Merge pull request #287 from dice-group/general_adjustments

General adjustments

MANIFEST.in

@@ -7,9 +7,5 @@ recursive-include examples *.py
 recursive-include examples *.json
 recursive-include examples *.conf
 recursive-include tests *.py
-include sortedcontainers-stubs/py.typed
-recursive-include sortedcontainers-stubs *.pyi
-include superprop/py.typed
-recursive-include superprop *.pyi
 prune *.egg-info
 prune .tox

README.md

@@ -59,12 +59,13 @@ the learning algorithms. Also in the [tests](https://github.com/dice-group/Ontol
 For more detailed instructions we suggest to follow the [guides](https://ontolearn-docs-dice-group.netlify.app/usage/03_algorithm.html) in the documentation.
 
 Below we give a simple example on using CELOE to learn class expressions for a small dataset.
+
 ```python
 from ontolearn.concept_learner import CELOE
 from ontolearn.model_adapter import ModelAdapter
-from owlapy.model import OWLNamedIndividual, IRI
-from owlapy.namespaces import Namespaces
-from owlapy.render import DLSyntaxObjectRenderer
+from ontolearn.owlapy.model import OWLNamedIndividual, IRI
+from ontolearn.owlapy.namespaces import Namespaces
+from ontolearn.owlapy.render import DLSyntaxObjectRenderer
 from examples.experiments_standard import ClosedWorld_ReasonerFactory
 
 NS = Namespaces('ex', 'http://example.com/father#')

deploy_cl.py

@@ -15,8 +15,8 @@
 from ontolearn.learning_problem import PosNegLPStandard
 from ontolearn.refinement_operators import ModifiedCELOERefinement
 from ontolearn.value_splitter import EntropyValueSplitter, BinningValueSplitter
-from owlapy.model import OWLNamedIndividual, IRI
-from owlapy.render import DLSyntaxObjectRenderer
+from ontolearn.owlapy.model import OWLNamedIndividual, IRI
+from ontolearn.owlapy.render import DLSyntaxObjectRenderer
 
 metrics = {'F1': F1,
            'Accuracy': Accuracy,

docs/usage/01_knowledge_base.md

@@ -68,13 +68,14 @@ before fitting a model.
 It can be done as follows:
 
 <!--pytest-codeblocks:cont-->
+
 ```python
-from owlapy.model import OWLClass
-from owlapy.model import IRI
+from ontolearn.owlapy.model import OWLClass
+from ontolearn.owlapy.model import IRI
 
-iri = IRI('http://example.com/father#', 'Father') 
+iri = IRI('http://example.com/father#', 'Father')
 father_concept = OWLClass(iri)
-concepts_to_ignore = {father_concept} # you can add more than 1
+concepts_to_ignore = {father_concept}  # you can add more than 1
 
 new_kb = kb.ignore_and_copy(ignored_classes=concepts_to_ignore)
 ```

docs/usage/02_learning_problem.md

@@ -33,9 +33,10 @@ describe) are stefan, markus, and martin. And our negative examples
 could write the following Python code:
 
 <!--pytest-codeblocks:cont-->
+
 ```python
-from owlapy.namespaces import Namespaces
-from owlapy.model import OWLNamedIndividual, IRI
+from ontolearn.owlapy.namespaces import Namespaces
+from ontolearn.owlapy.model import OWLNamedIndividual, IRI
 
 NS = Namespaces('ex', 'http://example.com/father#')
 

docs/usage/03_ontologies.md

@@ -13,8 +13,8 @@ To load an ontology as well as to manage it, you will need an [OWLOntologyManage
 To load an ontology, use the following Python code:
 
 ```python
-from owlapy.model import IRI
-from owlapy.owlready2 import OWLOntologyManager_Owlready2
+from ontolearn.owlapy.model import IRI
+from ontolearn.owlapy.owlready2 import OWLOntologyManager_Owlready2
 
 manager = OWLOntologyManager_Owlready2()
 onto = manager.load_ontology(IRI.create("file://KGs/father.owl"))
@@ -70,9 +70,10 @@ Let's suppose you want to add a new class in our example ontology `KGs/father.ow
 to see a description of it). It can be done as follows:
 
 <!--pytest-codeblocks:cont-->
+
 ```python
-from owlapy.model import OWLClass
-from owlapy.model import OWLDeclarationAxiom
+from ontolearn.owlapy.model import OWLClass
+from ontolearn.owlapy.model import OWLDeclarationAxiom
 
 iri = IRI('http://example.com/father#', 'child')
 child_class = OWLClass(iri)
@@ -98,16 +99,17 @@ you can use the class [OWLObjectProperty](owlapy.model.OWLObjectProperty) and fo
 properties you can use the class [OWLDataProperty](owlapy.model.OWLDataProperty).
 
