From 2ccd6e3a5bab098711f41f7549d11c2a8ff83bc2 Mon Sep 17 00:00:00 2001
From: Christian Diener <ch.diener@gmail.com>
Date: Wed, 20 Nov 2024 10:51:39 +0100
Subject: [PATCH 1/3] fix GPR copy overwrite

---
 src/cobra/core/gene.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/cobra/core/gene.py b/src/cobra/core/gene.py
index 4d8a13576..56733ec46 100644
--- a/src/cobra/core/gene.py
+++ b/src/cobra/core/gene.py
@@ -545,9 +545,13 @@ def to_string(self, names: dict = None) -> str:
         """
         return self._ast2str(self, names=names)
 
-    def copy(self):
+    def copy(self) -> "GPR":
         """Copy a GPR."""
-        return deepcopy(self)
+        cls = type(self)
+        gpr = cls()
+        gpr._genes = deepcopy(self._genes)
+        gpr.body = deepcopy(self.body)
+        return gpr
 
     def __copy__(self) -> "GPR":
         """Ensure a correct shallow copy."""

From 2ad4cc3c957620a46f8a7d743908e0d2277621a1 Mon Sep 17 00:00:00 2001
From: Christian Diener <ch.diener@gmail.com>
Date: Wed, 20 Nov 2024 10:57:26 +0100
Subject: [PATCH 2/3] add specific test

---
 tests/test_core/test_gpr.py | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/tests/test_core/test_gpr.py b/tests/test_core/test_gpr.py
index 31d95f561..e472226b6 100644
--- a/tests/test_core/test_gpr.py
+++ b/tests/test_core/test_gpr.py
@@ -27,6 +27,16 @@ def test_gpr() -> None:
     assert len(gpr1.genes) == 0
 
 
+def test_grp_copy() -> None:
+    """Test that copying a GPR works."""
+    gpr1 = GPR.from_string("(A and B) or C")
+    gpr2 = gpr1.copy()
+    assert gpr1 == gpr2
+    assert id(gpr1.body) is not id(gpr2.body)
+    assert gpr1._genes == gpr2._genes
+    assert id(gpr1._genes) is not id(gpr2._genes)
+
+
 @pytest.mark.parametrize("test_input", ["", "", None])
 def test_empty_gpr(test_input) -> None:
     """Test empty GPR."""
@@ -89,7 +99,6 @@ def test_and_gpr(gpr_input, num_genes, gpr_genes, gpr_output_string) -> None:
     for ko_genes in powerset_ne(gpr_genes):
         assert not gpr1.eval(ko_genes)
     assert gpr1.body
-    gpr1.copy()
 
 
 def all_except_one(iterable: Iterable[str]) -> Iterator[Tuple[str, ...]]:
@@ -132,7 +141,6 @@ def test_or_gpr(
         assert gpr1.eval(ko_genes)
     assert not gpr1.eval(gpr_genes)
     assert gpr1.body
-    gpr1.copy()
 
 
 @pytest.mark.parametrize(
@@ -158,7 +166,6 @@ def test_complicated_gpr(gpr_input: str) -> None:
     assert not gpr1.eval("c")
     assert not gpr1.eval(["a", "b"])
     assert not gpr1.eval(["a", "b", "c"])
-    gpr1.copy()
 
 
 @pytest.mark.parametrize(
@@ -185,7 +192,6 @@ def test_gpr_from_ast_or(
     for ko_genes in all_except_one(gpr_genes):
         assert gpr1.eval(ko_genes)
     assert not gpr1.eval(gpr_genes)
-    gpr1.copy()
 
 
 @pytest.mark.parametrize(
@@ -210,7 +216,6 @@ def test_gpr_from_ast_and(
     assert gpr1.eval()
     for ko_genes in powerset_ne(gpr_genes):
         assert not gpr1.eval(ko_genes)
-    gpr1.copy()
 
 
 @pytest.mark.parametrize("test_input", [["a", "b"], {"a", "b"}])

From b909c02cd376df765c4cb7877942ffce408994c8 Mon Sep 17 00:00:00 2001
From: Christian Diener <ch.diener@gmail.com>
Date: Wed, 20 Nov 2024 11:00:44 +0100
Subject: [PATCH 3/3] add RNs

---
 release-notes/next-release.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/release-notes/next-release.md b/release-notes/next-release.md
index 2ddd48ce4..3b41cdc8c 100644
--- a/release-notes/next-release.md
+++ b/release-notes/next-release.md
@@ -4,6 +4,8 @@
 
 ## Fixes
 
+Fixes failures of GPR.copy() in Python 3.13.
+
 ## Other
 
 ## Deprecated features