Added new stup for updating github pages (#294)

.github/workflows/cd_update_pages.yml

@@ -5,57 +5,119 @@ on:
     branches:
       - '[0-9]+.[0-9]+.[0-9]+'
       - '[0-9]+.[0-9]+.[0-9]+-*'
-      - update_pages
-      - fix-github-workflow
+      - cd_update_pages
+
+env:
+  GIT_USER_NAME: EMMO Developers
+  GIT_USER_EMAIL: "[email protected]"
 
 jobs:
 
   build:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+    - name: Checkout repository
+      uses: actions/checkout@v4
 
-    - name: Setup git identity
+    - name: Debug info
       run: |
-        git config --global user.email "[email protected]"
-        git config --global user.name "EMMO GitHub Action"
+        echo "GITHUB_REF_NAME=${GITHUB_REF_NAME}"
 
     - name: Setup Python 3.11
       uses: actions/setup-python@v5
       with:
         python-version: 3.11
 
-    - name: Debug info
+    - name: Install dependencies
       run: |
-        echo "GITHUB_REF_NAME=${GITHUB_REF_NAME}"
+        pip install --upgrade pip
+        pip install sphinx sphinxcontrib-globalsubs sphinx_design nbsphinx pydata-sphinx-theme
+        pip install git+https://github.com/emmo-repo/EMMOntoPy.git@ontodoc2
+        #pip install sphinx EMMOntoPy
 
-    - name: Install EMMO-python
+    - name: Create and prepare build and public directories
       run: |
-        pip install --upgrade pip
-        pip install EMMOntoPy
+        mkdir build public
+        if [ -d doc/_static ]; then cp -rf doc/_static/* build/. ; fi
 
-    - name: Install pandoc 2.1.2
+    - name: Create ontologies for publishing
       run: |
-        #sudo apt-get install pandoc  # we need v2.1.2
-        wget https://github.com/jgm/pandoc/releases/download/2.1.2/pandoc-2.1.2-1-amd64.deb
-        sudo apt-get install ./pandoc-2.1.2-1-amd64.deb
+        ontoconvert -sawe --base-iri="https://w3id.org/emmo#" --iri=https://w3id.org/emmo emmo.ttl public/emmo.ttl
+        ontoconvert public/emmo.ttl public/emmo.owl
 
-    - name: Install other dependencies
+    - name: Generate html documentation
       run: |
-        sudo apt-get install graphviz
-        sudo apt-get install texlive-xetex
-        sudo apt-get install texlive-latex-extra
-        pip install semver
+        ontodoc --iri-regex=https://w3id.org/emmo --imported emmo.ttl build/emmo.rst
+        sphinx-build "build/" "public/"
 
     - name: Checkout GitHub Pages for EMMO-repo
       uses: actions/checkout@v4
       with:
         repository: emmo-repo/emmo-repo.github.io
-        path: ".github/pages"
+        path: pages
         ssh-key: ${{ secrets.SSH_PRIVATE_KEY }}
         ssh-strict: no
 
-    - name: Update GitHub Pages
+    - name: Copy to GitHub Pages
       run: |
-        .github/scripts/update_pages.sh -v -V ${GITHUB_REF_NAME}
+        # Do not overwrite index.html
+        rm public/index.html
+        cp -rf public/* pages/.
+        # Tell GitHub that this site is not generated with jekyll
+        touch public/.nojekyll
+
+      # Domain repositories can use peaceiris/actions-gh-pages@v3.
+      # However, since EMMO for historical reasons uses a separate repo
+      # for its GitHub Pages, it is easier to use git directly.
+    - name: Push to GitHub Pages
+      run: |
+        cd pages
+        git config --global user.email "[email protected]"
+        git config --global user.name "EMMO Developer"
+        git add --all
+        if [ -n "$(git status --porcelain -uno)" ]; then \
+          git commit -m 'Updated releasetable'; \
+          git pull origin master; \
+          git push origin master; \
+        fi
+
+
+    #- name: Publish
+    #  uses: peaceiris/actions-gh-pages@v3
+    #  if: github.ref == 'refs/heads/master'
+    #  with:
+    #    github_token: ${{ secrets.GITHUB_TOKEN }}
+    #    publish_dir: ./public
+    #    #keep_files: true
+    #    #external_repository: emmo-repo emmo-repo.github.io
+    #
+    #    #publish_branch: master
+    #    #force_orphan: true
+
+
+
+#    - name: Install pandoc 2.1.2
+#      run: |
+#        #sudo apt-get install pandoc  # we need v2.1.2
+#        wget https://github.com/jgm/pandoc/releases/download/2.1.2/pandoc-2.1.2-1-amd64.deb
+#        sudo apt-get install ./pandoc-2.1.2-1-amd64.deb
+#
+#    - name: Install other dependencies
+#      run: |
+#        sudo apt-get install graphviz
+#        sudo apt-get install texlive-xetex
+#        sudo apt-get install texlive-latex-extra
+#        pip install semver
+#
+#    - name: Checkout GitHub Pages for EMMO-repo
+#      uses: actions/checkout@v4
+#      with:
+#        repository: emmo-repo/emmo-repo.github.io
+#        path: ".github/pages"
+#        ssh-key: ${{ secrets.SSH_PRIVATE_KEY }}
+#        ssh-strict: no
+#
+#    - name: Update GitHub Pages
+#      run: |
+#        .github/scripts/update_pages.sh -v -V ${GITHUB_REF_NAME}

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 = 'EMMO'
+copyright = '2024, EMMC'
+author = 'E. Ghedini, G. Goldbeck, J. Friis, A. Hashibon, G.J. Schmitz'
+release = '1.0.0-rc1'
+
+# -- 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);
+}