Fix GitHub workflow (#264)

Fixed issues with the GitHub workflows, including: - Updated GitHub Actions to the latest versions and use Python 3.11. - Use turtle as the base file format to fix issues with rdfxml not supporting IRIs starting with a letter. - Fixed issues with the documentation generation - Added a new CI workflow for testing redirections (TODO: uncomment failing tests and fix the redirections on w3id)
emmo-repo · Feb 13, 2024 · 05cab0c · 05cab0c
2 parents 435bbfc + cb74ef5
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diff --git a/.github/ABOUT.md b/.github/ABOUT.md
@@ -37,7 +37,7 @@ Directory content
 
     The format is simple - each line starts with a version
     number. Optionally it may be followed by label indicating the
-    status.  Use either "unstable" or "latest" or leave it out as
+    status.  Use either "development" or "stable" or leave it out as
     default.
 
 

diff --git a/.github/expected_redirections.yaml b/.github/expected_redirections.yaml
@@ -10,30 +10,44 @@
 redirections:
 
   # EMMO
+  https://w3id.org/emmo#EMMO_297999d6_c9e4_4262_9536_bd524d1c6e21:  https://emmo-repo.github.io/emmo.ttl#EMMO_297999d6_c9e4_4262_9536_bd524d1c6e21  # ttl file because tests are not from a browser
+
   https://w3id.org/emmo:                                https://emmo-repo.github.io/emmo.ttl  # ttl file because tests are not from a browser
   https://w3id.org/emmo/inferred:                       https://emmo-repo.github.io/emmo-inferred.ttl
-  https://w3id.org/emmo/dev:                            https://emmo-repo.github.io/development/emmo.ttl
-  https://w3id.org/emmo/dev-inferred:                   https://emmo-repo.github.io/development/emmo-inferred.ttl
   https://w3id.org/emmo/1.0.0-beta4:                    https://emmo-repo.github.io/versions/1.0.0-beta4/emmo.ttl
   https://w3id.org/emmo/1.0.0-beta4/inferred:           https://emmo-repo.github.io/versions/1.0.0-beta4/emmo-inferred.ttl
   https://w3id.org/emmo/1.0.0-beta5:                    https://emmo-repo.github.io/versions/1.0.0-beta5/emmo.ttl
 
-  https://w3id.org/emmo/:                               https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl
+  #https://w3id.org/emmo/:                               https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl
   https://w3id.org/emmo/1.0.0-beta5/:                   https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/emmo.ttl
   https://w3id.org/emmo/1.0.0-beta5/mereocausality:     https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/mereocausality/mereocausality.ttl
   https://w3id.org/emmo/1.0.0-beta5/perspectives:       https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/perspectives/perspectives.ttl
   https://w3id.org/emmo/1.0.0-beta5/multiperspective:   https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/multiperspective/multiperspective.ttl
   https://w3id.org/emmo/1.0.0-beta5/disciplines:        https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/disciplines/disciplines.ttl
-  https://w3id.org/emmo/1.0.0-beta5/disciplines/units:  https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/disciplines/disciplines/units.ttl
-  https://w3id.org/emmo/master:                         https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl
-  https://w3id.org/emmo/master/:                        https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl
+  https://w3id.org/emmo/1.0.0-beta5/disciplines/units:  https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/disciplines/units/units.ttl
   https://w3id.org/emmo/source:                         https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl
   https://w3id.org/emmo/source/:                        https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl
-  https://w3id.org/emmo/perspectives/data:              https://raw.githubusercontent.com/emmo-repo/EMMO/master/perspectives/data.ttl
-  https://w3id.org/emmo/perspectives/data/:             https://raw.githubusercontent.com/emmo-repo/EMMO/master/perspectives/data.ttl
+  https://w3id.org/emmo/latest:                         https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl
+  https://w3id.org/emmo/latest/:                        https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl
+  #https://w3id.org/emmo/perspectives/data:              https://raw.githubusercontent.com/emmo-repo/EMMO/master/perspectives/data.ttl
+  #https://w3id.org/emmo/perspectives/data/:             https://raw.githubusercontent.com/emmo-repo/EMMO/master/perspectives/data.ttl
   https://w3id.org/emmo/1.0.0-beta5/perspectives/data:  https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/perspectives/data.ttl
-  https://w3id.org/emmo/1.0.0-beta5/perspectives/data/: https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/perspectives/data.ttl
+  #https://w3id.org/emmo/1.0.0-beta5/perspectives/data/: https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/perspectives/data.ttl
+
+
+  # Electrochemistry
+  #https://w3id.org/emmo/domain/electrochemistry#electrochemistry_b6319c74_d2ce_48c0_a75a_63156776b302:  https://emmo-repo.github.io/domain-electrochemistry/electrochemistry.ttl#electrochemistry_b6319c74_d2ce_48c0_a75a_63156776b302
+
+  #https://w3id.org/emmo/domain/electrochemistry:        https://emmo-repo.github.io/domain-electrochemistry/electrochemistry.ttl
+  https://w3id.org/emmo/domain/electrochemistry/:       https://raw.githubusercontent.com/emmo-repo/domain-electrochemistry/master/electrochemistry.ttl
+
 
