Merge branch 'ci/dependabot-updates' into dependabot/pip/ci/dependabo…

…t-updates/mkdocstrings-python-legacy--approx-eq-0.25.1

.pre-commit-config.yaml

@@ -17,7 +17,7 @@ repos:
  args: [--markdown-linebreak-ext=md]
 
 - repo: https://github.com/ambv/black
- rev: 24.3.0
+ rev: 24.4.2
  hooks:
  - id: black
  name: Blacken

ontopy/excelparser.py

@@ -808,7 +808,7 @@ def _add_entities(
  or row["Other annotations"] == "nan"
  ):
  for annotation in row["Other annotations"].split(";"):
- key, value = annotation.split("=")
+ key, value = annotation.split("=", 1)
  entity[key.strip(" ")] = english(value.strip(" "))
 
  remaining_rows.difference_update(added_rows)

ontopy/ontology.py

@@ -871,6 +871,7 @@ def save(
  write_catalog_file=False,
  append_catalog=False,
  catalog_file="catalog-v001.xml",
+ **kwargs,
  ) -> Path:
  """Writes the ontology to file.
 
@@ -915,6 +916,7 @@ def save(
  # pylint: disable=redefined-builtin,too-many-arguments
  # pylint: disable=too-many-statements,too-many-branches
  # pylint: disable=too-many-locals,arguments-renamed,invalid-name
+
  if not _validate_installed_version(
  package="rdflib", min_version="6.0.0"
  ) and format == FMAP.get("ttl", ""):
@@ -940,7 +942,9 @@ def save(
  raise TypeError("`filename` and `format` cannot both be None.")
  else:
  file = filename
- filepath = os.path.join(dir, file)
+ filepath = os.path.join(
+ dir, file if isinstance(file, (str, Path)) else file.name
+ )
  returnpath = filepath
 
  dir = Path(filepath).resolve().parent
@@ -980,6 +984,7 @@ def save(
  recursive=False,
  squash=False,
  write_catalog_file=False,
+ **kwargs,
  )
 
  if write_catalog_file:
@@ -1045,7 +1050,7 @@ def save(
 
  graph.serialize(destination=filepath, format=format)
  elif format in OWLREADY2_FORMATS:
- super().save(file=filepath, format=fmt)
+ super().save(file=filepath, format=fmt, **kwargs)
  else:
  # The try-finally clause is needed for cleanup and because
  # we have to provide delete=False to NamedTemporaryFile
@@ -1056,7 +1061,7 @@ def save(
  suffix=".owl", delete=False
  ) as handle:
  tmpfile = handle.name
- super().save(tmpfile, format="ntriples")
+ super().save(tmpfile, format="ntriples", **kwargs)
  graph = rdflib.Graph()
  graph.parse(tmpfile, format="ntriples")
  graph.namespace_manager.bind(
@@ -1331,12 +1336,46 @@ def sync_reasoner(
 
  Keyword arguments are passed to the underlying owlready2 function.
  """
+ # pylint: disable=too-many-branches
+
+ removed_equivalent = defaultdict(list)
+ removed_subclasses = defaultdict(list)
+
  if reasoner == "FaCT++":
  sync = sync_reasoner_factpp
  elif reasoner == "Pellet":
  sync = owlready2.sync_reasoner_pellet
  elif reasoner == "HermiT":
  sync = owlready2.sync_reasoner_hermit
+
+ # Remove custom data propertyes, otherwise HermiT will crash
+ datatype_iri = "http://www.w3.org/2000/01/rdf-schema#Datatype"
+
+ for cls in self.classes(imported=include_imported):
+ remove_eq = []
+ for i, r in enumerate(cls.equivalent_to):
+ if isinstance(r, owlready2.Restriction):
+ if (
+ hasattr(r.value.__class__, "iri")
+ and r.value.__class__.iri == datatype_iri
+ ):
+ remove_eq.append(i)
+ removed_equivalent[cls].append(r)
+ for i in reversed(remove_eq):
+ del cls.equivalent_to[i]
+
+ remove_subcls = []
+ for i, r in enumerate(cls.is_a):
+ if isinstance(r, owlready2.Restriction):
+ if (
+ hasattr(r.value.__class__, "iri")
+ and r.value.__class__.iri == datatype_iri
+ ):
+ remove_subcls.append(i)
+ removed_subclasses[cls].append(r)
+ for i in reversed(remove_subcls):
+ del cls.is_a[i]
+
  else:
  raise ValueError(
  f"Unknown reasoner '{reasoner}'. Supported reasoners "
@@ -1353,6 +1392,12 @@ def sync_reasoner(
  else:
  sync(self, **kwargs)
 
