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here is the log from the commit of package python-biopython for
openSUSE:Factory checked in at 2023-01-04 17:53:47
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/python-biopython (Old)
and /work/SRC/openSUSE:Factory/.python-biopython.new.1563 (New)
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Package is "python-biopython"
Wed Jan 4 17:53:47 2023 rev:9 rq:1055870 version:1.80
Changes:
--------
--- /work/SRC/openSUSE:Factory/python-biopython/python-biopython.changes
2022-04-03 21:31:36.335415265 +0200
+++
/work/SRC/openSUSE:Factory/.python-biopython.new.1563/python-biopython.changes
2023-01-04 17:54:30.754857023 +0100
@@ -1,0 +2,48 @@
+Wed Jan 4 14:19:49 UTC 2023 - Dirk Müller <[email protected]>
+
+- update to 1.80:
+ * This release of Biopython supports Python 3.7, 3.8, 3.9, 3.10, 3.11. It
+ has also been tested on PyPy3.7 v7.3.5.
+ * Functions ``read``, ``parse``, and ``write`` were added to ``Bio.Align``
+ to read and write ``Alignment`` objects.
+ * Because dict retains the item order by default since Python3.6, all
+ instances of ``collections.OrderedDict`` have been replaced by either
standard
+ ``dict`` or where appropriate by ``collections.defaultsdict``.
+ * The ``Bio.motifs.jaspar.db`` now returns ``tf_family`` and ``tf_class``
+ as a string array since the JASPAR 2018 release.
+ * The Local Composition Complexity functions from ``Bio.SeqUtils`` now
+ uses base 4 log instead of 2 as stated in the original reference Konopka
+ (2005), * Sequence Complexity and Composition.
https://doi.org/10.1038/npg.els.0005260
+ * Append mode is now supported in ``Bio.bgzf`` (and a bug parsing blocked
+ GZIP files with an internal empty block fixed).
+ * The experimental warning was dropped from ``Bio.phenotype`` (which was
+ new in Biopython 1.67).
+ * Sequences now have a ``defined`` attribute that returns a boolean
+ indicating if the underlying data is defined or not.
+ * The ``Bio.PDB`` module now includes a structural alignment module, using
+ the combinatorial extension algorithm of Shindyalov and Bourne, commonly
+ known as CEAlign. The module allows for two structures to be aligned based
solely
+ on their 3D conformation, ie. in a sequence-independent manner. The method
+ is particularly powerful when the structures shared a very low degree of
+ sequence similarity. The new module is available in ``Bio.PDB.CEAligner``
with an
+ interface similar to other 3D superimposition modules.
+ * A new module ``Bio.PDB.qcprot`` implements the QCP superposition
+ algorithm in pure Python, deprecating the existing C implementation. This
leads to a
+ slight performance improvement and to much better maintainability. The
+ refactored ``qcprot.QCPSuperimposer`` class has small changes to its API,
to better
+ mirror that of ``Bio.PDB.Superimposer``.
+ * The ``Bio.PDB.PDBList`` module now allows downloading biological
+ assemblies, for one or more entries of the wwPDB.
+ * In the ``Bio.Restriction`` module, each restriction enzyme now includes
+ an `id` property giving the numerical identifier for the REBASE database
+ identifier from which the enzyme object was created, and a `uri` property
with a
+ canonical `identifiers.org` link to the database, for use in linked-data
+ representations.
+ * Add new ``gc_fraction`` function in ``SeqUtils`` and marks ``GC`` for
+ future deprecation.
+ * Support for the old format (dating back to 2004) of the GN line in
+ SwissProt files was dropped in ``Bio.SwissProt``.
+ * Additionally, a number of small bugs and typos have been fixed with
+ additions to the test suite.
+
+-------------------------------------------------------------------
Old:
----
biopython-1.79.tar.gz
New:
----
biopython-1.80.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ python-biopython.spec ++++++
--- /var/tmp/diff_new_pack.VTvwmy/_old 2023-01-04 17:54:31.266860041 +0100
+++ /var/tmp/diff_new_pack.VTvwmy/_new 2023-01-04 17:54:31.270860065 +0100
@@ -1,7 +1,7 @@
#
# spec file for package python-biopython
#
-# Copyright (c) 2022 SUSE LLC
+# Copyright (c) 2023 SUSE LLC
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
@@ -22,7 +22,7 @@
%define skip_python2 1
%define skip_python36 1
Name: python-biopython
-Version: 1.79
+Version: 1.80
Release: 0
Summary: Python Tools for Computational Molecular Biology
License: BSD-3-Clause AND MIT
++++++ biopython-1.79.tar.gz -> biopython-1.80.tar.gz ++++++
/work/SRC/openSUSE:Factory/python-biopython/biopython-1.79.tar.gz
/work/SRC/openSUSE:Factory/.python-biopython.new.1563/biopython-1.80.tar.gz
differ: char 5, line 1