 <!--pytest-codeblocks:cont-->
+
 ```python
-from owlapy.model import OWLObjectProperty
-from owlapy.model import OWLDataProperty
+from ontolearn.owlapy.model import OWLObjectProperty
+from ontolearn.owlapy.model import OWLDataProperty
 
 # adding the object property 'hasParent'
 hasParent_op = OWLObjectProperty(IRI('http://example.com/father#', 'hasParent'))
 hasParent_op_declaration_axiom = OWLDeclarationAxiom(hasParent_op)
 manager.add_axiom(onto, hasParent_op_declaration_axiom)
 
-#adding the data property 'hasAge' 
+# adding the data property 'hasAge' 
 hasAge_dp = OWLDataProperty(IRI('http://example.com/father#', 'hasAge'))
 hasAge_dp_declaration_axiom = OWLDeclarationAxiom(hasAge_dp)
 manager.add_axiom(onto, hasAge_dp_declaration_axiom)
@@ -120,11 +122,12 @@ See the [API documentation](owlapy.model) for more OWL entities that you can add
 To assign a class to a specific individual use the following code:
 
 <!--pytest-codeblocks:cont-->
+
 ```python
-from owlapy.model import OWLClassAssertionAxiom
+from ontolearn.owlapy.model import OWLClassAssertionAxiom
 
 individuals = list(onto.individuals_in_signature())
-heinz = individuals[1] # get the 2nd individual in the list which is 'heinz'
+heinz = individuals[1]  # get the 2nd individual in the list which is 'heinz'
 
 class_assertion_axiom = OWLClassAssertionAxiom(heinz, child_class)
 
@@ -142,9 +145,10 @@ Let's show one more example using a `OWLDataPropertyAssertionAxiom` to assign th
 heinz. 
 
 <!--pytest-codeblocks:cont-->
+
 ```python
-from owlapy.model import OWLLiteral
-from owlapy.model import OWLDataPropertyAssertionAxiom
+from ontolearn.owlapy.model import OWLLiteral
+from ontolearn.owlapy.model import OWLDataPropertyAssertionAxiom
 
 literal_17 = OWLLiteral(17)
 dp_assertion_axiom = OWLDataPropertyAssertionAxiom(heinz, hasAge_dp, literal_17)

docs/usage/04_reasoner.md

@@ -24,9 +24,9 @@ To load any reasoner, use the following code:
 <!--pytest-codeblocks:cont-->
 
 ```python
-from owlapy.owlready2 import OWLReasoner_Owlready2
-from owlapy.owlready2.complex_ce_instances import OWLReasoner_Owlready2_ComplexCEInstances
-from owlapy.fast_instance_checker import OWLReasoner_FastInstanceChecker
+from ontolearn.owlapy.owlready2 import OWLReasoner_Owlready2
+from ontolearn.owlapy.owlready2.complex_ce_instances import OWLReasoner_Owlready2_ComplexCEInstances
+from ontolearn.owlapy.fast_instance_checker import OWLReasoner_FastInstanceChecker
 
 structural_reasoner = OWLReasoner_Owlready2(onto)
 complex_reasoner = OWLReasoner_Owlready2_ComplexCEInstances(onto)
@@ -60,11 +60,13 @@ but a reasoner can give you more than that. You can get the subclasses, supercla
 equivalent classes of a class in the ontology:
 
