From a1803bf5ec1e103979d6ee1836e02bf9d8cef5cf Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 8 Oct 2024 01:49:04 +0000
Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v5.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.4.0...v5.0.0)
- [github.com/pycqa/isort: 5.10.1 → 5.13.2](https://github.com/pycqa/isort/compare/5.10.1...5.13.2)
- [github.com/psf/black: 22.3.0 → 24.10.0](https://github.com/psf/black/compare/22.3.0...24.10.0)
---
 .pre-commit-config.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b0b94e26..ed8f8cb5 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
       - id: check-json
       - id: check-yaml
@@ -11,13 +11,13 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+    rev: 5.13.2
     hooks:
       - id: isort
         args: [--profile, black, --filter-files, --line-length, "79"]
 
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 24.10.0
     hooks:
       - id: black
         args: [--line-length, "79"]

From 90e532c815d5bc05b7efac1d2f24aa6f04414c43 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 8 Oct 2024 01:49:19 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 examples/sessions.py                          |  2 +-
 examples/terminological_knowledge.py          |  8 +++--
 .../interfaces/dataspace/interface.py         |  1 +
 simphony_osp/interfaces/interface.py          | 14 +++++---
 simphony_osp/interfaces/remote/server.py      |  6 ++--
 simphony_osp/namespaces.py                    |  1 +
 simphony_osp/ontology/annotation.py           |  1 +
 simphony_osp/ontology/attribute.py            |  1 +
 simphony_osp/ontology/composition.py          |  1 +
 simphony_osp/ontology/entity.py               |  9 ++++--
 simphony_osp/ontology/individual.py           | 27 +++++++++-------
 simphony_osp/ontology/namespace.py            |  1 +
 simphony_osp/ontology/oclass.py               |  1 +
 simphony_osp/ontology/operations/container.py |  1 +
 simphony_osp/ontology/operations/file.py      |  1 +
 .../ontology/operations/operations.py         |  1 +
 simphony_osp/ontology/parser/parser.py        |  1 +
 simphony_osp/ontology/relationship.py         |  1 +
 simphony_osp/ontology/restriction.py          |  1 +
 simphony_osp/ontology/utils.py                | 18 +++++------
 simphony_osp/session/session.py               |  1 +
 simphony_osp/tools/import_export.py           |  1 +
 simphony_osp/tools/pretty_print.py            | 32 ++++++++++++-------
 simphony_osp/utils/datatypes.py               |  1 +
 tests/benchmark.py                            |  1 +
 tests/test_api.py                             |  1 +
 26 files changed, 85 insertions(+), 49 deletions(-)

diff --git a/examples/sessions.py b/examples/sessions.py
index 51808e24..65b7de13 100644
--- a/examples/sessions.py
+++ b/examples/sessions.py
@@ -132,7 +132,7 @@
         }}
     """
     )(citizen=OntologyIndividual, age=int)
-    for (citizen, age) in result:
+    for citizen, age in result:
         print(citizen.name, age)
 
 # Session contents can be exported to RDF,
diff --git a/examples/terminological_knowledge.py b/examples/terminological_knowledge.py
index 61c23375..004fd7a4 100644
--- a/examples/terminological_knowledge.py
+++ b/examples/terminological_knowledge.py
@@ -115,9 +115,11 @@
 print("  - restriction type", restriction.rtype)
 print(
     "  - affected predicate",
-    restriction.attribute
-    if restriction.rtype == RESTRICTION_TYPE.ATTRIBUTE_RESTRICTION
-    else restriction.relationship,
+    (
+        restriction.attribute
+        if restriction.rtype == RESTRICTION_TYPE.ATTRIBUTE_RESTRICTION
+        else restriction.relationship
+    ),
 )
 print("\n`Integer` ontology class object from the `emmo` namespace")
 composition = tuple(
diff --git a/simphony_osp/interfaces/dataspace/interface.py b/simphony_osp/interfaces/dataspace/interface.py
index 4457d42b..a39770df 100644
--- a/simphony_osp/interfaces/dataspace/interface.py
+++ b/simphony_osp/interfaces/dataspace/interface.py
@@ -1,4 +1,5 @@
 """The data space store connects SimPhoNy to a data space."""
+
 import os
 import pathlib
 from base64 import b64encode
diff --git a/simphony_osp/interfaces/interface.py b/simphony_osp/interfaces/interface.py
index 9d737630..7bf215f4 100644
--- a/simphony_osp/interfaces/interface.py
+++ b/simphony_osp/interfaces/interface.py
@@ -1,4 +1,5 @@
 """Universal interface for wrapper developers."""
+
 from __future__ import annotations
 
