Script 'mail_helper' called by obssrc Hello community, 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) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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 <dmuel...@suse.com> + +- 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+ * Because dict retains the item order by default since Python3.6, all + instances of ``collections.OrderedDict`` have been replaced by either standard + ``dict`` or where appropriate by ``collections.defaultsdict``.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