[med-svn] [Git][med-team/python-cobra][master] add Python3.13 patch (Closes: #1092791)

[Alexandre Detiste (@detiste-guest)]

Alexandre Detiste pushed to branch master at Debian Med / python-cobra


Commits:
37fdc5cc by Alexandre Detiste at 2025-05-18T11:27:19+02:00
add Python3.13 patch (Closes: #1092791)

- - - - -


2 changed files:

- + debian/patches/a2b9d00a04b85b8c8eb12e4deba29ce2147896cf.patch
- debian/patches/series


Changes:

=====================================
debian/patches/a2b9d00a04b85b8c8eb12e4deba29ce2147896cf.patch
=====================================
@@ -0,0 +1,110 @@
+From a2b9d00a04b85b8c8eb12e4deba29ce2147896cf Mon Sep 17 00:00:00 2001
+From: Christian Diener <ch.diener at gmail.com>
+Date: Mon, 25 Nov 2024 12:46:45 +0100
+Subject: [PATCH] Fix the GPR copy in Python 3.13 (#1412)
+
+* fix GPR copy overwrite
+
+* add specific test
+
+* add RNs
+---
+ release-notes/next-release.md |  2 ++
+ src/cobra/core/gene.py        |  8 ++++++--
+ tests/test_core/test_gpr.py   | 15 ++++++++++-----
+ 3 files changed, 18 insertions(+), 7 deletions(-)
+
+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
+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."""
+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"}])


=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ ignore_tests.patch
 32-bit-test.patch
 no_future_dependency.patch
 remove-appdirs.patch
+a2b9d00a04b85b8c8eb12e4deba29ce2147896cf.patch



View it on GitLab: https://salsa.debian.org/med-team/python-cobra/-/commit/37fdc5cc85f064e4a0fcb6214830faef1292f86b

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-cobra/-/commit/37fdc5cc85f064e4a0fcb6214830faef1292f86b
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