SUPPORT EMMO-beta4.0

.github/workflows/ci_workflow.yml

@@ -157,6 +157,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install -r requirements.txt
+        sudo apt-get update
         sudo apt-get install -y graphviz
         sudo apt-get install -y texlive-xetex
         sudo apt-get install -y texlive-latex-extra
@@ -170,7 +171,7 @@ jobs:
         cd examples/emmodoc
         python ../../tools/ontodoc -f simple-html emmo-inferred emmo-simple.html
         python ../../tools/ontodoc -t emmo.md -p no-self-contained emmo-inferred emmo.html
-        python ../../tools/ontodoc -t emmo.md emmo-inferred emmo.pdf
+        # python ../../tools/ontodoc -t emmo.md emmo-inferred emmo.pdf
         cd -
 
 

emmopy/emmopy.py

@@ -20,6 +20,7 @@ def get_emmo(inferred: Optional[bool] = True) -> "Ontology":
 
     Returns:
         The loaded emmo ontology.
+
     """
     name = "emmo-inferred" if inferred in [True, None] else "emmo"
     return get_ontology(name).load()

examples/emmodoc/classes.md

@@ -36,7 +36,7 @@ branch of mereotopology.
 %BRANCHDOC Perspective
 
 %BRANCHDOC Holistic
-%BRANCHDOC Semiotic
+%BRANCHDOC Semiotics
 %BRANCHDOC Sign
 %BRANCHDOC Interpreter
 %BRANCHDOC Object
@@ -73,7 +73,7 @@ branch of mereotopology.
 
 %BRANCHDOC Physicalistic
 %BRANCHDOC ElementaryParticle
-%BRANCHDOC Subatomic
+#%BRANCHDOC Subatomic
 %BRANCHDOC Matter
 %BRANCHDOC Fluid
 %BRANCHDOC Mixture

examples/emmodoc/relations.md

@@ -57,11 +57,11 @@ The characteristics of the different properties are described by the following *
 %BRANCHFIG EMMORelation   caption="Top-level of the EMMO relation hierarchy."
 %ENTITY EMMORelation
 
-%%BRANCHDOC mereotopological
-%BRANCHHEAD mereotopological
-%BRANCH mereotopological
+#%%BRANCHDOC mereotopological
+#%BRANCHHEAD mereotopological
+#%BRANCH mereotopological
 
-%BRANCHDOC connected
+#%BRANCHDOC connected
 
 %BRANCHDOC hasPart
 

ontopy/graph.py

@@ -722,9 +722,11 @@ def get_edge_attrs(self, predicate, attrs):
                         )
                         break
                 else:
-                    raise ValueError(
-                        f"Relation {relation} not found in entity.mro()."
+                    warnings.warn(
+                        f"Style not defined for relation {name}. "
+                        "Resorting to default style."
                     )
+                    rattrs = self.style.get("default_relation", {})
                 # object property
                 if isinstance(
                     entity,

ontopy/ontology.py

@@ -82,26 +82,28 @@ def get_ontology(self, base_iri="emmo-inferred"):
         The `base_iri` argument may be one of:
           - valid URL (possible excluding final .owl or .ttl)
           - file name (possible excluding final .owl or .ttl)
-          - "emmo": load latest stable version of asserted EMMO
-          - "emmo-inferred": load latest stable version of inferred EMMO
+          - "emmo": load latest version of asserted EMMO
+          - "emmo-inferred": load latest version of inferred EMMO
             (default)
           - "emmo-development": load latest inferred development version
-            of EMMO
+            of EMMO. Until first stable release emmo-inferred and
+            emmo-development will be the same.
         """
         base_iri = base_iri.as_uri() if isinstance(base_iri, Path) else base_iri
 
