Accepting request 1252765 from devel:languages:python:numeric

OBS-URL: https://build.opensuse.org/request/show/1252765
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-biopython?expand=0&rev=15

biopython-1.83.tar.gz

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

biopython-1.85.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:5dafab74059de4e78f49f6b5684eddae6e7ce46f09cfa059c1d1339e8b1ea0a6
+size 19909902

python-biopython.changes

@@ -1,3 +1,42 @@
+Wed Mar 12 23:26:04 UTC 2025 - Friedrich Haubensak <hsk17@mail.de>
+
+- 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 <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

@@ -16,13 +16,11 @@
 #
 
 
-%{?!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:        1.85
 Release:        0
 Summary:        Python Tools for Computational Molecular Biology
 License:        BSD-3-Clause AND MIT
@@ -53,7 +51,7 @@ 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