diff --git a/py313-support.patch b/py313-support.patch new file mode 100644 index 0000000..bded3ab --- /dev/null +++ b/py313-support.patch @@ -0,0 +1,26 @@ +From 22ebf951e736bd44f04e3552a4a39723ccb3c219 Mon Sep 17 00:00:00 2001 +From: Sandro +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); + diff --git a/python-biopython.changes b/python-biopython.changes index bf1764c..a27b9a6 100644 --- a/python-biopython.changes +++ b/python-biopython.changes @@ -1,3 +1,8 @@ +------------------------------------------------------------------- +Fri Nov 22 12:13:40 UTC 2024 - Dirk Müller + +- add py313-support.patch to fix build with python 3.13 + ------------------------------------------------------------------- Thu Oct 10 15:36:36 UTC 2024 - Dirk Müller diff --git a/python-biopython.spec b/python-biopython.spec index 5d72903..2feec91 100644 --- a/python-biopython.spec +++ b/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 -%define skip_python36 1 +%{?sle15_python_module_pythons} 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