Accepting request 819448 from devel:languages:python:numeric

OBS-URL: https://build.opensuse.org/request/show/819448
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-biopython?expand=0&rev=5

biopython-1.75.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:5060e4ef29c2bc214749733634051be5b8d11686c6590fa155c3443dcaa89906
-size 16449672

biopython-1.77.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:fb1936e9ca9e7af8de1050e84375f23328e04b801063edf0ad73733494d8ec42
+size 16837021

python-biopython.changes

@@ -1,3 +1,33 @@
+-------------------------------------------------------------------
+Wed Jul  8 07:31:29 UTC 2020 - Marketa Calabkova <mcalabkova@suse.com>
+
+- Update to version 1.77
+  * **We have dropped support for Python 2 now.**
+  * ``pairwise2`` now allows the input of parameters with keywords and returns the
+    alignments as a list of ``namedtuples``.
+  * The codon tables have been updated to NCBI genetic code table version 4.5,
+    which adds Cephalodiscidae mitochondrial as table 33.
+  * Updated ``Bio.Restriction`` to the January 2020 release of REBASE.
+  * A major contribution by Rob Miller to ``Bio.PDB`` provides new methods to
+    handle protein structure transformations using dihedral angles (internal
+    coordinates). The new framework supports lossless interconversion between
+    internal and cartesian coordinates, which, among other uses, simplifies the
+    analysis and manipulation of coordinates of proteins structures.
+  * ``PDBParser`` and ``PDBIO`` now support PQR format file parsing and input/
+    output.
+  * In addition to the mainstream ``x86_64`` aka ``AMD64`` CPU architecture, we
+    now also test every contribution on the ``ARM64``, ``ppc64le``, and ``s390x``
+    CPUs under Linux thanks to Travis CI. Further post-release testing done by
+    Debian and other packagers and distributors of Biopython also covers these
+    CPUs.
+  * ``Bio.motifs.PositionSpecificScoringMatrix.search()`` method has been
+    re-written: it now applies ``.calculate()`` to chunks of the sequence
+    to maintain a low memory footprint for long sequences.
+  * Additionally, a number of small bugs and typos have been fixed with further
+    additions to the test suite. There has been further work to follow the Python
+    PEP8, PEP257 and best practice standard coding style, and more of the code
+    style has been reformatted with the ``black`` tool.
+
 -------------------------------------------------------------------
 Wed Nov 20 20:17:31 UTC 2019 - Todd R <toddrme2178@gmail.com>
 

python-biopython.spec

@@ -1,7 +1,7 @@
 #
 # spec file for package python-biopython
 #
-# Copyright (c) 2019 SUSE LINUX GmbH, Nuernberg, Germany.
+# Copyright (c) 2020 SUSE LLC
 #
 # All modifications and additions to the file contributed by third parties
 # remain the property of their copyright owners, unless otherwise agreed
@@ -19,8 +19,9 @@
 %{?!python_module:%define python_module() python-%{**} python3-%{**}}
 # Tests require a network connection
 %bcond_with test
+%define skip_python2 1
 Name:           python-biopython
-Version:        1.75
+Version:        1.77
 Release:        0
 Summary:        Python Tools for Computational Molecular Biology
 License:        MIT AND BSD-3-Clause
@@ -34,7 +35,6 @@ BuildRequires:  %{python_module xml}
 BuildRequires:  fdupes
 BuildRequires:  flex
 BuildRequires:  python-rpm-macros
-BuildRequires:  python3-2to3
 Requires:       python-numpy
 Requires:       python-xml
 Recommends:     python-matplotlib