Merge pull request #61 from dice-group/develop

New Release 1.2.1
dice-group · Aug 22, 2024 · 3f6f75e · 3f6f75e
2 parents f988897 + e3c2663
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diff --git a/.coveragerc b/.coveragerc
@@ -0,0 +1,18 @@
+[run]
+omit =
+    tests/*
+
+[report]
+exclude_lines =
+    pragma: no cover
+    def __repr__
+    if self.debug:
+    if settings.DEBUG
+    raise AssertionError
+    raise NotImplementedError
+    if 0:
+    if __name__ == .__main__.:
+    if TYPE_CHECKING:
+    class .*\bProtocol\):
+    @(abc\.)?abstractmethod
+    pass
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -24,3 +24,9 @@ jobs:
           wget https://files.dice-research.org/projects/Ontolearn/KGs.zip
           unzip KGs.zip
           python -m pytest -p no:warnings -x
+
+      - name: Coverage report
+        run: |
+          pip install coverage
+          coverage run -m pytest
+          coverage report -m
diff --git a/README.md b/README.md
@@ -1,4 +1,9 @@
 # OWLAPY
+[![Coverage](https://img.shields.io/badge/coverage-78%25-green)](https://dice-group.github.io/owlapy/usage/further_resources.html#coverage-report)
+[![Pypi](https://img.shields.io/badge/pypi-1.2.0-blue)](https://pypi.org/project/owlapy/1.2.0/)
+[![Docs](https://img.shields.io/badge/documentation-1.2.0-yellow)](https://dice-group.github.io/owlapy/usage/main.html)
+
+![OWLAPY](docs/_static/images/owlapy_logo.png)
 
 OWLAPY is a Python Framework for creating and manipulating OWL Ontologies.
 
@@ -17,10 +22,17 @@ pip3 install owlapy
 ```
 
 
+```shell
+# To download RDF knowledge graphs
+wget https://files.dice-research.org/projects/Ontolearn/KGs.zip -O ./KGs.zip && unzip KGs.zip
+pytest -p no:warnings -x # Running 103 tests takes ~ 30 mins
+```
+
 ## Usage
 
-In this example we start with a simple atomic class expression and move to some more complex 
-ones and finally render and print the last of them in description logics syntax.
+
+### Creating OWL Class Expressions
+<details><summary> Click me! </summary>
 
 ```python
 from owlapy.class_expression import OWLClass, OWLObjectIntersectionOf, OWLObjectSomeValuesFrom
@@ -29,17 +41,13 @@ from owlapy import owl_expression_to_sparql, owl_expression_to_dl
 
 # Create the male class
 male = OWLClass("http://example.com/society#male")
-
 # Create an object property using the iri as a string for 'hasChild' property.
 hasChild = OWLObjectProperty("http://example.com/society#hasChild")
-
 # Create an existential restrictions
 hasChild_male = OWLObjectSomeValuesFrom(hasChild, male)
-
 # Let's make it more complex by intersecting with another class
 teacher = OWLClass("http://example.com/society#teacher")
 teacher_that_hasChild_male = OWLObjectIntersectionOf([hasChild_male, teacher])
-
 # You can render and print owl class expressions in description logics syntax (and vice-versa)
 print(owl_expression_to_dl(teacher_that_hasChild_male))
 # (∃ hasChild.male) ⊓ teacher
@@ -57,7 +65,56 @@ class. In the above examples we have introduced 3 types of class expressions:
 Like we showed in this example, you can create all kinds of class expressions using the 
 OWL objects in [owlapy api](https://dice-group.github.io/owlapy/autoapi/owlapy/index.html).
 