 import logging
@@ -974,12 +975,15 @@ def __call__(self, subject: Node):
             if s not in added_subjects and s in tracker.existing_subjects:
                 deleted_subjects[s] = deleted_subjects.get(s, 0) + 1
         deleted_subjects = {
-            s: True
-            if count
-            >= sum(
-                1 for _ in self.interface.old_graph.triples((s, None, None))
+            s: (
+                True
+                if count
+                >= sum(
+                    1
+                    for _ in self.interface.old_graph.triples((s, None, None))
+                )
+                else False
             )
-            else False
             for s, count in deleted_subjects.items()
         }
         deleted_subjects = {
diff --git a/simphony_osp/interfaces/remote/server.py b/simphony_osp/interfaces/remote/server.py
index 1d7629ce..0eee84d2 100644
--- a/simphony_osp/interfaces/remote/server.py
+++ b/simphony_osp/interfaces/remote/server.py
@@ -35,9 +35,9 @@ def __init__(
         )
         self._interfaces: Dict[UUID, Interface] = dict()
         self._directories: Dict[UUID, tempfile.TemporaryDirectory] = dict()
-        self._interface_generator: Callable[
-            [str, str], Interface
-        ] = generate_interface
+        self._interface_generator: Callable[[str, str], Interface] = (
+            generate_interface
+        )
 
     def listen(self) -> None:
         """Listen for connections from clients."""
diff --git a/simphony_osp/namespaces.py b/simphony_osp/namespaces.py
index 8dae36ae..13eb4507 100644
--- a/simphony_osp/namespaces.py
+++ b/simphony_osp/namespaces.py
@@ -1,4 +1,5 @@
 """You can import the installed namespaces from this module."""
+
 from __future__ import annotations
 
 import logging as _logging
diff --git a/simphony_osp/ontology/annotation.py b/simphony_osp/ontology/annotation.py
index c4304f6d..2b03aaa4 100644
--- a/simphony_osp/ontology/annotation.py
+++ b/simphony_osp/ontology/annotation.py
@@ -1,4 +1,5 @@
 """An annotation property defined in the ontology."""
+
 from __future__ import annotations
 
 import logging
diff --git a/simphony_osp/ontology/attribute.py b/simphony_osp/ontology/attribute.py
index e39e110a..aca78c5a 100644
--- a/simphony_osp/ontology/attribute.py
+++ b/simphony_osp/ontology/attribute.py
@@ -1,4 +1,5 @@
 """An attribute defined in the ontology."""
+
 from __future__ import annotations
 
 import logging
diff --git a/simphony_osp/ontology/composition.py b/simphony_osp/ontology/composition.py
index 473a38b1..518984db 100644
--- a/simphony_osp/ontology/composition.py
+++ b/simphony_osp/ontology/composition.py
@@ -1,4 +1,5 @@
 """This files defines composition of classes."""
+
 from __future__ import annotations
 
 import logging
diff --git a/simphony_osp/ontology/entity.py b/simphony_osp/ontology/entity.py
index c36e8ea3..fb85f53c 100644
--- a/simphony_osp/ontology/entity.py
+++ b/simphony_osp/ontology/entity.py
@@ -1,4 +1,5 @@
 """Abstract superclass of any entity in the ontology."""
+
 from __future__ import annotations
 
 import logging
@@ -348,9 +349,11 @@ def __repr__(self) -> str:
         """Transform the entity into a string."""
         header = f"{self.__class__.__name__}"
         elements = [
-            f"{self.label}"
-            if hasattr(self, "label") and self.label is not None
-            else None,
+            (
+                f"{self.label}"
+                if hasattr(self, "label") and self.label is not None
+                else None
+            ),
             f"{self.uid}",
         ]
         elements = filter(lambda x: x is not None, elements)
diff --git a/simphony_osp/ontology/individual.py b/simphony_osp/ontology/individual.py
index 0afba601..eb045b45 100644
--- a/simphony_osp/ontology/individual.py
+++ b/simphony_osp/ontology/individual.py
@@ -1,4 +1,5 @@
 """An ontology individual."""
+
 from __future__ import annotations
 
 import functools
@@ -391,11 +392,13 @@ def __iter__(self) -> Iterator[OntologyIndividual]:
 
         if self._uid_filter:
             yield from (
-                self._individual.session.from_identifier_typed(
-                    identifier, typing=OntologyIndividual
+                (
+                    self._individual.session.from_identifier_typed(
+                        identifier, typing=OntologyIndividual
+                    )
+                    if identifier in connected
+                    else None
                 )
-                if identifier in connected
-                else None
                 for identifier in identifiers
             )
         else:
@@ -1518,7 +1521,7 @@ def get(
                 )
         else:
             result = []
-            for (i, r, t) in relationship_set.iter_low_level():
+            for i, r, t in relationship_set.iter_low_level():
                 if not t:
                     continue
                 session = self.session
@@ -1650,16 +1653,16 @@ def iter(
             iterator = iter(relationship_set)
         else:
 
-            def iterator() -> Iterator[
-                Tuple[OntologyIndividual, OntologyRelationship]
-            ]:
+            def iterator() -> (
+                Iterator[Tuple[OntologyIndividual, OntologyRelationship]]
+            ):
                 """Helper iterator.
 
