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Accepting request 874100 from home:andythe_great:branches:devel:languages:python:numeric

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- Update to version 1.7.8.
  * The main change is that Bio.Alphabet is no longer used. In some
    cases you will now have to specify expected letters, molecule 
    type (DNA, RNA, protein), or gap character explicitly.
  * Bio.SeqIO.parse() is faster with "fastq" format due to small 
    improvements in the Bio.SeqIO.QualityIO module.
  * The SeqFeature object's .extract() method can now be used for 
    trans-spliced locations via an optional dictionary of references.
  * 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.
  * Additionally, a number of small bugs and typos have been fixed
    with additions to the test suite. There has been further work to
    follow the Python PEP8, PEP257 and best practice standard coding
    style, and all of the tests have been reformatted with the black
    tool to match the main code base.
- Skip python36 because numpy no longer support it.

OBS-URL: https://build.opensuse.org/request/show/874100
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python-biopython?expand=0&rev=13
This commit is contained in:
Matej Cepl 2021-02-21 06:56:38 +00:00 committed by Git OBS Bridge
parent 38ef6639e1
commit 30a50e8f9e
4 changed files with 28 additions and 6 deletions
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3
biopython-1.77.tar.gz
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biopython-1.78.tar.gz Normal file
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python-biopython.changes
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@ -1,3 +1,25 @@
-------------------------------------------------------------------
Sat Feb 20 19:29:23 UTC 2021 - andy great <andythe_great@pm.me>
- Update to version 1.7.8.
* The main change is that Bio.Alphabet is no longer used. In some
cases you will now have to specify expected letters, molecule
type (DNA, RNA, protein), or gap character explicitly.
* Bio.SeqIO.parse() is faster with "fastq" format due to small
improvements in the Bio.SeqIO.QualityIO module.
* The SeqFeature object's .extract() method can now be used for
trans-spliced locations via an optional dictionary of references.
* 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.
* Additionally, a number of small bugs and typos have been fixed
with additions to the test suite. There has been further work to
follow the Python PEP8, PEP257 and best practice standard coding
style, and all of the tests have been reformatted with the black
tool to match the main code base.
- Skip python36 because numpy no longer support it.
-------------------------------------------------------------------
Tue Nov 3 15:58:16 UTC 2020 - Matej Cepl <mcepl@suse.com>

6
python-biopython.spec
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@ -1,7 +1,7 @@
#
# spec file for package python-biopython
#
# Copyright (c) 2020 SUSE LLC
# Copyright (c) 2021 SUSE LLC
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
@ -20,8 +20,9 @@
# Tests require a network connection
%bcond_with test
%define skip_python2 1
%define skip_python36 1
Name: python-biopython
Version: 1.77
Version: 1.78
Release: 0
Summary: Python Tools for Computational Molecular Biology
License: MIT AND BSD-3-Clause
@ -54,7 +55,6 @@ available Python tools for computational molecular biology.
%prep
%setup -q -n biopython-%{version}
find -type f -name "*.py" -exec sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' {} 2>/dev/null ';'
sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' Scripts/Structure/hsexpo
# Example scripts cannot be in a subdirectory
mv -v Doc/examples examples