Merge branch 'master' into 406-harmonize-get_descendants-and-get_ance…

…stors

ontopy/graph.py

@@ -678,7 +678,7 @@ def get_node_attrs(self, name, nodeattrs, attrs):
         label = get_label(entity)
         # class
         if isinstance(entity, owlready2.ThingClass):
-            if self.ontology.is_defined(entity):
+            if entity.is_defined:
                 kwargs = self.style.get("defined_class", {})
             else:
                 kwargs = self.style.get("class", {})

ontopy/ontology.py

@@ -1363,7 +1363,17 @@ def is_individual(self, entity):
     # FIXME - deprecate this method as soon the ThingClass property
     #         `defined_class` works correct in Owlready2
     def is_defined(self, entity):
-        """Returns true if the entity is a defined class."""
+        """Returns true if the entity is a defined class.
+
+        Deprecated, use the `is_defined` property of the classes
+        (ThingClass subclasses) instead.
+        """
+        warnings.warn(
+            "This method is deprecated.  Use the `is_defined` property of "
+            "the classes instad.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
         if isinstance(entity, str):
             entity = self.get_by_label(entity)
         return hasattr(entity, "equivalent_to") and bool(entity.equivalent_to)

ontopy/patch.py

@@ -136,13 +136,31 @@ def get_indirect_is_a(self, skip_classes=True):
     return subclass_relations
 
 
+is_defined = property(
+    fget=lambda self: (
+        hasattr(self, "equivalent_to") and bool(self.equivalent_to)
+    ),
+    doc="""Is true if this class is a defined class.
+
+    For a "defined class" both necessary and sufficient conditions for
+    membership in that class are given.  Hence, classes declared with
+    `owl:equivalentTo` are defined classes.
+
+    Note that this method is different from the `defined_class`
+    property provided by Owlready2, who's boolean value is set by the
+    user.
+    """,
+)
+
+
 # Inject methods into ThingClass
 setattr(ThingClass, "__dir__", _dir)
 setattr(ThingClass, "get_preferred_label", get_preferred_label)
 setattr(ThingClass, "get_parents", get_parents)
 setattr(ThingClass, "get_annotations", get_annotations)
 setattr(ThingClass, "disjoint_with", disjoint_with)
 setattr(ThingClass, "get_indirect_is_a", get_indirect_is_a)
+setattr(ThingClass, "is_defined", is_defined)
 
 
 #

requirements_dev.txt

@@ -1,5 +1,5 @@
 pre-commit>=2.21.0,<3; python_version<"3.8"
-pre-commit~=3.2; python_version>="3.8"
+pre-commit~=3.3; python_version>="3.8"
 pylint~=2.17
 pytest~=7.3
 pytest-cov~=4.0

tests/ontopy_tests/test_patch.py

@@ -0,0 +1,61 @@
+"""Tests Owlready2 patches implemented in ontopy/patch.py
+
+Implemented as a script, such that it easy to understand and use for debugging.
+"""
+from ontopy import get_ontology
+
+from owlready2 import owl, Inverse
+
+
+emmo = get_ontology().load()
+
+
+# Test some ThingClass extensions implemented in patch.py
+assert emmo.Atom.get_preferred_label() == "Atom"
+
+assert emmo.Atom.get_parents() == {
+    emmo.CausalSystem,
+    emmo.CompositeParticle,
+    emmo.MolecularEntity,
+}
+
+assert set(emmo.Atom.get_annotations().keys()) == {
+    "prefLabel",
+    "altLabel",
+    "elucidation",
+}
+
+# TODO: Fix disjoint_with().
+# It seems not to take into account disjoint unions.
+# assert set(emmo.Collection.disjoint_with()) == {emmo.Item}
+
+assert set(str(s) for s in emmo.CausalChain.get_indirect_is_a()) == set(
+    str(s)
+    for s in {
+        Inverse(emmo.hasPart).value(emmo.universe),
+        emmo.CausalObject,
+        emmo.Particle,
+        emmo.hasPart.some(emmo.Quantum),
+        emmo.hasTemporalPart.only(emmo.CausalChain | emmo.Quantum),
+        emmo.hasTemporalPart.some(emmo.CausalChain | emmo.Quantum),
+    }
+)
+assert set(
+    str(s) for s in emmo.CausalChain.get_indirect_is_a(skip_classes=False)
+) == set(
+    str(s)
+    for s in {
+        Inverse(emmo.hasPart).value(emmo.universe),
+        emmo.CausalObject,
+        emmo.EMMO,
+        emmo.Item,
+        emmo.Particle,
+        emmo.hasPart.some(emmo.Quantum),
+        emmo.hasTemporalPart.only(emmo.CausalChain | emmo.Quantum),
+        emmo.hasTemporalPart.some(emmo.CausalChain | emmo.Quantum),
+        owl.Thing,
+    }
+)
+
+assert emmo.Atom.is_defined == False
+assert emmo.Holistic.is_defined == True