Updated oteio.ttl

.github/emmocheck_conf.yml

@@ -0,0 +1,11 @@
+# Configurations used when running emmocheck from the ci_emmocheck workflow
+skip:
+  - test_description
+
+test_number_of_labels:
+  exceptions:
+    - 0.1.Person  # foaf:Person
+    - 0.1.mbox  # foaf:mbox
+    - 22-rdf-syntax-ns.Statement  # rdf:Statement
+    - dcat.Distribution
+    - dcat.Dataset

.github/workflows/cd_publish.yml

@@ -2,13 +2,9 @@ name: CD_publish
 
 on:
   push:
+    branches:
+      - master
 
-#on:
-#  push:
-#    branches:
-#      - '[0-9]+.[0-9]+.[0-9]+'
-#      - '[0-9]+.[0-9]+.[0-9]+-*'
-#
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
@@ -24,37 +20,70 @@ jobs:
         with:
           python-version: 3.11
 
-      - name: Install EMMOntoPy and pyvode
+      - name: Install ROBOT
+        run: |
+          mkdir bin
+          wget -nv https://github.com/ontodev/robot/releases/download/v1.9.6/robot.jar
+          mv robot.jar bin/.
+          curl https://raw.githubusercontent.com/ontodev/robot/master/bin/robot > bin/robot
+          chmod +x bin/robot
+          ls -l bin/
+
+      - name: Install EMMOntoPy and Sphinx
         run: |
           pip install --upgrade pip
-          pip install pylode==2.13.2 git+https://github.com/EMMO-REPO/EMMOntoPy.git
-
-      - name: Create build directory
-        run: mkdir build
-
-      - name: Copy json-ld context
-        run: cp -r context build/.
-
-      - name: Generate squashed ontology
-        run: ontoconvert -saw
-          -c 'http://www.w3.org/2004/02/skos/core#prefLabel-->http://www.w3.org/2000/01/rdf-schema#label'
-          -c 'elucidation-->http://www.w3.org/2000/01/rdf-schema#comment'
-          -c 'definition-->http://www.w3.org/2000/01/rdf-schema#comment'
-          oteio.ttl build/oteio.ttl
-          #-c 'comment-->http://www.w3.org/2000/01/rdf-schema#comment'
-
-      - name: Generate inferred ontology
-        run: ontoconvert -saw --reasoner=HermiT
-          -c 'http://www.w3.org/2004/02/skos/core#prefLabel-->http://www.w3.org/2000/01/rdf-schema#label'
-          -c 'elucidation-->http://www.w3.org/2000/01/rdf-schema#comment'
-          -c 'definition-->http://www.w3.org/2000/01/rdf-schema#comment'
-          oteio.ttl build/oteio-inferred.ttl
-          #-c 'comment-->http://www.w3.org/2000/01/rdf-schema#comment'
-
-      - name: Generate documentation
-        run: pylode -i build/oteio-inferred.ttl -o build/oteio.html -p ontdoc
-
-      - name: Deploy
-        uses: JamesIves/github-pages-deploy-action@v4
-        with:
-          folder: build  # The folder the action should deploy.
+          #pip install pylode==2.13.2 git+https://github.com/EMMO-REPO/EMMOntoPy.git
+          pip install sphinx sphinxcontrib-globalsubs sphinx_design nbsphinx pydata-sphinx-theme
+          pip install git+https://github.com/emmo-repo/EMMOntoPy.git@master
+          #pip install git+https://github.com/emmo-repo/EMMOntoPy.git@fix-rename-iris
+
+      - name: Create and prepare build and public directories
+        run: |
+          mkdir -p build public
+          if [ -d doc/_static ]; then cp -rf doc/_static/* build/. ; fi
+
+      - name: Create ontologies for publishing
+        run: |
+          ontoconvert -sawe --base-iri="https://w3id.org/emmo/domain/oteio#" --iri=https://w3id.org/emmo/domain/oteio oteio.ttl public/oteio.ttl
+          #ontoconvert -sawe --base-iri="https://w3id.org/emmo/domain/oteio#" --iri=https://w3id.org/emmo/domain/oteio --reasoner=HermiT public/oteio.ttl public/oteio-inferred.ttl
+          bin/robot reason --reasoner HermiT --input public/oteio.ttl --output public/oteio-inferred.ttl
+
+      - name: Generate html documentation (based on emmo-full)
+        run: |
+          ontodoc --iri-regex='.*/oteio.*' oteio.ttl build/oteio.rst
+          sphinx-build "build/" "public/"
+
+
+
+
+
+#      - name: Create build directory
+#        run: mkdir build
+#
+#      - name: Copy json-ld context
+#        run: cp -r context build/.
+#
+#      - name: Generate squashed ontology
+#        run: ontoconvert -saw
+#          -c 'http://www.w3.org/2004/02/skos/core#prefLabel-->http://www.w3.org/2000/01/rdf-schema#label'
+#          -c 'elucidation-->http://www.w3.org/2000/01/rdf-schema#comment'
+#          -c 'definition-->http://www.w3.org/2000/01/rdf-schema#comment'
+#          oteio.ttl build/oteio.ttl
+#          #-c 'comment-->http://www.w3.org/2000/01/rdf-schema#comment'
+#
+#      - name: Generate inferred ontology
+#        run: ontoconvert -saw --reasoner=HermiT
+#          -c 'http://www.w3.org/2004/02/skos/core#prefLabel-->http://www.w3.org/2000/01/rdf-schema#label'
+#          -c 'elucidation-->http://www.w3.org/2000/01/rdf-schema#comment'
+#          -c 'definition-->http://www.w3.org/2000/01/rdf-schema#comment'
+#          oteio.ttl build/oteio-inferred.ttl
+#          #-c 'comment-->http://www.w3.org/2000/01/rdf-schema#comment'
+#
+#      - name: Generate documentation
+#        run: pylode -i build/oteio-inferred.ttl -o build/oteio.html -p ontdoc
+#
+#      - name: Deploy
+#        uses: JamesIves/github-pages-deploy-action@v4
+#        with:
+#          folder: build  # The folder the action should deploy.
+#

