Fixed generation of documentation and redirectionscheck

emmo-repo · Feb 12, 2024 · 3400287 · 3400287
1 parent 89eb7c7
commit 3400287
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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
@@ -55,9 +55,8 @@ ${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.
+  "Compacted ontology" means that all the top and middle level modules
+  are joint together into a single file with no imports.
 </sup>
 
 </body>

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"
@@ -83,35 +83,35 @@ 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
+        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 "$d/emmo-inferred.owl" "$d/emmo-renamed.ttl" \
-                    -s -a -R -b http://emmo.info/emmo-renamed || true
+        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
 

diff --git a/.github/workflows/ci_redirectioncheck.yml b/.github/workflows/ci_redirectioncheck.yml
@@ -0,0 +1,24 @@
+name: Check conventions
+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/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