Merge branch '1.0.0-rc3'

emmo-repo · Dec 19, 2024 · 788b567 · 788b567
2 parents 42b67bc + e5e09d2
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diff --git a/.github/expected_redirections.yaml b/.github/expected_redirections.yaml
@@ -9,6 +9,26 @@
 ---
 redirections:
 
+
+  # CHAMEO
+  https://w3id.org/emmo/domain/characterisation-methodology/chameo:             https://emmo-repo.github.io/domain-characterisation-methodology/chameo.ttl
+  https://w3id.org/emmo/domain/characterisation-methodology/chameo#:            https://emmo-repo.github.io/domain-characterisation-methodology/chameo.ttl
+  https://w3id.org/emmo/domain/characterisation-methodology/chameo/inferred:    https://emmo-repo.github.io/domain-characterisation-methodology/chameo-inferred.ttl
+  https://w3id.org/emmo/domain/characterisation-methodology/chameo/turtle:      https://emmo-repo.github.io/domain-characterisation-methodology/chameo.ttl
+  #https://w3id.org/emmo/domain/characterisation-methodology/chameo/context:     https://emmo-repo.github.io/domain-characterisation-methodology/context/chameo.json
+  #https://w3id.org/emmo/domain/characterisation-methodology/chameo/context/ch:  https://emmo-repo.github.io/domain-characterisation-methodology/context/ch.json
+
+  #https://w3id.org/emmo/domain/characterisation-methodology/chameo/:            https://raw.githubusercontent.com/emmo-repo/domain-characterisation-methodology/master/chameo.ttl
+  https://w3id.org/emmo/domain/characterisation-methodology/chameo/latest:      https://raw.githubusercontent.com/emmo-repo/domain-characterisation-methodology/master/chameo.ttl
+  https://w3id.org/emmo/domain/characterisation-methodology/chameo/latest/:     https://raw.githubusercontent.com/emmo-repo/domain-characterisation-methodology/master/chameo.ttl
+  https://w3id.org/emmo/domain/characterisation-methodology/chameo/source:      https://raw.githubusercontent.com/emmo-repo/domain-characterisation-methodology/master/chameo.ttl
+  https://w3id.org/emmo/domain/characterisation-methodology/chameo/source/:     https://raw.githubusercontent.com/emmo-repo/domain-characterisation-methodology/master/chameo.ttl
+
+  #https://w3id.org/emmo/domain/characterisation-methodology/chameo/1.0.0-beta3: https://emmo-repo.github.io/domain-characterisation-methodology/versions/1.0.0-beta3/chameo.ttl
+
+  https://w3id.org/emmo/domain/characterisation-methodology/chameo/1.0.0-beta3/source:  https://raw.githubusercontent.com/emmo-repo/domain-characterisation-methodology/1.0.0-beta3/chameo.ttl
+
+
   # EMMO
   https://w3id.org/emmo#fragment:                       https://emmo-repo.github.io/emmo.ttl#fragment  # ttl file because tests are not from a browser
 

diff --git a/.github/scripts/makedoc.sh b/.github/scripts/makedoc.sh
@@ -19,9 +19,19 @@ outdir=$3
 [ $# -ne 3 ] && echo "Usage: makedoc.sh inferred version outdir" && exit 1
 
 set -x
-cd "$rootdir/doc/emmodoc"
-ontodoc --template=emmo.md --format=html -p variable=version:$version \
-        "$inferred" "$outdir/emmo.html"
 
-ontodoc --template=emmo.md -p variable=version:$version \
-        "$inferred" "$outdir/emmo.pdf"
+tmpdir=/tmp
+
+
+mkdir -p $tmpdir
+ontodoc --iri-regex=https://w3id.org/emmo --imported emmo-full.ttl "${tmpdir}/emmo.rst"
+
+mkdir -p public
+sphinx-build "${tmpdir}/" "${outdir}/"
+
+#cd "$rootdir/doc/emmodoc"
+#ontodoc --template=emmo.md --format=html -p variable=version:$version \
+#        "$inferred" "$outdir/emmo.html"
+#
+#ontodoc --template=emmo.md -p variable=version:$version \
+#        "$inferred" "$outdir/emmo.pdf"
diff --git a/.github/versions.txt b/.github/versions.txt
@@ -1,8 +1,10 @@
-1.0.0-rc1      development
+1.0.0-rc3      development
+1.0.0-rc2      stable
+1.0.0-rc1
 1.0.0-beta7
 1.0.0-beta6
 1.0.0-beta5
-1.0.0-beta4    stable
+1.0.0-beta4
 1.0.0-beta3
 1.0.0-beta2
 1.0.0-beta

