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Accepting request 819377 from home:mcalabkova:branches:devel:languages:python:numeric

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- 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.

OBS-URL: https://build.opensuse.org/request/show/819377
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python-biopython?expand=0&rev=9
This commit is contained in:
Tomáš Chvátal 2020-07-08 10:10:38 +00:00 committed by Git OBS Bridge
parent e0e5d221c6
commit 52977e93ef
4 changed files with 36 additions and 6 deletions
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3
biopython-1.75.tar.gz
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size 16449672

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biopython-1.77.tar.gz Normal file
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python-biopython.changes
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@ -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>

6
python-biopython.spec
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@ -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