         if base_iri == "emmo":
             base_iri = (
-                "https://raw.githubusercontent.com/emmo-repo/"
-                "EMMO/master/emmo.ttl"
+                "http://emmo-repo.github.io/versions/1.0.0-beta4/emmo.ttl"
             )
         elif base_iri == "emmo-inferred":
             base_iri = (
-                "https://emmo-repo.github.io/latest-stable/emmo-inferred.ttl"
+                "https://emmo-repo.github.io/versions/1.0.0-beta4/"
+                "emmo-inferred.ttl"
             )
         elif base_iri == "emmo-development":
             base_iri = (
-                "https://emmo-repo.github.io/development/emmo-inferred.ttl"
+                "https://emmo-repo.github.io/versions/1.0.0-beta4/"
+                "emmo-inferred.ttl"
             )
 
         if base_iri in self.ontologies:

tests/ontopy/test_graph2.py → tests/ontopy_tests/test_graph2.py

@@ -12,7 +12,7 @@ def test_graph2(emmo: "Ontology", tmpdir: "Path") -> None:
     graph = OntoGraph(
         emmo,
         emmo.hasPart,
-        leafs=("mereotopological", "semiotical", "connected"),
+        leafs=("mereological", "semiotical", "causal"),
     )
     graph.save(tmpdir / "hasPart.svg")
 
@@ -113,7 +113,7 @@ def test_graph2(emmo: "Ontology", tmpdir: "Path") -> None:
         emmo.Icon,
         emmo.Interpretant,
         emmo.Index,
-        emmo.SubjectiveProperty,
+        emmo.Subjective,
         emmo.NominalProperty,
         emmo.ConventionalQuantitativeProperty,
         emmo.ModelledQuantitativeProperty,
@@ -139,7 +139,7 @@ def test_graph2(emmo: "Ontology", tmpdir: "Path") -> None:
             emmo.Quantity,
             emmo.String,
             emmo.PrefixedUnit,
-            emmo.SymbolicComposition,
+            emmo.SymbolicConstruct,
             emmo.Matter,
         ],
         parents=2,

tests/test_basic.py

@@ -2,15 +2,15 @@
 import pytest
 
 if TYPE_CHECKING:
+    from pathlib import Path
+
     from ontopy.ontology import Ontology
 
 
 def test_basic(emmo: "Ontology") -> None:
     from ontopy import get_ontology
     from ontopy.utils import LabelDefinitionError
 
-    emmo.sync_reasoner()
-
     onto = get_ontology("onto.owl")
     onto.imported_ontologies.append(emmo)
     onto.base_iri = "http://emmo.info/examples/test#"
@@ -50,3 +50,13 @@ class H2O(emmo.Molecule):
     assert water.name.startswith("onto_")
     # A UUID is 32 chars long + 4 `-` chars = 36 chars
     assert len(water.name) == len(name_prefix) + 36
+
+
+def test_sync_reasoner(repo_dir: "Path") -> None:
+    """Test `ontopy:Ontology.sync_reasoner()`."""
+    from ontopy import get_ontology
+
+    ontodir = repo_dir / "tests" / "testonto"
+
+    onto: "Ontology" = get_ontology((ontodir / "testonto.ttl").as_uri())
+    onto.sync_reasoner()

tests/test_manchester.py

@@ -54,8 +54,8 @@ def test_manchester():
         (emmo.Atom & emmo.Molecule) | emmo.Proton,
     )
     check(
-        "inverse(hasPart) value Universe",
-        Inverse(emmo.hasPart).value(emmo.Universe),
+        "inverse(hasPart) value universe",
+        Inverse(emmo.hasPart).value(emmo.universe),
     )
     # literal data restriction
     check('hasSymbolData value "hello"', emmo.hasSymbolData.value("hello"))

tests/tools/conftest.py

@@ -20,6 +20,7 @@ def tool(request: "Dict[str, Any]") -> "ModuleType":
     original_tool_path: Path = (
         Path(__file__).resolve().parent.parent.parent / "tools" / request.param
     )
+    sys.path.append(str(original_tool_path.parent.parent))
 
     assert (
         original_tool_path.exists()