                 The purpose of defining this iterator is to be able to
                 return it, instead of using the `yield` keyword on the main
                 function, as described on the comment above.
                 """
-                for (i, r, t) in relationship_set.iter_low_level():
+                for i, r, t in relationship_set.iter_low_level():
                     if not t:
                         continue
                     session = self.session
@@ -2242,9 +2245,9 @@ def relationships_iter(
             Iterator with the queried ontology individuals.
         """
 
-        def individuals_and_relationships() -> Iterator[
-            OntologyIndividual, OntologyEntity
-        ]:
+        def individuals_and_relationships() -> (
+            Iterator[OntologyIndividual, OntologyEntity]
+        ):
             for s, p, o in self.session.graph.triples(
                 (
                     self.identifier,
diff --git a/simphony_osp/ontology/namespace.py b/simphony_osp/ontology/namespace.py
index baea1cb5..03168380 100644
--- a/simphony_osp/ontology/namespace.py
+++ b/simphony_osp/ontology/namespace.py
@@ -1,4 +1,5 @@
 """An ontology namespace."""
+
 from __future__ import annotations
 
 import itertools
diff --git a/simphony_osp/ontology/oclass.py b/simphony_osp/ontology/oclass.py
index 99aaab93..90301aab 100644
--- a/simphony_osp/ontology/oclass.py
+++ b/simphony_osp/ontology/oclass.py
@@ -1,4 +1,5 @@
 """A class defined in the ontology."""
+
 from __future__ import annotations
 
 import logging
diff --git a/simphony_osp/ontology/operations/container.py b/simphony_osp/ontology/operations/container.py
index df15d0c6..23661da1 100644
--- a/simphony_osp/ontology/operations/container.py
+++ b/simphony_osp/ontology/operations/container.py
@@ -1,4 +1,5 @@
 """Special kind of ontology individual designed to organize entities."""
+
 from __future__ import annotations
 
 import logging
diff --git a/simphony_osp/ontology/operations/file.py b/simphony_osp/ontology/operations/file.py
index e828bfaa..f0a3926e 100644
--- a/simphony_osp/ontology/operations/file.py
+++ b/simphony_osp/ontology/operations/file.py
@@ -1,4 +1,5 @@
 """Special kind of ontology individual designed to organize entities."""
+
 from __future__ import annotations
 
 import logging
diff --git a/simphony_osp/ontology/operations/operations.py b/simphony_osp/ontology/operations/operations.py
index 5fb72492..de06bdcd 100644
--- a/simphony_osp/ontology/operations/operations.py
+++ b/simphony_osp/ontology/operations/operations.py
@@ -11,6 +11,7 @@
 individual has an associated instance of the subclass of `Operations` that the
 wrapper or package developer has defined.
 """
+
 from __future__ import annotations
 
 import os
diff --git a/simphony_osp/ontology/parser/parser.py b/simphony_osp/ontology/parser/parser.py
index 68b087b0..82466496 100644
--- a/simphony_osp/ontology/parser/parser.py
+++ b/simphony_osp/ontology/parser/parser.py
@@ -2,6 +2,7 @@
 
 Also contains a `Parser` class for backwards compatibility.
 """
+
 from __future__ import annotations
 
 import logging
diff --git a/simphony_osp/ontology/relationship.py b/simphony_osp/ontology/relationship.py
index aca7c29f..b5fd49ac 100644
--- a/simphony_osp/ontology/relationship.py
+++ b/simphony_osp/ontology/relationship.py
@@ -1,4 +1,5 @@
 """A relationship defined in the ontology."""
+
 from __future__ import annotations
 
 import logging
diff --git a/simphony_osp/ontology/restriction.py b/simphony_osp/ontology/restriction.py
index bbc28d4f..532491f7 100644
--- a/simphony_osp/ontology/restriction.py
+++ b/simphony_osp/ontology/restriction.py
@@ -1,4 +1,5 @@
 """Restrictions on ontology classes."""
+
 from __future__ import annotations
 
 import logging
diff --git a/simphony_osp/ontology/utils.py b/simphony_osp/ontology/utils.py
index f78b9eb3..0a78a876 100644
--- a/simphony_osp/ontology/utils.py
+++ b/simphony_osp/ontology/utils.py
@@ -1,4 +1,5 @@
 """Utility resources for the ontology module."""
+
 from __future__ import annotations
 