 <!--pytest-codeblocks:cont-->
+
 ```python
-from owlapy.model import OWLClass
-from owlapy.model import IRI
+from ontolearn.owlapy.model import OWLClass
+from ontolearn.owlapy.model import IRI
+
 namespace = "http://example.com/father#"
-male = OWLClass(IRI(namespace,"male"))
+male = OWLClass(IRI(namespace, "male"))
 
 male_super_classes = fast_instance_checker.super_classes(male)
 male_sub_classes = fast_instance_checker.sub_classes(male)
@@ -87,12 +89,14 @@ upon the class, object property, or data property hierarchy.
 You can get all the types of a certain individual using `types` method:
 
 <!--pytest-codeblocks:cont-->
+
 ```python
-from owlapy.owlready2 import OWLOntologyManager_Owlready2
+from ontolearn.owlapy.owlready2 import OWLOntologyManager_Owlready2
 
 manager = OWLOntologyManager_Owlready2()
 onto = manager.load_ontology(IRI.create("KGs/father.owl"))
-anna = list(onto.individuals_in_signature()).pop() # getting the 1st individual in the list of individuals which is 'anna'
+anna = list(
+    onto.individuals_in_signature()).pop()  # getting the 1st individual in the list of individuals which is 'anna'
 
 anna_types = fast_instance_checker.types(anna)
 ```
@@ -146,10 +150,11 @@ specified individual.
 In the same way as with classes, you can also get the sub object properties or equivalent object properties.
 
 <!--pytest-codeblocks:cont-->
+
 ```python
-from owlapy.model import OWLObjectProperty
+from ontolearn.owlapy.model import OWLObjectProperty
 
-hasChild = OWLObjectProperty(IRI(namespace,"hasChild"))
+hasChild = OWLObjectProperty(IRI(namespace, "hasChild"))
 
 equivalent_to_hasChild = fast_instance_checker.equivalent_object_properties(hasChild)
 hasChild_sub_properties = fast_instance_checker.sub_object_properties(hasChild)

docs/usage/05_concept_learners.md

@@ -137,13 +137,14 @@ each individual (stored as `string`) from the set `positive_examples `
 and `negative_examples` to `OWLNamedIndividual`: 
 
 <!--pytest-codeblocks:cont-->
+
 ```python
     from ontolearn.learning_problem import PosNegLPStandard
-    from owlapy.model import IRI,OWLNamedIndividual
-    
-    typed_pos = set(map(OWLNamedIndividual, map(IRI.create, p)))  
-    typed_neg = set(map(OWLNamedIndividual, map(IRI.create, n)))
-    lp = PosNegLPStandard(pos=typed_pos, neg=typed_neg)
+from ontolearn.owlapy.model import IRI, OWLNamedIndividual
+
+typed_pos = set(map(OWLNamedIndividual, map(IRI.create, p)))
+typed_neg = set(map(OWLNamedIndividual, map(IRI.create, n)))
+lp = PosNegLPStandard(pos=typed_pos, neg=typed_neg)
 ```
 
 To construct an [OWLNamedIndividual](owlapy.model.OWLNamedIndividual) object an [IRI](owlapy.model.IRI) is required as an input. 

docs/usage/09_model_adapter.md

@@ -10,12 +10,11 @@ from ontolearn.concept_learner import CELOE
 from ontolearn.heuristics import CELOEHeuristic
 from ontolearn.metrics import Accuracy
 from ontolearn.model_adapter import ModelAdapter
-from owlapy.model import OWLNamedIndividual, IRI
-from owlapy.namespaces import Namespaces
-from owlapy.owlready2 import OWLOntologyManager_Owlready2
-from owlapy.owlready2.complex_ce_instances import OWLReasoner_Owlready2_ComplexCEInstances
-from owlapy.render import DLSyntaxObjectRenderer
-
+from ontolearn.owlapy.model import OWLNamedIndividual, IRI
+from ontolearn.owlapy.namespaces import Namespaces
+from ontolearn.owlapy.owlready2 import OWLOntologyManager_Owlready2
+from ontolearn.owlapy.owlready2.complex_ce_instances import OWLReasoner_Owlready2_ComplexCEInstances
+from ontolearn.owlapy.render import DLSyntaxObjectRenderer
 
 manager = OWLOntologyManager_Owlready2()
 onto = manager.load_ontology(IRI.create("KGs/father.owl"))
@@ -32,10 +31,10 @@ negative_examples = {OWLNamedIndividual(IRI.create(NS, 'heinz')),
 
