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Accepting request 662924 from devel:languages:python:numeric

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OBS-URL: https://build.opensuse.org/request/show/662924
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-biopython?expand=0&rev=2
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Dominique Leuenberger 2019-01-21 09:46:29 +00:00 committed by Git OBS Bridge
parent 061a2d5331
commit 562201f9d3
5 changed files with 68 additions and 14 deletions
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biopython-1.71.tar.gz
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version https://git-lfs.github.com/spec/v1
oid sha256:4f1770a29a5b18fcaca759bbc888083cdde2b301f073439ff640570d4a93e033
size 16031832

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biopython-1.73.tar.gz Normal file
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version https://git-lfs.github.com/spec/v1
oid sha256:70c5cc27dc61c23d18bb33b6d38d70edc4b926033aea3b7434737c731c94a5e0
size 15715102

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python-biopython-rpmlintrc Normal file
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addFilter("devel-file-in-non-devel-package .*\.c")
addFilter("devel-file-in-non-devel-package .*\.h")

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python-biopython.changes
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-------------------------------------------------------------------
Fri Jan 4 17:31:38 UTC 2019 - Todd R <toddrme2178@gmail.com>
- Update to version 1.73
* As in recent releases, more of our code is now explicitly available under
either our original "Biopython License Agreement", or the very similar but
more commonly used "3-Clause BSD License". See the ``LICENSE.rst`` file for
more details.
* The dictionary-like indexing in SeqIO and SearchIO will now explicitly preserve
record order to match a behaviour change in the Python standard dict object.
This means looping over the index will load the records in the on-disk order,
which will be much faster (previously it would be effectively at random, based
on the key hash sorting).
* The "grant" matrix in Bio.SubsMat.MatrixInfo has been replaced as our original
values taken from Gerhard Vogt's old webpages at EMBL Heidelberg were
discovered to be in error. The new values have been transformed following
Vogt's approach, taking the global maximum 215 minus the similarity scores
from the original paper Grantham (1974), to give a distance measure.
* Additionally, a number of small bugs and typos have been fixed with further
additions to the test suite, and there has been further work to follow the
Python PEP8, PEP257 and best practice standard coding style.
* Double-quote characters in GenBank feature qualifier values in ``Bio.SeqIO``
are now escaped as per the NCBI standard. Improperly escaped values trigger a
warning on parsing.
* There is a new command line wrapper for the BWA-MEM sequence mapper.
* The string-based FASTA parsers in ``Bio.SeqIO.FastaIO`` have been optimised,
which also speeds up parsing FASTA files using ``Bio.SeqIO.parse()``.
- Update to version 1.72
* Internal changes to Bio.SeqIO have sped up the SeqRecord .format method and
SeqIO.write (especially when used in a for loop).
* The MAF alignment indexing in Bio.AlignIO.MafIO has been updated to use
inclusive end co-ordinates to better handle searches at end points. This
will require you to rebuild any existing MAF index files.
* In this release more of our code is now explicitly available under either our
original "Biopython License Agreement", or the very similar but more commonly
used "3-Clause BSD License". See the ``LICENSE.rst`` file for more details.
* The Entrez module now supports the NCBI API key. Also you can now set a custom
directory for DTD and XSD files. This allows Entrez to be used in environments
like AWS Lambda, which restricts write access to specific directories.
Improved support for parsing NCBI Entrez XML files that use XSD schemas.
* Internal changes to our C code mean that NumPy is no longer required at
compile time - only at run time (and only for those modules which use NumPy).
* Seq, UnknownSeq, MutableSeq and derived classes now support integer
multiplication methods, matching native Python string methods.
* A translate method has been added to Bio.SeqFeature that will extract a
feature and translate it using the codon_start and transl_table qualifiers
of the feature if they are present.
* Bio.SearchIO is no longer considered experimental, and so it does not raise
warnings anymore when imported.
* A new pairwise sequence aligner is available in Bio.Align, as an alternative
to the existing pairwise sequence aligner in Bio.pairwise2.
------------------------------------------------------------------- -------------------------------------------------------------------
Wed May 9 03:23:14 UTC 2018 - toddrme2178@gmail.com Wed May 9 03:23:14 UTC 2018 - toddrme2178@gmail.com

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python-biopython.spec
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# #
# spec file for package python-biopython # spec file for package python-biopython
# #
# Copyright (c) 2018 SUSE LINUX GmbH, Nuernberg, Germany. # Copyright (c) 2019 SUSE LINUX GmbH, Nuernberg, Germany.
# #
# All modifications and additions to the file contributed by third parties # All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed # remain the property of their copyright owners, unless otherwise agreed
@ -12,7 +12,7 @@
# license that conforms to the Open Source Definition (Version 1.9) # license that conforms to the Open Source Definition (Version 1.9)
# published by the Open Source Initiative. # published by the Open Source Initiative.
# Please submit bugfixes or comments via http://bugs.opensuse.org/ # Please submit bugfixes or comments via https://bugs.opensuse.org/
# #
@ -21,21 +21,22 @@
%{?!python_module:%define python_module() python-%{**} python3-%{**}} %{?!python_module:%define python_module() python-%{**} python3-%{**}}
Name: python-biopython Name: python-biopython
Version: 1.71 Version: 1.73
Release: 0 Release: 0
Summary: Python Tools for Computational Molecular Biology Summary: Python Tools for Computational Molecular Biology
License: MIT License: MIT
Group: Development/Libraries/Python Group: Development/Libraries/Python
Url: http://www.biopython.org Url: http://www.biopython.org
Source: https://files.pythonhosted.org/packages/source/b/biopython/biopython-%{version}.tar.gz Source0: https://files.pythonhosted.org/packages/source/b/biopython/biopython-%{version}.tar.gz
BuildRequires: flex Source100: python-biopython-rpmlintrc
BuildRequires: %{python_module devel}
BuildRequires: %{python_module numpy-devel}
BuildRequires: %{python_module setuptools}
BuildRequires: %{python_module xml}
BuildRequires: fdupes BuildRequires: fdupes
BuildRequires: flex
BuildRequires: python-rpm-macros BuildRequires: python-rpm-macros
BuildRequires: python3-2to3 BuildRequires: python3-2to3
BuildRequires: %{python_module devel}
BuildRequires: %{python_module setuptools}
BuildRequires: %{python_module numpy-devel}
BuildRequires: %{python_module xml}
Requires: python-numpy Requires: python-numpy
Requires: python-xml Requires: python-xml
Recommends: python-matplotlib Recommends: python-matplotlib
@ -69,7 +70,7 @@ export LANG=en_US.UTF-8
%install %install
export LANG=en_US.UTF-8 export LANG=en_US.UTF-8
%python_install %python_install
%python_expand %fdupes %{buildroot}%{$python_sitelib} %python_expand %fdupes %{buildroot}%{$python_sitearch}
%if %{with test} %if %{with test}
%check %check
@ -78,7 +79,6 @@ export LANG=en_US.UTF-8
%endif %endif
%files %{python_files} %files %{python_files}
%defattr(-,root,root)
%doc CONTRIB.rst DEPRECATED.rst NEWS.rst README.rst %doc CONTRIB.rst DEPRECATED.rst NEWS.rst README.rst
%doc Doc/ %doc Doc/
%license LICENSE.rst %license LICENSE.rst