diff --git a/.github/workflows/cd_update_pages.yml b/.github/workflows/cd_update_pages.yml
@@ -42,8 +42,9 @@ jobs:
       run: |
         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@master
-        #pip install sphinx EMMOntoPy
+        #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: |
@@ -56,12 +57,15 @@ jobs:
         ontoconvert -sawe --base-iri="https://w3id.org/emmo#" --iri=https://w3id.org/emmo emmo-full.ttl public/emmo-full.ttl
         #ontoconvert --reasoner=Pellet public/emmo.ttl public/emmo-inferred.ttl
         #ontoconvert --reasoner=Pellet public/emmo-full.ttl public/emmo-full-inferred.ttl
-        bin/robot reason --reasoner ELK --input public/emmo.ttl --output public/emmo-inferred.ttl
-        bin/robot reason --reasoner ELK --input public/emmo-full.ttl --output public/emmo-full-inferred.ttl
+        #bin/robot reason --reasoner ELK --input public/emmo.ttl --output public/emmo-inferred.ttl
+        #bin/robot reason --reasoner ELK --input public/emmo-full.ttl --output public/emmo-full-inferred.ttl
+        bin/robot reason --reasoner HermiT --input public/emmo.ttl --output public/emmo-inferred.ttl
+        bin/robot reason --reasoner JFact --input public/emmo-full.ttl --output public/emmo-full-inferred.ttl
         ontoconvert public/emmo.ttl public/emmo.owl
         ontoconvert public/emmo-full.ttl public/emmo-full.owl
         ontoconvert public/emmo-inferred.ttl public/emmo-inferred.owl
         ontoconvert public/emmo-full-inferred.ttl public/emmo-full-inferred.owl
+        ontoconvert --rename-iris -- public/emmo.ttl public/emmo-for-humans.ttl
 
     - name: Generate html documentation (based on emmo-full)
       run: |

diff --git a/.github/workflows/ci_emmocheck.yml b/.github/workflows/ci_emmocheck.yml
@@ -4,7 +4,7 @@ on: [push]
 jobs:
 
   build:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     strategy:
       max-parallel: 1
       matrix:
@@ -21,7 +21,8 @@ jobs:
     - name: Install EMMOntoPy
       run: |
         pip install --upgrade pip
-        pip install EMMOntoPy
+        #pip install EMMOntoPy
+        pip install git+https://github.com/emmo-repo/EMMOntoPy.git@update-emmocheck2
 
     - name: Check EMMO
       run: |

diff --git a/README.md b/README.md
@@ -125,14 +125,14 @@ The reference ontologies are intended to be used by domain ontologies and import
 
 | Reference ontology | IRI                                                                                                                                               |
 | ------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------- |
-| Materials          | [https://w3id.org/emmo/multiperspective/materials](https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-rc1/multiperspective/materials.ttl)   |
-| Math               | [https://w3id.org/emmo/multiperspective/math](https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-rc1/multiperspective/math.ttl)             |
-| Models             | [https://w3id.org/emmo/multiperspective/models](https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-rc1/multiperspective/models.ttl)         |
-| Properties         | [https://w3id.org/emmo/multiperspective/properties](https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-rc1/multiperspective/properties.ttl) |
-| Metrology          | [https://w3id.org/emmo/multiperspective/metrology](https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-rc1/multiperspective/metrology.ttl)   |
-| Isq                | [https://w3id.org/emmo/multiperspective/isq](https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-rc1/multiperspective/isq.ttl)               |
-| Siunits            | [https://w3id.org/emmo/domain/siunits](https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-rc1/domain/siunits.ttl)                           |
-| Chemistry          | [https://w3id.org/emmo/multiperspective/chemistry](https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-rc1/multiperspective/chemistry.ttl)   |
+| Materials          | [https://w3id.org/emmo/reference/materials](https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-rc3/reference/materials.ttl)   |
+| Math               | [https://w3id.org/emmo/reference/math](https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-rc3/reference/math.ttl)             |
+| Models             | [https://w3id.org/emmo/reference/models](https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-rc3/reference/models.ttl)         |
+| Properties         | [https://w3id.org/emmo/disciplines/properties](https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-rc3/disciplines/properties.ttl) |
+| Metrology          | [https://w3id.org/emmo/reference/metrology](https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-rc3/reference/metrology.ttl)   |
+| Isq                | [https://w3id.org/emmo/reference/isq](https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-rc3/reference/isq.ttl)               |
+| Siunits            | [https://w3id.org/emmo/domain/siunits](https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-rc3/domain/siunits.ttl)                           |
+| Chemistry          | [https://w3id.org/emmo/reference/chemistry](https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-rc3/reference/chemistry.ttl)   |
 
 
 ### Domain Ontologies
@@ -199,7 +199,7 @@ Protégé will automatically download all the necessary dependencies.
 
 The EMMO hierarchy will be visible only after reasoning inference: use *ctrl-R* to start the reasoner and under the *Entities* tab, select the *Classes* subtab and *Inferred* in the scroll button.
 
-From EMMO 1.0.0-rc1 it is recommended to use HermiT as reasoner (distributed by default with Protege).
+From EMMO 1.0.0-rc3 it is recommended to use HermiT as reasoner (distributed by default with Protege).
 For earlier EMMO versions is FaCT++ the recommended reasoner.
 You can select it through the menu *Reasoner*.
 An instruction for how to install the FaCT++ plugin on Protege 5.5.0 on Windows can be found in the [doc subdirectory](doc/installing_factplusplus.md).