Merge branch 'main' into unnecessary-pass

Author: GeneCodeSavvy

sbol3/document.py

@@ -180,7 +180,7 @@ def _parse_objects(self, graph: rdflib.Graph) -> Dict[str, SBOLObject]:
         # 6.11 of the spec) and we instantiate it specially.
         #
         identity_types: Dict[str, List[str]] = collections.defaultdict(list)
-        for s, p, o in graph.triples((None, rdflib.RDF.type, None)):
+        for s, _, o in graph.triples((None, rdflib.RDF.type, None)):
             str_o = str(o)
             str_s = str(s)
             identity_types[str_s].append(str_o)
@@ -238,7 +238,7 @@ def _clean_up_singletons(objects: Dict[str, SBOLObject]):
         # in multiple values in a singleton property. Only the first value
         # is used, so the value read from file is ignored.
         for _, obj in objects.items():
-            for name, attr in obj.__dict__.items():
+            for _, attr in obj.__dict__.items():
                 if isinstance(attr, SingletonProperty):
                     prop_uri = attr.property_uri
                     store = attr._storage()
@@ -472,7 +472,7 @@ def write(self, fpath: Union[Path, str], file_format: str = None) -> None:
             file_format = self._guess_format(_fpath)
         if file_format is None:
             raise ValueError('Unable to determine file format')
-        with open(_fpath, 'w') as outfile:
+        with open(_fpath, 'w', encoding='utf-8') as outfile:
             outfile.write(self.write_string(file_format))
 
     def graph(self) -> rdflib.Graph:

sbol3/object.py

@@ -55,16 +55,19 @@ def _make_identity(name: str) -> Union[str, None]:
         """
         if name is None:
             return None
-        name_is_url = SBOLObject._is_url(name)
-        if name_is_url:
+
+        # Case 1: The name is already a valid URL
+        if SBOLObject._is_url(name):
             return name.strip(posixpath.sep)
+
+        # Case 2: The name is a valid UUID
         try:
-            # If it is a UUID, accept it as the identity
-            identity_uuid = uuid.UUID(name)
+            uuid.UUID(name)
             return name
         except ValueError:
             pass
-        # Not a URL or a UUID, so append to the namespace
+
+        # Case 3: The name is neither a URL or a UUID, so append to the namespace
         base_uri = get_namespace()
         if base_uri is None:
             # See https://github.com/SynBioDex/pySBOL3/issues/254

sbol3/toplevel.py

@@ -228,7 +228,7 @@ def update_references_traverser(x):
         # Use the identity map to update references.
         # References to objects outside of the object
         # being cloned will be left as is.
-        for k, v in x.__dict__.items():
+        for _, v in x.__dict__.items():
             if not isinstance(v, Property):
                 continue
             if v.property_uri not in x._properties:

setup.cfg

@@ -38,10 +38,8 @@ disable = abstract-class-instantiated,
           too-many-positional-arguments,
           too-many-public-methods,
           undefined-variable,
-          unspecified-encoding,
           unused-argument,
           unused-import,
-          unused-variable,
           unused-wildcard-import,
           useless-parent-delegation,
           useless-return,

test/test_custom.py

@@ -8,7 +8,6 @@
 
 import sbol3
 
-
 PYSBOL3_CUSTOM_TOP = 'https://github.com/synbiodex/pysbol3#customTop'
 PYSBOL3_CUSTOM_UNREGISTERED_TOP = 'https://github.com/synbiodex/pysbol3#customUnregisteredTop'
 PYSBOL3_CUSTOM_BOOL = 'https://github.com/synbiodex/pysbol3#customBool'
@@ -136,11 +135,11 @@ def test_none_identity(self):
         # as a CustomTopLevel identity. And also if identity
         # is an empty string or not a string.
         with self.assertRaises(ValueError):
-            obj = CustomTopClass(None)
+            _ = CustomTopClass(None)
         with self.assertRaises(ValueError):
-            obj = CustomTopClass('')
+            _ = CustomTopClass('')
         with self.assertRaises(ValueError):
-            obj = CustomTopClass(3)
+            _ = CustomTopClass(3)
 
 
 class TestCustomIdentified(unittest.TestCase):

test/test_document.py

@@ -52,7 +52,7 @@ def test_file_extension(self):
         self.assertEqual(extension_2, '.xml')
         # 3. for invalid file formats, valueError must be raised
         with self.assertRaises(ValueError):
-            extension_3 = sbol3.Document.file_extension(file_format_3)
+            _ = sbol3.Document.file_extension(file_format_3)
 
     def test_read_ntriples(self):
         # Initial test of Document.read
@@ -218,7 +218,7 @@ def test_write_string(self):
         with tempfile.TemporaryDirectory() as tmpdirname:
             test_file = os.path.join(tmpdirname, filename)
             doc.write(test_file, sbol3.SORTED_NTRIPLES)
-            with open(test_file, 'r') as infile:
+            with open(test_file, 'r', encoding='utf-8') as infile:
                 expected = infile.read()
         actual = doc.write_string(sbol3.SORTED_NTRIPLES)
         self.assertEqual(expected, actual)

test/test_object.py

@@ -62,7 +62,6 @@ def test_replace_namespace(self):
     def test_copy_is_deprecated(self):
         namespace = 'https://github.com/synbiodex/pysbol3'
         sbol3.set_namespace(namespace)
-        name = 'ed1'
         ed1 = sbol3.ExternallyDefined(types=[sbol3.SBO_DNA],
                                       definition='https://example.org/other')
         with self.assertWarns(DeprecationWarning):

test/test_subcomponent.py

@@ -56,7 +56,7 @@ def test_list_wrapping(self):
         instance_uri = 'https://example.org/instance'
         seq1 = sbol3.Sequence('seq1')
         test_loc = sbol3.EntireSequence(seq1)
-        seq2 = sbol3.Sequence('seq2')
+        _ = sbol3.Sequence('seq2')
         test_source_loc = sbol3.EntireSequence(seq1)
         subcomp1 = sbol3.SubComponent(instance_of=instance_uri,
                                       locations=test_loc,

test/test_varcomp.py

@@ -78,7 +78,7 @@ def test_list_wrapping(self):
         # See https://github.com/SynBioDex/pySBOL3/issues/301
         sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
         seq = sbol3.Sequence('seq1')
-        test_loc = sbol3.EntireSequence(seq)
+        _ = sbol3.EntireSequence(seq)
         variable_uri = 'https://example.org/variable'
         var_coll_uri = 'https://example.org/collection'
         var_feat1 = sbol3.VariableFeature(cardinality=sbol3.SBOL_ZERO_OR_MORE,