From 30a50e8f9e58d4bc9f76b406aaf2013a7d3e03b17575152929e9055ff016da0b Mon Sep 17 00:00:00 2001 From: Matej Cepl Date: Sun, 21 Feb 2021 06:56:38 +0000 Subject: [PATCH] Accepting request 874100 from home:andythe_great:branches:devel:languages:python:numeric - 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 --- biopython-1.77.tar.gz | 3 --- biopython-1.78.tar.gz | 3 +++ python-biopython.changes | 22 ++++++++++++++++++++++ python-biopython.spec | 6 +++--- 4 files changed, 28 insertions(+), 6 deletions(-) delete mode 100644 biopython-1.77.tar.gz create mode 100644 biopython-1.78.tar.gz diff --git a/biopython-1.77.tar.gz b/biopython-1.77.tar.gz deleted file mode 100644 index 263b264..0000000 --- a/biopython-1.77.tar.gz +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:fb1936e9ca9e7af8de1050e84375f23328e04b801063edf0ad73733494d8ec42 -size 16837021 diff --git a/biopython-1.78.tar.gz b/biopython-1.78.tar.gz new file mode 100644 index 0000000..e358ea7 --- /dev/null +++ b/biopython-1.78.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1ee0a0b6c2376680fea6642d5080baa419fd73df104a62d58a8baf7a8bbe4564 +size 16895184 diff --git a/python-biopython.changes b/python-biopython.changes index 57d9f15..08d1e66 100644 --- a/python-biopython.changes +++ b/python-biopython.changes @@ -1,3 +1,25 @@ +------------------------------------------------------------------- +Sat Feb 20 19:29:23 UTC 2021 - andy great + +- 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 diff --git a/python-biopython.spec b/python-biopython.spec index 94e8eaf..59f89a4 100644 --- a/python-biopython.spec +++ b/python-biopython.spec @@ -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