.github/workflows/ci_emmocheck.yml

@@ -0,0 +1,30 @@
+name: Check conventions
+on: [push]
+
+jobs:
+
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 1
+      matrix:
+        python-version: [3.11]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install EMMOntoPy
+      run: |
+        pip install --upgrade pip
+        #pip install EMMOntoPy
+        pip install git+https://github.com/emmo-repo/EMMOntoPy.git@master
+
+    - name: Check EMMO
+      run: |
+        emmocheck --local --url-from-catalog --verbose --check-imported \
+          --configfile=.github/emmocheck_conf.yml  oteio.ttl

.gitignore

@@ -0,0 +1,4 @@
+build/
+public/
+
+pylode.log

doc/_static/conf.py

@@ -0,0 +1,75 @@
+
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'OTEIO'
+copyright = '2025, EMMC'
+author = 'J. Friis, F.L. Bleken'
+release = '0.4.0'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+autoclass_content = 'both'
+autodoc_member_order = 'bysource'
+
+extensions = ['sphinxcontrib.globalsubs',
+              'sphinx.ext.intersphinx',
+              'sphinx.ext.autosectionlabel',
+              'sphinx_design',
+              'nbsphinx']
+
+autosectionlabel_prefix_document = True
+
+global_substitutions = {
+}
+
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#html_theme = 'alabaster'
+html_theme = 'pydata_sphinx_theme'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+html_theme_options = {
+  # "show_nav_level": 4
+}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['../doc/_static']
+html_css_files = ['custom.css']
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = '../doc/emmo-logo.png'
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_flavicon = '../doc/figs/emmo-logo.ico'

doc/_static/custom.css

@@ -0,0 +1,39 @@
+td.element-table-key, td.element-table-value {
+    vertical-align: top;
+}
+
+td.element-table-key {
+    text-align: right;
+    padding-right: 2mm;
+    width: 20%;
+}
+
+span.element-table-key {
+    font-weight: bold;
+}
+
+table.element-table {
+    width: 100%;
+    text-align: left;
+}
+
+html table.element-table tr:nth-child(odd) td{
+   background-color: Gainsboro;
+}
+
+table.element-table tr:nth-child(even) td{
+   background-color: GhostWhite;
+}
+
+html[data-theme=dark] table.element-table tr:nth-child(odd) td{
+   background-color: black;
+}
+
+html[data-theme=dark] table.element-table tr:nth-child(even) td{
+   background-color: black;
+}
+/* this fixes darkmode within the json-ld playground iframe
+by inverting all colors if darkmode is active */
+html[data-theme="dark"] iframe[src*="json-ld.org/playground"] {
+   filter: invert(0.9);
+}

doc/_static/index.rst

@@ -0,0 +1,6 @@
+
+.. toctree::
+   :includehidden:
+   :hidden:
+
+   Reference Index <oteio>