*
 
 Here are the steps for submitting updates in Excel.
 
@@ -47,7 +47,7 @@ Here are the steps for submitting updates in Excel.
   - or why the proposed change may not fit.
 - If you need to fix something update the pull request branch. This will trigger the pipeline to run again.
 
-Finally, when the proposed merge request is accepted, your changes will be integrated in the vocabulary in the folder [vocabularies](https://github.com/nfdi4cat/voc4cat/tree/main/vocabularies).
+Finally, when the proposed merge request is accepted, your changes will be integrated in the vocabulary in the folder [vocabularies](https://github.com/nfdi4cat/voc4cat/tree/main/vocabularies). The vocabulary is stored in split form using a folder of turtle files. Each concept, collection and concept scheme is stored in a separate file using the ID-part of the IRI as file name.
 
 See [inbox-excel-vocabs/README.md](inbox-excel-vocabs/README.md) for a minimal example how to test the submission process.
 

templates/README.md

@@ -4,6 +4,11 @@ The templates here match structure-wise with the templates in [Voc4Cat-tool](htt
 
 ### Version 0.4.3
 
+#### Revision 2023-08a
+
+- Changed included example data to be consistent with improved validation.
+- Updated help on filling out provenance fields.
+
 #### Revision 2023-07a
 
 - Fixed typos.