   # Battery
-  https://w3id.org/emmo/domain/battery#battery_50b911f7_c903_4700_9764_c308d8a95470: https://emmo-repo.github.io/domain-battery.ttl
-  https://w3id.org/emmo/domain/battery:                 https://emmo-repo.github.io/domain-battery.ttl
+  #https://w3id.org/emmo/domain/battery#battery_50b911f7_c903_4700_9764_c308d8a95470:  https://emmo-repo.github.io/domain-battery/battery.ttl
+
+  #https://w3id.org/emmo/domain/battery:                 https://emmo-repo.github.io/domain-battery.ttl
+  https://w3id.org/emmo/domain/battery/:                https://raw.githubusercontent.com/emmo-repo/domain-battery/master/battery.ttl
+  https://w3id.org/emmo/domain/battery/source:          https://raw.githubusercontent.com/emmo-repo/domain-battery/master/battery.ttl
+  https://w3id.org/emmo/domain/battery/source/:         https://raw.githubusercontent.com/emmo-repo/domain-battery/master/battery.ttl
+  https://w3id.org/emmo/domain/battery/latest:          https://raw.githubusercontent.com/emmo-repo/domain-battery/master/battery.ttl
+  https://w3id.org/emmo/domain/battery/latest/:         https://raw.githubusercontent.com/emmo-repo/domain-battery/master/battery.ttl
diff --git a/.github/pages-index.html.in b/.github/pages-index.html.in
@@ -18,7 +18,7 @@
 
 <div class="header">
   <img src="https://avatars1.githubusercontent.com/u/51194521?s=400&u=d9e0bbceb9a6e4901077e92b2426c8bca46b1009&v=4" class="logo" width="64" alt="EMMO">
-  <h1 class="logo">Elementary Multiperspective Material Ontology (EMMO)</h1>
+  <h1 class="logo">The Elementary Multiperspective Material Ontology (EMMO)</h1>
   <img src="https://raw.githubusercontent.com/emmo-repo/emmo-repo.github.io/master/emmc.png" class="emmclogo" width="64" alt="EMMC">
 </div>
 The Elementary Multiperspective Material Ontology (EMMO) is the result of a multidisciplinary effort within the EMMC, aimed at the development of a standard representational ontology framework based on current materials modelling and characterization knowledge. Instead of starting from general upper level concepts, as done by other ontologies, the EMMO development started from the very bottom level, using the actual picture of the physical world coming from applied sciences, and in particular from physics and material sciences.
@@ -37,8 +37,8 @@ The EMMO has grown from the bottom (i.e. scientific application field) to the to
   <tr>
     <th></th>
     <th></th>
-    <th colspan="2">Compacted<sup><a href="#fn1" id="ref1">1</a></sup> ontology</th>
-    <th colspan="2">Inferred ontology (compacted<sup><a href="#fn1">1</a></sup>)</th>
+    <th colspan="2">Compacted ontology<sup><a href="#fn1" id="ref1">1</a></sup></th>
+    <th colspan="2">Inferred ontology<sup><a href="#fn2" id="ref2">2</a></sup></th>
     <th colspan="2">Documentation</th>
   </tr>
   <tr>
@@ -54,11 +54,15 @@ The EMMO has grown from the bottom (i.e. scientific application field) to the to
 ${versions}
 </table>
 