 # Only the class of the learning algorithm is specified
 model = ModelAdapter(learner_type=CELOE,
-                     reasoner=complex_ce_reasoner, # (*)
+                     reasoner=complex_ce_reasoner,  # (*)
                      path="KGs/father.owl",
                      quality_type=Accuracy,
-                     heuristic_type=CELOEHeuristic, # (*)
+                     heuristic_type=CELOEHeuristic,  # (*)
                      expansionPenaltyFactor=0.05,
                      startNodeBonus=1.0,
                      nodeRefinementPenalty=0.01,

examples/concept_learning_drill_train.py

@@ -12,16 +12,16 @@
 from ontolearn.concept_learner import Drill
 from ontolearn.metrics import F1
 from ontolearn.heuristics import Reward
-from owlapy.model import OWLOntology, OWLReasoner
+from ontolearn.owlapy.model import OWLOntology, OWLReasoner
 from ontolearn.utils import setup_logging
 
 setup_logging()
 
 
 def ClosedWorld_ReasonerFactory(onto: OWLOntology) -> OWLReasoner:
-    from owlapy.owlready2 import OWLOntology_Owlready2
-    from owlapy.owlready2.complex_ce_instances import OWLReasoner_Owlready2_ComplexCEInstances
-    from owlapy.fast_instance_checker import OWLReasoner_FastInstanceChecker
+    from ontolearn.owlapy.owlready2 import OWLOntology_Owlready2
+    from ontolearn.owlapy.owlready2.complex_ce_instances import OWLReasoner_Owlready2_ComplexCEInstances
+    from ontolearn.owlapy.fast_instance_checker import OWLReasoner_FastInstanceChecker
     assert isinstance(onto, OWLOntology_Owlready2)
     base_reasoner = OWLReasoner_Owlready2_ComplexCEInstances(ontology=onto)
     reasoner = OWLReasoner_FastInstanceChecker(ontology=onto,

examples/concept_learning_with_celoe_heuristic.py

@@ -8,7 +8,7 @@
 from ontolearn.heuristics import CELOEHeuristic
 from ontolearn.learning_problem import PosNegLPStandard
 from ontolearn.metrics import Accuracy
-from owlapy.model import OWLClass, OWLNamedIndividual, IRI
+from ontolearn.owlapy.model import OWLClass, OWLNamedIndividual, IRI
 from ontolearn.refinement_operators import ModifiedCELOERefinement
 from ontolearn.utils import setup_logging
 

examples/concept_learning_with_celoe_heuristic_ma.py

@@ -5,10 +5,10 @@
 from ontolearn.concept_learner import CELOE
 from ontolearn.knowledge_base import KnowledgeBase
 from ontolearn.model_adapter import ModelAdapter
-from owlapy.model import OWLClass, OWLNamedIndividual, IRI
+from ontolearn.owlapy.model import OWLClass, OWLNamedIndividual, IRI
 from ontolearn.utils import setup_logging
-from owlapy.owlready2 import BaseReasoner_Owlready2, OWLOntology_Owlready2
-from owlapy.owlready2.complex_ce_instances import OWLReasoner_Owlready2_ComplexCEInstances
+from ontolearn.owlapy.owlready2 import BaseReasoner_Owlready2, OWLOntology_Owlready2
+from ontolearn.owlapy.owlready2.complex_ce_instances import OWLReasoner_Owlready2_ComplexCEInstances
 from typing import cast
 setup_logging()
 

examples/concept_learning_with_evolearner.py

@@ -4,7 +4,7 @@
 from ontolearn.knowledge_base import KnowledgeBase
 from ontolearn.concept_learner import EvoLearner
 from ontolearn.learning_problem import PosNegLPStandard
-from owlapy.model import OWLClass, OWLNamedIndividual, IRI
+from ontolearn.owlapy.model import OWLClass, OWLNamedIndividual, IRI
 from ontolearn.utils import setup_logging
 
 setup_logging()

examples/concept_learning_with_ocel.py

@@ -5,7 +5,7 @@
 from ontolearn.concept_learner import OCEL
 from ontolearn.learning_problem import PosNegLPStandard
 from ontolearn.utils import setup_logging
-from owlapy.model import OWLClass, IRI, OWLNamedIndividual
+from ontolearn.owlapy.model import OWLClass, IRI, OWLNamedIndividual
 
 setup_logging()
 

examples/example_knowledge_base.py

@@ -1,3 +1,4 @@
+from ontolearn.concept_generator import ConceptGenerator
 from ontolearn.knowledge_base import KnowledgeBase
 import os
 