 import importlib
@@ -372,22 +373,19 @@ def recursive_iterator(class_):
             else {subclass.rdf_type}
         )
         for rdf_type in rdf_types:
-            mapping_rdf_to_python_class[
-                rdf_type
-            ] = mapping_rdf_to_python_class.get(rdf_type, set()) | {subclass}
+            mapping_rdf_to_python_class[rdf_type] = (
+                mapping_rdf_to_python_class.get(rdf_type, set()) | {subclass}
+            )
         rdf_identifiers = (
             subclass.rdf_identifier
             if isinstance(subclass.rdf_identifier, set)
             else {subclass.rdf_identifier}
         )
         for rdf_identifier in rdf_identifiers:
-            mapping_identifier_to_python_class[
-                rdf_identifier
-            ] = mapping_identifier_to_python_class.get(
-                rdf_identifier, set()
-            ) | {
-                subclass
-            }
+            mapping_identifier_to_python_class[rdf_identifier] = (
+                mapping_identifier_to_python_class.get(rdf_identifier, set())
+                | {subclass}
+            )
     return mapping_rdf_to_python_class, mapping_identifier_to_python_class
 
 
diff --git a/simphony_osp/session/session.py b/simphony_osp/session/session.py
index f8b9d019..73277a11 100644
--- a/simphony_osp/session/session.py
+++ b/simphony_osp/session/session.py
@@ -1,4 +1,5 @@
 """Abstract Base Class for all Sessions."""
+
 from __future__ import annotations
 
 import itertools
diff --git a/simphony_osp/tools/import_export.py b/simphony_osp/tools/import_export.py
index c97a0389..7d4264fe 100644
--- a/simphony_osp/tools/import_export.py
+++ b/simphony_osp/tools/import_export.py
@@ -1,4 +1,5 @@
 """Tools for importing and exporting data."""
+
 from __future__ import annotations
 
 import io
diff --git a/simphony_osp/tools/pretty_print.py b/simphony_osp/tools/pretty_print.py
index 2cb659a1..209c6617 100644
--- a/simphony_osp/tools/pretty_print.py
+++ b/simphony_osp/tools/pretty_print.py
@@ -184,15 +184,19 @@ def _pp_individual_subelements(
                 "\0"
                 + str(
                     sorted(
-                        class_.label
-                        if class_.label is not None
-                        else class_.identifier
+                        (
+                            class_.label
+                            if class_.label is not None
+                            else class_.identifier
+                        )
                         for class_ in x[0].classes
                     )[0]
                 ),
-                f"\0{x[1].label}"
-                if x[1].label is not None
-                else f"{x[1].identifier}",
+                (
+                    f"\0{x[1].label}"
+                    if x[1].label is not None
+                    else f"{x[1].identifier}"
+                ),
                 f"\0{x[0].label}" if x[0].label is not None else f"{x[0].uid}",
             ),
         )
@@ -241,9 +245,11 @@ def _pp_individual_values(cuds_object, indentation="\n          "):
     sorted_attributes = sorted(
         cuds_object.attributes.items(),
         key=lambda x: (
-            f"\0{x[0].label}"
-            if x[0].label is not None
-            else f"{x[0].identifier}",
+            (
+                f"\0{x[0].label}"
+                if x[0].label is not None
+                else f"{x[0].identifier}"
+            ),
             str(x[1]),
         ),
     )
@@ -251,9 +257,11 @@ def _pp_individual_values(cuds_object, indentation="\n          "):
         result.append(
             "%s: %s"
             % (
-                f"\0{attribute.label}"
-                if attribute.label is not None
-                else f"{attribute.identifier}",
+                (
+                    f"\0{attribute.label}"
+                    if attribute.label is not None
+                    else f"{attribute.identifier}"
+                ),
                 value if not len(value) == 1 else next(iter(value)),
             )
         )
diff --git a/simphony_osp/utils/datatypes.py b/simphony_osp/utils/datatypes.py
index 452e2200..9dd1736a 100644
--- a/simphony_osp/utils/datatypes.py
+++ b/simphony_osp/utils/datatypes.py
@@ -1,4 +1,5 @@
 """This module contains methods for datatype conversions."""
+
 from __future__ import annotations
 
 import logging
diff --git a/tests/benchmark.py b/tests/benchmark.py
index d9cd2a0d..69e96caa 100644
--- a/tests/benchmark.py
+++ b/tests/benchmark.py
@@ -1,4 +1,5 @@
 """Contains an abstract class that serves as a base for defining benchmarks."""
+
 import time
 from abc import ABC, abstractmethod
 from typing import Union
diff --git a/tests/test_api.py b/tests/test_api.py
index 6b3aecd7..d50ab594 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -3,6 +3,7 @@
 The public API methods are the methods that are available to the users,
 and available in the user documentation.
 """
+
 import io
 import json
 import os