From eb08cc4768293faca82bf3f1a60c02d105249e20 Mon Sep 17 00:00:00 2001
From: GeneCodeSavvy <hxrsh.09@gmail.com>
Date: Mon, 3 Mar 2025 00:47:55 +0530
Subject: [PATCH 1/5] range replaced with enumerate

---
 sbol3/toplevel.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/sbol3/toplevel.py b/sbol3/toplevel.py
index 7cca28d..46f4e45 100644
--- a/sbol3/toplevel.py
+++ b/sbol3/toplevel.py
@@ -3,11 +3,11 @@
 import copy
 import math
 import posixpath
+import typing
 import urllib.parse
 import uuid
 import warnings
-from typing import Dict, Callable, Optional, Any
-import typing
+from typing import Any, Callable, Dict, Optional
 
 from . import *
 from .typing import *
@@ -234,10 +234,10 @@ def update_references_traverser(x):
             if v.property_uri not in x._properties:
                 continue
             items = x._properties[v.property_uri]
-            for i in range(len(items)):
-                str_item = str(items[i])
-                if str_item in identity_map:
-                    new_reference = identity_map[str_item].identity
+            for i, item in enumerate(items):
+                str_item = str(item)
+                if str(item) in identity_map:
+                    new_reference = identity_map[str(item)].identity
                     # The item is probably an rdflib.URIRef. We take
                     # the type of the item and use that type to
                     # construct a new instance of the same type.

From d0157b00775e95ec6dc87010ab543f8ff547b9d4 Mon Sep 17 00:00:00 2001
From: GeneCodeSavvy <hxrsh.09@gmail.com>
Date: Mon, 3 Mar 2025 01:28:31 +0530
Subject: [PATCH 2/5] test files

---
 test/test_component.py | 3 +--
 test/test_module.py    | 4 ++--
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/test/test_component.py b/test/test_component.py
index 8486d92..846f030 100644
--- a/test/test_component.py
+++ b/test/test_component.py
@@ -148,8 +148,7 @@ def test_cloning_references(self):
         doc2 = sbol3.Document()
         doc2.add(toggle_clone)
         self.assertEqual(len(toggle.constraints), len(toggle_clone.constraints))
-        for i in range(len(toggle.constraints)):
-            c = toggle.constraints[i]
+        for i, c in enumerate(toggle.constraints):
             c_clone = toggle_clone.constraints[i]
             self.assertNotEqual(c.identity, c_clone.identity)
             s = c.subject.lookup()
diff --git a/test/test_module.py b/test/test_module.py
index d315266..acee7ef 100644
--- a/test/test_module.py
+++ b/test/test_module.py
@@ -100,9 +100,9 @@ def test_identified_constructors(self):
             try:
                 item(*arg_list)
             except TypeError as e:
-                self.fail('Unable to construct sbol3.%s: %s' % (name, e))
+                self.fail(f'Unable to construct sbol3.{name}: {e}')
             except sbol3.ValidationError as e:
-                self.fail('Constructed invalid sbol3.%s: %s' % (name, e))
+                self.fail(f'Constructed invalid sbol3.{name}: {e}')
             if item in abstract_list:
                 # Skip over abstract classes when checking for the
                 # accept method

From a4179728cab76bc8c0eda88c35e4310944af29c8 Mon Sep 17 00:00:00 2001
From: GeneCodeSavvy <hxrsh.09@gmail.com>
Date: Mon, 3 Mar 2025 01:35:50 +0530
Subject: [PATCH 3/5] revert test/test_module.py

---
 test/test_module.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/test_module.py b/test/test_module.py
index acee7ef..d315266 100644
--- a/test/test_module.py
+++ b/test/test_module.py
@@ -100,9 +100,9 @@ def test_identified_constructors(self):
             try:
                 item(*arg_list)
             except TypeError as e:
-                self.fail(f'Unable to construct sbol3.{name}: {e}')
+                self.fail('Unable to construct sbol3.%s: %s' % (name, e))
             except sbol3.ValidationError as e:
-                self.fail(f'Constructed invalid sbol3.{name}: {e}')
+                self.fail('Constructed invalid sbol3.%s: %s' % (name, e))
             if item in abstract_list:
                 # Skip over abstract classes when checking for the
                 # accept method

From e024fbcd668c3a7ead7e12ce989bd48733a386d3 Mon Sep 17 00:00:00 2001
From: GeneCodeSavvy <hxrsh.09@gmail.com>
Date: Mon, 3 Mar 2025 23:17:47 +0530
Subject: [PATCH 4/5] update setup.cfg

---
 setup.cfg | 1 -
 1 file changed, 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index 3cf21b6..be0b274 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -20,7 +20,6 @@ disable = abstract-class-instantiated,
           implicit-str-concat,
           import-outside-toplevel,
           logging-not-lazy,
-          consider-using-enumerate,
           consider-using-f-string,
           cyclic-import,
           duplicate-code,

From 625cfd03b5febccce9cc685bc94e69864a0aba03 Mon Sep 17 00:00:00 2001
From: GeneCodeSavvy <hxrsh.09@gmail.com>
Date: Mon, 3 Mar 2025 23:23:12 +0530
Subject: [PATCH 5/5] cleanup

---
 sbol3/toplevel.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sbol3/toplevel.py b/sbol3/toplevel.py
index 46f4e45..a892ed3 100644
--- a/sbol3/toplevel.py
+++ b/sbol3/toplevel.py
@@ -236,8 +236,8 @@ def update_references_traverser(x):
             items = x._properties[v.property_uri]
             for i, item in enumerate(items):
                 str_item = str(item)
-                if str(item) in identity_map:
-                    new_reference = identity_map[str(item)].identity
+                if str_item in identity_map:
+                    new_reference = identity_map[str_item].identity
                     # The item is probably an rdflib.URIRef. We take
                     # the type of the item and use that type to
                     # construct a new instance of the same type.