Accepting request 1055870 from devel:languages:python:numeric

- 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    instances of ``collections.OrderedDict`` have been replaced by either standard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

OBS-URL: https://build.opensuse.org/request/show/1055870
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-biopython?expand=0&rev=9

biopython-1.79.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:edb07eac99d3b8abd7ba56ff4bedec9263f76dfc3c3f450e7d2e2bcdecf8559b
-size 16738730

biopython-1.80.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:52805e9af88767e450e2df8113b5bc59e964e2e8a7bb803a83570bdbb51c0e43
+size 17924553

python-biopython.changes

@@ -1,3 +1,51 @@
+-------------------------------------------------------------------
+Wed Jan  4 14:19:49 UTC 2023 - Dirk Müller <dmueller@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.
+
 -------------------------------------------------------------------
 Sun Mar 27 13:57:19 UTC 2022 - Dirk Müller <dmueller@suse.com>
 

python-biopython.spec

@@ -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