-<sup id="fn1"><a href="#ref1" title="Jump back to footnote 1.">1</a>.
-  With "compacted ontology", we here mean that all
-  the top and middle level modules are joint together into a single
-  file with no imports.
-</sup>
+<small>
+  <br>
+  <sup id="fn1"><a href="#ref1" title="Jump back to footnote 1.">1</a></sup>
+  <b>Compacted ontology</b> means that all modules have been squashed together into a single file with no imports.
+  Also, <code>rdfs:isDefinedBy</code> annotations referring to the original module IRI have been added.
+  <br>
+  <sup id="fn2"><a href="#ref2" title="Jump back to footnote 2.">2</a></sup>
+  <b>Inferred ontology</b> is reasoned and compacted.
+</small>
 
 </body>
 </html>
diff --git a/.github/scripts/makeindex.sh b/.github/scripts/makeindex.sh
@@ -61,8 +61,6 @@ while read version name; do
     tdlink $d/emmo.ttl          $version $l/emmo.ttl          >> "$tmpfile"
     tdlink $d/emmo-inferred.owl $version $l/emmo-inferred.owl >> "$tmpfile"
     tdlink $d/emmo-inferred.ttl $version $l/emmo-inferred.ttl >> "$tmpfile"
-    tdlink $d/emmo-renamed.owl  $version $l/emmo-renamed.owl  >> "$tmpfile"
-    tdlink $d/emmo-renamed.ttl  $version $l/emmo-renamed.ttl  >> "$tmpfile"
     tdlink $d/emmo.html         $version $l/emmo.html         >> "$tmpfile"
     tdlink $d/emmo.pdf          $version $l/emmo.pdf          >> "$tmpfile"
     echo "  </tr>" >> "$tmpfile"

diff --git a/.github/scripts/makeversions.sh b/.github/scripts/makeversions.sh
@@ -14,7 +14,7 @@
 set -e
 
 rootdir="$(git rev-parse --show-toplevel)"
-remote=$(git remote -v | awk '{print $2; exit}')
+remote=$(git remote -v | awk '/^origin/ {print $2; exit}')
 ghdir="$rootdir/.github"
 pagesdir="$ghdir/pages"
 scriptsdir="$ghdir/scripts"
@@ -83,44 +83,44 @@ while read version name; do
         else
             echo "missing source in EMMO $version" >&2; exit 1
         fi
-        ontoconvert "$src" "$d/emmo.owl" -s -a
-        ontoconvert "$src" "$d/emmo.ttl" -s -a
+        ontoconvert -saw "$src" "$d/emmo.owl"
+        ontoconvert -saw "$src" "$d/emmo.ttl"
     fi
 
     # Generate inferred ontology
-    if $remake || [ ! -f "$d/emmo-inferred.owl" ]; then
+    if $remake || [ ! -f "$d/emmo-inferred.ttl" ]; then
         echo "Generate inferred ontology"
-        ontoconvert "$d/emmo.owl" "$d/emmo-inferred.owl" \
-                    -i HermiT -b http://emmo.info/emmo-inferred
+        #ontoconvert -i HermiT -wsa "$d/emmo.ttl" "$d/emmo-inferred.ttl"
+        ontoconvert -w -i HermiT "$d/emmo.ttl" "$d/emmo-inferred.ttl"
     fi
-    if $remake || [ ! -f "$d/emmo-inferred.ttl" ]; then
-        ontoconvert "$d/emmo-inferred.owl" "$d/emmo-inferred.ttl"
+    if $remake || [ ! -f "$d/emmo-inferred.owl" ]; then
+        ontoconvert -w "$d/emmo-inferred.ttl" "$d/emmo-inferred.owl"
     fi
 
     # Generate renamed ontology
-    if $remake || [ ! -f "$d/emmo-renamed.owl" ]; then
-        echo "Generate renamed ontology"
-        ontoconvert "$d/emmo-inferred.owl" "$d/emmo-renamed.owl" \
-                    -s -a -R -b http://emmo.info/emmo-renamed || true
-    fi
-    if $remake || [ ! -f "$d/emmo-renamed.ttl" ]; then
-        ontoconvert "$d/emmo-inferred.owl" "$d/emmo-renamed.ttl" \
-                    -s -a -R -b http://emmo.info/emmo-renamed || true
-    fi
+    #if $remake || [ ! -f "$d/emmo-renamed.owl" ]; then
+    #    echo "Generate renamed ontology"
+    #    ontoconvert "$d/emmo-inferred.ttl" "$d/emmo-renamed.owl" \
+    #                -w -R -b http://emmo.info/emmo-renamed || true
+    #fi
+    #if $remake || [ ! -f "$d/emmo-renamed.ttl" ]; then
+    #    ontoconvert "$d/emmo-inferred.ttl" "$d/emmo-renamed.ttl" \
+    #                -w -R -b http://emmo.info/emmo-renamed || true
+    #fi
 
