Fix style errors

SynBioDex · Oct 15, 2023 · 6e2ea5e · 6e2ea5e
1 parent 9bd4921
commit 6e2ea5e
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Showing 4 changed files with 17 additions and 12 deletions.
diff --git a/sbol3/document.py b/sbol3/document.py
@@ -376,7 +376,7 @@ def assign_document(x: Identified):
 
         # Update any external references to this object
         # replacing stub SBOLObjects with this one
-        self._resolve_references(obj) 
+        self._resolve_references(obj)
         return obj
 
     def _add_all(self, objects: pytyping.Sequence[TopLevel]) -> pytyping.Sequence[TopLevel]:

diff --git a/sbol3/object.py b/sbol3/object.py
@@ -108,6 +108,7 @@ def find(self, search_string: str) -> Optional['SBOLObject']:
 
     def _resolve_references(self, new_obj):
         NEW_OBJ = new_obj
+
         def resolve_references(x):
             for property_id, references in x._referenced_objects.items():
                 needs_updating = False
@@ -118,6 +119,7 @@ def resolve_references(x):
                 if needs_updating:
                     references.remove(ref_obj)
                     references.append(new_obj)
+
         self.traverse(resolve_references)
 
     def copy(self, target_doc=None, target_namespace=None):
@@ -180,19 +182,20 @@ def copy(self, target_doc=None, target_namespace=None):
                     if referenced_obj:
                         new_obj._referenced_objects[property_uri].append(referenced_obj)
                     else:
-                        new_obj._referenced_objects[property_uri].append(SBOLObject(o.identity)) 
+                        new_obj._referenced_objects[property_uri].append(SBOLObject(o.identity))
         else:
             # If the copy does not belong to a Document, then treat all references
             # like external references
             for property_uri, object_store in self._referenced_objects.items():
                 for o in object_store:
-                    new_obj._referenced_objects[property_uri].append(SBOLObject(o.identity))             
+                    new_obj._referenced_objects[property_uri].append(SBOLObject(o.identity))
 
         return new_obj
 
     def lookup(self):
         return self
 
+
 def replace_namespace(old_uri, target_namespace, rdf_type):
 
     # Flag as not working to ensure nobody calls this function thinking

diff --git a/sbol3/refobj_property.py b/sbol3/refobj_property.py
@@ -110,7 +110,7 @@ def __init__(self, property_owner: Any, property_uri: str,
 
     def __setitem__(self, key: Union[int, slice], value: Any) -> None:
         replaced_obj = self._storage()[self.property_uri].__getitem__(key)
-        replaced_obj._references.remove(self.property_owner) 
+        replaced_obj._references.remove(self.property_owner)
         super().__setitem__(key, value)
 
     def __delitem__(self, key: Union[int, slice]) -> None:

diff --git a/test/test_referenced_object.py b/test/test_referenced_object.py
@@ -119,7 +119,6 @@ def test_uri_assignment_not_resolved(self):
         component.sequences.append(sequence.identity)
         self.assertNotEqual(sequence, component.sequences[0])
         self.assertTrue(type(component.sequences[0]) is sbol3.SBOLObject)
-
 
     def test_instance_append(self):
         # Test assignment to a ReferencedObject attribute with an
@@ -203,7 +202,7 @@ def test_equality(self):
         foo = sbol3.SBOLObject('foo')
         self.assertEqual(foo, foo.identity)
         self.assertEqual(foo.identity, foo)
- 
+
     def test_singleton_property_reference_counter(self):
         sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
         doc = sbol3.Document()
@@ -227,7 +226,7 @@ def test_list_property_reference_counter(self):
         self.assertListEqual(seq1._references, [])
         doc.add(component)
         doc.add(seq1)
-        
+
         # Test that the reference counter is working
         component.sequences = [seq1.identity]
         self.assertListEqual(seq1._references, [component])
@@ -269,7 +268,7 @@ def setUp(self) -> None:
                              file_format=TestExternalReferences.TEST_FORMAT)
 
     def test_parse_external_reference(self):
-        # When parsing a document, if we encounter a reference to an object 
+        # When parsing a document, if we encounter a reference to an object
         # not in this document, create a stub object using SBOLObject
         component = self.doc.find('toggle_switch')
         model = component.models[0]
@@ -278,11 +277,14 @@ def test_parse_external_reference(self):
         self.assertListEqual(model._references, [component])
 
     def test_serialize_external_reference(self):
-        # When serializing a document, if we encounter a reference to an object 
+        # When serializing a document, if we encounter a reference to an object
         # not in this document, serialize it as a URI
 
         roundtrip_doc = sbol3.Document()
-        roundtrip_doc.read_string(self.doc.write_string(file_format=TestExternalReferences.TEST_FORMAT), file_format=TestExternalReferences.TEST_FORMAT)
+        roundtrip_doc.read_string(
+            self.doc.write_string(file_format=TestExternalReferences.TEST_FORMAT),
+            file_format=TestExternalReferences.TEST_FORMAT
+        )
         component = roundtrip_doc.find('toggle_switch')
         model = component.models[0]
 
@@ -300,7 +302,7 @@ def test_update(self):
         self.assertEqual(model.identity, 'https://sbolstandard.org/examples/model1')
         self.doc.add(model)
 
-        # Check whether dereferencing now returns a Model 
+        # Check whether dereferencing now returns a Model
         # instead of SBOLObject
         model = component.models[0]
         self.assertFalse(type(model) is sbol3.SBOLObject)
@@ -318,7 +320,7 @@ def test_remove(self):
         model = component.models[0]
         self.assertFalse(type(model) is sbol3.Model)
         self.assertTrue(type(model) is sbol3.SBOLObject)
-        
+
 
 if __name__ == '__main__':
     unittest.main()