diff --git a/biopython-1.84.tar.gz b/biopython-1.84.tar.gz deleted file mode 100644 index c4ee00f..0000000 --- a/biopython-1.84.tar.gz +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:60fbe6f996e8a6866a42698c17e552127d99a9aab3259d6249fbaabd0e0cc7b4 -size 25793001 diff --git a/biopython-1.85.tar.gz b/biopython-1.85.tar.gz new file mode 100644 index 0000000..53688f4 --- /dev/null +++ b/biopython-1.85.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5dafab74059de4e78f49f6b5684eddae6e7ce46f09cfa059c1d1339e8b1ea0a6 +size 19909902 diff --git a/py313-support.patch b/py313-support.patch deleted file mode 100644 index bded3ab..0000000 --- a/py313-support.patch +++ /dev/null @@ -1,26 +0,0 @@ -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 a27b9a6..dd2932b 100644 --- a/python-biopython.changes +++ b/python-biopython.changes @@ -1,3 +1,19 @@ +Wed Mar 12 23:26:04 UTC 2025 - Friedrich Haubensak + +- update to 1.85: + * Some optimisation work was done for "Bio.SeqIO" + * "Bio.motifs" now supports reading PFM from Cys2His2 Zinc Finger + Proteins PWM Predictor + * "Bio.motifs" now supports reverse complementing RNA motifs + and correctly generating degenerate consensus sequences for + RNA motifs + * "Bio.motifs.minimal" now supports parsing RNA motifs and + parsing motifs for which not all statistics are provided + * "Bio.motifs.clusterbuster" now supports parsing GAP and WEIGHT + parameters and can optionally write Cluster Buster motif files + with floats instead of integers +- drop patch py313-support.patch, now upstream + ------------------------------------------------------------------- Fri Nov 22 12:13:40 UTC 2024 - Dirk Müller diff --git a/python-biopython.spec b/python-biopython.spec index 2feec91..87c2bac 100644 --- a/python-biopython.spec +++ b/python-biopython.spec @@ -20,14 +20,13 @@ %bcond_with test %{?sle15_python_module_pythons} Name: python-biopython -Version: 1.84 +Version: 1.85 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}