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

biopython-1.83.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:78e6bfb78de63034037afd35fe77cb6e0a9e5b62706becf78a7d922b16ed83f7
-size 19431530

biopython-1.84.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:60fbe6f996e8a6866a42698c17e552127d99a9aab3259d6249fbaabd0e0cc7b4
+size 25793001

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 +1,26 @@
+-------------------------------------------------------------------
+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>
+
+- update to 1.84:
+  * The old parser stores information in a
+    Bio.Blast.NCBIXML.Blast object, with attribute names based on
+    plain-text Blast output. The new parser stores information in
+    a Bio.Blast.Record object. This class follows the DTD that
+    describes the XML in terms of attribute names and dictionary
+    key names, class structure, and object types. This makes it
+    easier to find the detailed description of each field in the
+    NCBI Blast documentation.
+  * The old parser stores alignment information directly as seen
+    in the BLAST XML output, i.e. as strings with dashes to
+    represent gaps. The new parser stores the alignment
+    information as a Bio.Align.Alignment object, which can then
+    be used to e.g. print the alignment in a different format.
+
 -------------------------------------------------------------------
 Sat Jan 20 12:29:01 UTC 2024 - Dirk Müller <dmueller@suse.com>
 

python-biopython.spec

@@ -16,19 +16,18 @@
 #
 
 
-%{?!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:        1.83
+Version:        1.84
 Release:        0
 Summary:        Python Tools for Computational Molecular Biology
 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