-Check also the [examples](https://github.com/dice-group/owlapy/tree/develop/examples) folder.
+</details>
+
+### Logical Inference
+
+<details><summary> Click me! </summary>
+
+```python
+from owlapy.owl_ontology_manager import OntologyManager
+from owlapy.owlapi_adaptor import OWLAPIAdaptor
+
+ontology_path = "KGs/Family/family-benchmark_rich_background.owl"
+# Available OWL Reasoners: 'HermiT', 'Pellet', 'JFact', 'Openllet'
+owlapi_adaptor = OWLAPIAdaptor(path=ontology_path, name_reasoner="Pellet")
+onto = OntologyManager().load_ontology(ontology_path)
+# Iterate over defined owl Classes in the signature
+for i in onto.classes_in_signature():
+    # Performing type inference with Pellet
+    instances=owlapi_adaptor.instances(i,direct=False)
+    print(f"Class:{i}\t Num instances:{len(instances)}")
+owlapi_adaptor.stopJVM()
+```
+
+</details>
+
+### Ontology Enrichment
+
+<details><summary> Click me! </summary>
+
+An Ontology can be enriched by inferring many different axioms.
+```python
+from owlapy.owlapi_adaptor import OWLAPIAdaptor
+
+adaptor = OWLAPIAdaptor(path="KGs/Family/family-benchmark_rich_background.owl", name_reasoner="Pellet")
+# Infer missing class assertions
+adaptor.infer_axioms_and_save(output_path="KGs/Family/inferred_family-benchmark_rich_background.ttl",
+                       output_format="ttl",
+                       inference_types=[
+                           "InferredClassAssertionAxiomGenerator",
+                           "InferredEquivalentClassAxiomGenerator",
+                           "InferredDisjointClassesAxiomGenerator",
+                                        "InferredSubClassAxiomGenerator",
+                                        "InferredInverseObjectPropertiesAxiomGenerator",
+                                        "InferredEquivalentClassAxiomGenerator"])
+adaptor.stopJVM()
+```
+
+</details>
+
+
+Check also the [examples](https://github.com/dice-group/owlapy/tree/develop/examples) and [tests](https://github.com/dice-group/owlapy/tree/develop/tests) folders.
 
 ## How to cite
 Currently, we are working on our manuscript describing our framework.
diff --git a/docs/_static/images/favicon.ico b/docs/_static/images/favicon.ico
diff --git a/docs/_static/images/owlapy_logo.png b/docs/_static/images/owlapy_logo.png
diff --git a/docs/conf.py b/docs/conf.py
@@ -13,7 +13,7 @@
 
 project = 'OWLAPY'
 author = 'Ontolearn Team'
-release = '1.1.1'
+release = '1.2.0'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
@@ -66,6 +66,12 @@
 
 html_static_path = ['_static']
 
+html_logo = '_static/images/owlapy_logo.png'
+
+html_favicon = '_static/images/favicon.ico'
+
+html_extra_path = ["googlec4c425077889c69c.html"]
+
 if stanford_theme_mod:
     html_theme = 'sphinx_rtd_theme'
 