+ # Restore removed custom data properties
+ for cls, eqs in removed_equivalent.items():
+ cls.extend(eqs)
+ for cls, subcls in removed_subclasses.items():
+ cls.extend(subcls)
+
  def sync_attributes( # pylint: disable=too-many-branches
  self,
  name_policy=None,

tests/test_excelparser/result_ontology/fromexcelonto.ttl

@@ -72,7 +72,7 @@
 
 :EMMO_7c8ba943-15cf-5621-98a3-ed1e7e68fee8 a owl:Class ;
  emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "A special boundary."@en ;
- :EMMO_98871837-aa90-5eef-9a56-926ae8beebbb "\"A text about this type of boundary\""@en ;
+ :EMMO_98871837-aa90-5eef-9a56-926ae8beebbb "\"A text about this type of=boundary\""@en ;
  rdfs:subClassOf :EMMO_1b2bfe71-5da9-5c46-b137-be45c3e3f9c3 ;
  skos:prefLabel "SpecialBoundary"@en .
 

tests/testonto/domainonto.ttl

@@ -43,6 +43,11 @@ emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 a owl:AnnotationProperty ;
  skos:prefLabel "elucidation"@en ;
  rdfs:comment "Short enlightening explanation aimed to facilitate the user in drawing the connection (interpretation) between a OWL entity and the real world object(s) for which it stands."@en .
 
+emmo:EMMO_c7b62dd7_063a_4c2a_8504_42f7264ba83f a owl:AnnotationProperty ;
+ rdfs:subPropertyOf rdfs:comment ;
+ skos:prefLabel "comment"@en ;
+ rdfs:comment "A text that add some information about the entity."@en .
+
 :EMMO_70fe84ff_99b6_4206_a9fc_9a8931836d84 a owl:AnnotationProperty ;
  rdfs:subPropertyOf rdfs:comment ;
  skos:prefLabel "definition"@en ;

tools/ontoconvert

@@ -9,6 +9,9 @@ from rdflib.util import guess_format
 from ontopy import get_ontology
 from ontopy.utils import annotate_source, rename_iris, copy_annotation
 
+import owlready2 # pylint: disable=wrong-import-order
+import owlready2.reasoning # pylint: disable=wrong-import-order
+
 
 def main(argv: list = None):
  """Main run function.
@@ -84,8 +87,10 @@ def main(argv: list = None):
  "http://www.w3.org/2004/02/skos/core#prefLabel"
  "-->http://www.w3.org/2000/01/rdf-schema#label "
  "--copy-annotation=elucidation"
- "-->http://www.w3.org/2000/01/rdf-schema#comment`"
+ "-->http://www.w3.org/2000/01/rdf-schema#comment` "
  "--copy-annotation=definition"
+ "-->http://www.w3.org/2000/01/rdf-schema#comment` "
+ "--copy-annotation=comment"
  "-->http://www.w3.org/2000/01/rdf-schema#comment`"
  ),
  )
@@ -107,7 +112,7 @@ def main(argv: list = None):
  metavar="NAME",
  help=(
  "Add additional relations inferred by the reasoner. Supported "
- 'reasoners are "FaCT++" (default), "HermiT" and "Pellet".'
+ 'reasoners are "HermiT" (default), "Pellet" and "FaCT++".'
  ),
  )
  parser.add_argument(
@@ -116,7 +121,14 @@ def main(argv: list = None):
  action="store_true",
  help="Do not infer imported ontologies.",
  )
- # To be implemented...
+ parser.add_argument(
+ "--java-executable",
+ help="Path to Java executable to use. Default is `java`.",
+ )
+ parser.add_argument(
+ "--java-memory",
+ help="Maximum memory allocated to Java in MB. Default is 2000.",
+ )
  parser.add_argument(
  "--iri",
  "-I",
@@ -218,6 +230,12 @@ def main(argv: list = None):
  if not output_format:
  output_format = "xml"
 
+ # Settings for running Java
+ if args.java_executable:
+ owlready2.JAVA_EXE = args.java_executable
+ if args.java_memory:
+ owlready2.reasoning.JAVA_MEMORY = int(args.java_memory)
+
  # Annotations to copy with --copy-emmo-annotations
  if args.copy_emmo_annotations:
  args.copy_annotation.extend(
@@ -226,6 +244,7 @@ def main(argv: list = None):
  "-->http://www.w3.org/2000/01/rdf-schema#label",
  "elucidation-->http://www.w3.org/2000/01/rdf-schema#comment",
  "definition-->http://www.w3.org/2000/01/rdf-schema#comment",
+ "comment-->http://www.w3.org/2000/01/rdf-schema#comment",
  ]
  )