@@ -8,7 +9,7 @@
 
 kb_path = '../KGs/Family/family-benchmark_rich_background.owl'
 kb = KnowledgeBase(path=kb_path)
-
+generator = ConceptGenerator()
 
 # All concepts.
 for i in kb.get_concepts():
@@ -42,23 +43,23 @@
 print('*' * 100)
 
 
-for concept in kb.most_general_existential_restrictions(domain=kb.thing):
+for concept in kb.most_general_existential_restrictions(domain=generator.thing):
     print(concept)
 
 print('*' * 100)
-for concept in kb.most_general_universal_restrictions(domain=kb.thing):
+for concept in kb.most_general_universal_restrictions(domain=generator.thing):
     print(concept)
 
 print('*' * 100)
-for concept in kb.most_general_existential_restrictions(domain=kb.nothing):
+for concept in kb.most_general_existential_restrictions(domain=generator.nothing):
     print(concept)
 
 print('*' * 100)
-for concept in kb.most_general_universal_restrictions(domain=kb.nothing):
+for concept in kb.most_general_universal_restrictions(domain=generator.nothing):
     print(concept)
 
 print('*' * 100)
 for c in kb.get_concepts():
-    neg_c = kb.negation(c)
-    neg_neg_c = kb.negation(neg_c)
+    neg_c = generator.negation(c)
+    neg_neg_c = generator.negation(neg_c)
     assert neg_neg_c == c

examples/example_reasoner.py

@@ -1,11 +1,9 @@
-from owlapy.model import OWLSubClassOfAxiom, OWLEquivalentClassesAxiom, \
-    OWLEquivalentObjectPropertiesAxiom, OWLObjectPropertyDomainAxiom, OWLDataProperty
-from owlapy.owlready2._base import OWLReasoner_Owlready2, BaseReasoner_Owlready2
-from owlapy.fast_instance_checker import OWLReasoner_FastInstanceChecker
+from ontolearn.owlapy.model import OWLSubClassOfAxiom, OWLEquivalentObjectPropertiesAxiom, OWLObjectPropertyDomainAxiom, OWLDataProperty
+from ontolearn.owlapy.owlready2 import OWLReasoner_Owlready2, BaseReasoner_Owlready2
 from ontolearn.knowledge_base import KnowledgeBase
-from owlapy.model import OWLObjectProperty, IRI, OWLObjectSomeValuesFrom, \
+from ontolearn.owlapy.model import OWLObjectProperty, IRI, OWLObjectSomeValuesFrom, \
     OWLObjectIntersectionOf, OWLClass, OWLNamedIndividual
-from owlapy.owlready2.complex_ce_instances import OWLReasoner_Owlready2_ComplexCEInstances
+from ontolearn.owlapy.owlready2.complex_ce_instances import OWLReasoner_Owlready2_ComplexCEInstances
 
 data_file = '../KGs/test_ontology.owl'
 NS = 'http://www.semanticweb.org/stefan/ontologies/2023/1/untitled-ontology-11#'

examples/experiments_standard.py

@@ -27,7 +27,7 @@
 from ontolearn.metrics import F1
 from ontolearn.refinement_operators import LengthBasedRefinement
 from ontolearn.utils import setup_logging
-from owlapy.model import OWLOntology, OWLReasoner
+from ontolearn.owlapy.model import OWLOntology, OWLReasoner
 
 setup_logging()
 full_computation_time = time.time()
@@ -44,9 +44,9 @@ def sanity_checking_args(args):
 
 
 def ClosedWorld_ReasonerFactory(onto: OWLOntology) -> OWLReasoner:
-    from owlapy.owlready2 import OWLOntology_Owlready2
-    from owlapy.owlready2.complex_ce_instances import OWLReasoner_Owlready2_ComplexCEInstances
-    from owlapy.fast_instance_checker import OWLReasoner_FastInstanceChecker
+    from ontolearn.owlapy.owlready2 import OWLOntology_Owlready2
+    from ontolearn.owlapy.owlready2.complex_ce_instances import OWLReasoner_Owlready2_ComplexCEInstances
+    from ontolearn.owlapy.fast_instance_checker import OWLReasoner_FastInstanceChecker
     assert isinstance(onto, OWLOntology_Owlready2)
     base_reasoner = OWLReasoner_Owlready2_ComplexCEInstances(ontology=onto)
     reasoner = OWLReasoner_FastInstanceChecker(ontology=onto,