diff --git a/docs/googlec4c425077889c69c.html b/docs/googlec4c425077889c69c.html
@@ -0,0 +1 @@
+google-site-verification: googlec4c425077889c69c.html
diff --git a/docs/index.rst b/docs/index.rst
@@ -14,6 +14,6 @@ Welcome to OWLAPY!
    usage/usage_examples
    usage/ontologies
    usage/reasoner
-   usage/reasoning_details
    usage/owlapi_adaptor
+   usage/further_resources
    autoapi/owlapy/index
diff --git a/docs/usage/further_resources.md b/docs/usage/further_resources.md
@@ -0,0 +1,59 @@
+# Further Resources
+
+Currently, we are working on our manuscript describing our framework. 
+If you want to attribute our library, please use our 
+[GitHub page](https://github.com/dice-group/owlapy) for reference.
+
+## More Inside the Project
+
+Examples and test cases provide a good starting point to get to know
+the project better. Find them in the folders 
+[examples](https://github.com/dice-group/owlapy/tree/develop/examples) and [tests](https://github.com/dice-group/owlapy/tree/develop/tests).
+
+## Contribution
+
+Feel free to create a pull request and we will take a look on it. 
+Your commitment is well appreciated!
+
+## Questions
+
+In case you have any question, please contact: `caglardemir8@gmail.com`
+or open an issue on our [GitHub issues page](https://github.com/dice-group/owlapy/issues).
+
+## Coverage Report
+The coverage report is generated using [coverage.py](https://coverage.readthedocs.io/en/7.6.1/).
+
+```
+Name                                                 Stmts   Miss  Cover   Missing
+----------------------------------------------------------------------------------
+owlapy/__init__.py                                       4      0   100%
+owlapy/class_expression/__init__.py                      8      0   100%
+owlapy/class_expression/class_expression.py             34      2    94%   58, 62
+owlapy/class_expression/nary_boolean_expression.py      24      0   100%
+owlapy/class_expression/owl_class.py                    33      1    97%   44
+owlapy/class_expression/restriction.py                 313     26    92%   41, 49, 68, 71, 89, 170, 245-246, 302, 305, 335, 340, 343, 426, 451, 499, 502, 579-580, 616, 659, 662, 700, 703, 751, 823
+owlapy/converter.py                                    397    189    52%   52-68, 75-76, 79, 82, 152, 157, 169, 176, 184, 246-257, 264-282, 294, 304-307, 313-359, 366-387, 394-401, 417-420, 431, 451, 460-481, 489-491, 498-511, 515-521, 525-548, 552-555, 559-560, 564-576, 580-587, 591-592, 620, 624-628
+owlapy/iri.py                                           79      7    91%   54, 69, 82, 97, 128, 133, 150
+owlapy/meta_classes.py                                  11      0   100%
+owlapy/namespaces.py                                    27      3    89%   36, 40, 43
+owlapy/owl_annotation.py                                17      4    76%   17, 25, 43, 51
+owlapy/owl_axiom.py                                    518    157    70%   36, 39, 42, 45, 59, 111-113, 116, 136-138, 141, 144, 147-150, 153, 182-184, 187, 190, 193, 196-200, 203, 253-256, 259-261, 264, 288, 291, 294, 332-335, 338-340, 343, 398-401, 404-406, 409, 533-536, 539, 561-563, 566, 569, 572, 575, 578-581, 584, 620-623, 626, 645-648, 652, 656, 674-675, 683, 692, 695-697, 700, 711, 733-737, 745, 753, 761, 764-766, 769, 786-788, 791, 794, 797-800, 803, 822-824, 827, 830, 833-836, 839, 858-860, 863, 866, 869-872, 875, 905-908, 911, 982-985, 988, 1018, 1044, 1071-1073, 1076, 1091, 1103, 1116, 1129, 1142, 1157, 1172, 1185-1187, 1190, 1208, 1227-1230, 1233, 1254-1257, 1260
+owlapy/owl_data_ranges.py                               40      1    98%   46
+owlapy/owl_datatype.py                                  20      2    90%   33-34
+owlapy/owl_individual.py                                20      1    95%   37
+owlapy/owl_literal.py                                  286     73    74%   49, 77, 86, 90, 99, 103, 112, 116, 125, 129, 138, 142, 151, 155, 164, 169, 173, 203, 208, 217, 221, 244, 247-249, 252, 258, 262, 288, 293, 302, 306, 311, 323, 329, 332-334, 337, 340, 346, 350, 355, 373, 376-378, 381, 387, 391, 415, 418-420, 423, 429, 433, 454, 459, 462-464, 467, 473, 477, 489-491, 494, 497-499, 502
+owlapy/owl_object.py                                    27      4    85%   24, 79-81
+owlapy/owl_ontology.py                                 391     40    90%   86, 97-100, 103, 109-111, 249, 292-295, 304, 312, 329, 341, 345, 358, 371, 376, 379-381, 384, 423, 433, 449-450, 473-474, 553-554, 595, 599, 603, 629, 736, 742, 750
+owlapy/owl_ontology_manager.py                         568    167    71%   48, 140, 151, 155, 168-169, 177, 200, 208-211, 312-318, 341-350, 355-376, 396, 466, 469, 474-496, 501-511, 521-527, 539, 542-543, 583, 588-593, 603, 608, 625, 634-645, 650-665, 676, 681, 691, 703, 707, 743, 749, 760, 766, 771-795, 800-807, 825-831, 850, 853, 859-862, 888
+owlapy/owl_property.py                                  69     11    84%   17, 24, 32, 40, 67, 76, 126, 158, 162, 174, 193
+owlapy/owl_reasoner.py                                 841    175    79%   452-455, 572, 584-586, 591-597, 604, 653-659, 665-669, 727-734, 760, 795-799, 825-828, 856-858, 860-862, 871, 884-886, 888-890, 897, 902-904, 924, 928-929, 942-944, 965, 1010-1012, 1113, 1121, 1124, 1127, 1130, 1133, 1136, 1139, 1142, 1145, 1160-1162, 1168, 1172, 1175, 1178, 1181, 1184, 1187, 1193, 1196, 1210, 1240-1243, 1251-1290, 1305, 1318-1328, 1353-1356, 1372, 1386, 1456-1460, 1488, 1498-1502, 1510-1514, 1555-1561, 1573, 1632, 1635, 1638, 1641, 1644, 1647, 1650, 1653, 1657, 1661, 1665, 1668, 1671, 1674, 1677, 1680, 1683, 1687, 1691, 1694, 1697
+owlapy/owlapi_adaptor.py                               130     65    50%   18, 74-76, 91-96, 110-115, 151-152, 164-165, 179-180, 195-196, 214, 232, 251, 271, 287, 305, 320, 333, 346, 361, 376, 390, 404, 419, 434, 450, 454-483, 511
+owlapy/owlapi_mapper.py                                103     14    86%   35, 51, 72, 76, 80, 84, 88, 133-136, 141, 145, 149
+owlapy/parser.py                                       371     16    96%   316, 327, 400-401, 416, 577, 618, 656, 667, 721, 723, 751-752, 763, 779-780
+owlapy/providers.py                                     38      3    92%   41, 54, 56
+owlapy/render.py                                       290     46    84%   79-114, 143-158, 176, 180, 186, 206, 222, 231, 236, 241, 375, 379, 386, 405, 421, 430, 435, 440
+owlapy/utils.py                                        766    227    70%   164, 168, 172, 178, 184-188, 192-196, 200, 204, 208, 214, 218, 222, 226, 230, 236, 242, 248, 252, 256, 260, 264-267, 271-274, 278, 285, 300-302, 305-314, 317, 320, 323, 326, 329, 333-339, 343, 354, 358, 362, 366, 370, 374-378, 382-386, 390-394, 398-402, 406, 410, 414-419, 423-428, 432-437, 441, 445, 449-453, 457-461, 465-469, 473-477, 481-485, 489, 493-497, 501, 505-510, 514-519, 523-528, 532, 536-540, 545, 554, 558, 562, 566, 570, 574, 578, 582-587, 591-597, 601, 605, 609, 614, 619, 624, 628, 632, 636, 640, 644-647, 651-654, 658, 662, 666, 671, 676, 681, 685, 736, 740, 746, 748, 751, 753, 796, 852, 866-868, 877, 919-920, 940, 1039, 1044, 1049, 1071, 1075, 1083, 1087, 1092, 1164-1182, 1195-1197, 1202-1206
+owlapy/vocab.py                                         92      4    96%   32, 35, 113-114
+----------------------------------------------------------------------------------
+TOTAL                                                 5517   1238    78%
+```
diff --git a/docs/usage/main.md b/docs/usage/main.md
@@ -1,6 +1,6 @@
 # About owlapy
 