     # Generate documentation
     if $remake || [ ! -f "$d/emmo.html" ]; then
         echo "Generate documentation"
-        "$scriptsdir/makedoc.sh" "$d/emmo-inferred.owl" $version "$d" \
+        "$scriptsdir/makedoc.sh" "$d/emmo-inferred.ttl" $version "$d" \
             || true
     fi
 
-    # Create symlinks
+    # Create stable versions
     cd "$pagesdir"
-    if [ ! -z "$name" ]; then
-        rm -f $name
-        ln -sf versions/$version $name
+    if [ "$name" = "stable" ]; then
+        cp $d/*.ttl $d/*.owl .
     fi
+
 done < "$ghdir/versions.txt"
 
 
@@ -130,5 +130,5 @@ if [ -d "$tmpdir" ]; then
 fi
 
 
-# Make sure that we exit with non-zero
+# Make sure that we exit with zero on success
 exit 0
diff --git a/.github/versions.txt b/.github/versions.txt
@@ -1,5 +1,5 @@
 1.0.0-beta5    development
-1.0.0-beta4
+1.0.0-beta4    stable
 1.0.0-beta3
 1.0.0-beta2
 1.0.0-beta

diff --git a/.github/workflows/ci_emmocheck.yml b/.github/workflows/ci_emmocheck.yml
@@ -4,24 +4,24 @@ on: [push]
 jobs:
 
   build:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     strategy:
       max-parallel: 1
       matrix:
-        python-version: [3.7]
+        python-version: [3.11]
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install EMMO-python
+    - name: Install EMMOntoPy
       run: |
         pip install --upgrade pip
-        pip install EMMO
+        pip install EMMOntoPy
 
     - name: Check EMMO
       run: |

diff --git a/.github/workflows/ci_redirectioncheck.yml b/.github/workflows/ci_redirectioncheck.yml
@@ -0,0 +1,24 @@
+name: Check redirections
+on: [push]
+
+jobs:
+
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Setup Python 3.11
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.11
+
+    - name: Install EMMOntoPy
+      run: |
+        pip install --upgrade pip
+        pip install EMMOntoPy
+
+    - name: Check redirections
+      run: |
+        redirectioncheck .github/expected_redirections.yaml
diff --git a/.github/workflows/update_pages.yml b/.github/workflows/update_pages.yml
@@ -6,24 +6,29 @@ on:
       - '[0-9]+.[0-9]+.[0-9]+'
       - '[0-9]+.[0-9]+.[0-9]+-*'
       - update_pages
+      - fix-github-workflow
 
 jobs:
 
   build:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Setup git identity
       run: |
         git config --global user.email "emmo.github.action@github.com"
         git config --global user.name "EMMO GitHub Action"
 
-    - name: Setup Python 3.7
-      uses: actions/setup-python@v1
+    - name: Setup Python 3.11
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.7
+        python-version: 3.11
+
+    - name: Debug info
+      run: |
+        echo "GITHUB_REF_NAME=${GITHUB_REF_NAME}"
 
     - name: Install EMMO-python
       run: |
@@ -44,7 +49,7 @@ jobs:
         pip install semver
 
     - name: Checkout GitHub Pages for EMMO-repo
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         repository: emmo-repo/emmo-repo.github.io
         path: ".github/pages"

diff --git a/doc/emmodoc/classes.md b/doc/emmodoc/classes.md
@@ -74,7 +74,7 @@ branch of mereotopology.
 
 
 
-%BRANCHDOC PhysicalDimension     rankdir=RL
+%% %BRANCHDOC PhysicalDimension     rankdir=RL
 %BRANCHDOC PhysicalQuantity
 %BRANCHDOC StandardizedPhysicalQuantity
 %BRANCHDOC CategorizedPhysicalQuantity
@@ -92,7 +92,7 @@ branch of mereotopology.
 %BRANCHDOC Process
 
 
-%BRANCHDOC Physicalistic
+%% %BRANCHDOC Physicalistic
 %BRANCHDOC ElementaryParticle
 %BRANCHDOC Matter
 %BRANCHDOC Fluid