Accepting request 1225807 from devel:languages:python:numeric

- add py313-support.patch to fix build with python 3.13

OBS-URL: https://build.opensuse.org/request/show/1225807
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-biopython?expand=0&rev=14

py313-support.patch

@@ -0,0 +1,26 @@
+From 22ebf951e736bd44f04e3552a4a39723ccb3c219 Mon Sep 17 00:00:00 2001
+From: Sandro <devel@penguinpee.nl>
+Date: Fri, 19 Apr 2024 14:41:38 +0200
+Subject: [PATCH] Python 3.13: Replace deprecated PyEval_CallObject()
+
+The function has been deprecated since Python 3.9 and will be removed
+from Python 3.13.
+
+See: https://docs.python.org/3.13/whatsnew/3.13.html#id9
+---
+ Bio/cpairwise2module.c | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/Bio/cpairwise2module.c b/Bio/cpairwise2module.c
+index af7843ed4bc..ada6663ccd5 100644
+--- a/Bio/cpairwise2module.c
++++ b/Bio/cpairwise2module.c
+@@ -57,7 +57,7 @@ static double _get_match_score(PyObject *py_sequenceA, PyObject *py_sequenceB,
+     if(!(py_arglist = Py_BuildValue("(OO)", py_A, py_B)))
+         goto _get_match_score_cleanup;
+ 
+-    if(!(py_result = PyEval_CallObject(py_match_fn, py_arglist)))
++    if(!(py_result = PyObject_CallObject(py_match_fn, py_arglist)))
+         goto _get_match_score_cleanup;
+     score = PyFloat_AsDouble(py_result);
+ 

python-biopython.changes

@@ -1,3 +1,8 @@
+-------------------------------------------------------------------
+Fri Nov 22 12:13:40 UTC 2024 - Dirk Müller <dmueller@suse.com>
+
+- add py313-support.patch to fix build with python 3.13
+
 -------------------------------------------------------------------
 Thu Oct 10 15:36:36 UTC 2024 - Dirk Müller <dmueller@suse.com>
 

python-biopython.spec

@@ -16,11 +16,9 @@
 #
 
 
-%{?!python_module:%define python_module() python-%{**} python3-%{**}}
 # Tests require a network connection
 %bcond_with test
-%define skip_python2 1
+%{?sle15_python_module_pythons}
-%define skip_python36 1
 Name:           python-biopython
 Version:        1.84
 Release:        0
@@ -29,6 +27,7 @@ License:        BSD-3-Clause AND MIT
 URL:            https://biopython.org/
 Source0:        https://files.pythonhosted.org/packages/source/b/biopython/biopython-%{version}.tar.gz
 Source100:      python-biopython-rpmlintrc
+Patch1:         https://github.com/biopython/biopython/commit/22ebf951e736bd44f04e3552a4a39723ccb3c219.patch#/py313-support.patch
 BuildRequires:  %{python_module devel}
 BuildRequires:  %{python_module numpy-devel}
 BuildRequires:  %{python_module setuptools}
@@ -53,7 +52,7 @@ The Biopython Project is an international association of developers of freely
 available Python tools for computational molecular biology.
 
 %prep
-%setup -q -n biopython-%{version}
+%autosetup -p1 -n biopython-%{version}
 find -type f -name "*.py" -exec sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' {} 2>/dev/null ';'
 # Example scripts cannot be in a subdirectory
 mv -v Doc/examples examples