-**Version:** owlapy 1.1.1
+**Version:** owlapy 1.2.0
 
 **GitHub repository:** [https://github.com/dice-group/owlapy](https://github.com/dice-group/owlapy)
 

diff --git a/docs/usage/ontologies.md b/docs/usage/ontologies.md
@@ -202,10 +202,10 @@ When an _OWLOntologyManager_ object is created, a new world is also created as a
 By calling the method `load_ontology(iri)` the ontology is loaded to this world. 
 
 It possible to create several isolated “worlds”, sometimes
-called “universe of speech”. This makes it possible in particular to load
+called “universe of speech”. This makes it possible, in particular, to load
 the same ontology several times, independently, that is to say, without
-the modifications made on one copy affecting the other copy. Sometimes the need to [isolate an ontology](reasoning_details.md#isolated-world) 
-arise. What that means is that you can have multiple reference of the same ontology in different
+the modifications made on one copy affecting the other copy. Sometimes the need to isolate 
+an ontology arise. What that means is that you can have multiple reference of the same ontology in different
 worlds.
 
 -------------------------------------------------------------------------------------

diff --git a/docs/usage/owlapi_adaptor.md b/docs/usage/owlapi_adaptor.md
@@ -48,6 +48,10 @@ Isn't that awesome!
 `OWLAPIAdaptor` uses HermiT reasoner by default. You can choose between:
 "HermiT", "Pellet", "JFact" and "Openllet".
 
+You can use the reasoning method directly from the adaptor but 
+for classes that require an [OWLReasoner](owlapi.owl_reasoner.OWLReasoner)
+you can use [SyncReasoner](https://dice-group.github.io/owlapy/autoapi/owlapy/owl_reasoner/index.html#owlapy.owl_reasoner.SyncReasoner).
+
 _**owlapi version**: 5.1.9_
 
 ## Examples