From 562201f9d30ab8b247dda10f2cd6fea9ef06024bb1eb14586a673dbdedfd2fa2 Mon Sep 17 00:00:00 2001 From: Dominique Leuenberger Date: Mon, 21 Jan 2019 09:46:29 +0000 Subject: [PATCH] Accepting request 662924 from devel:languages:python:numeric 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 --- biopython-1.71.tar.gz | 3 --- biopython-1.73.tar.gz | 3 +++ python-biopython-rpmlintrc | 2 ++ python-biopython.changes | 52 ++++++++++++++++++++++++++++++++++++++ python-biopython.spec | 22 ++++++++-------- 5 files changed, 68 insertions(+), 14 deletions(-) delete mode 100644 biopython-1.71.tar.gz create mode 100644 biopython-1.73.tar.gz create mode 100644 python-biopython-rpmlintrc diff --git a/biopython-1.71.tar.gz b/biopython-1.71.tar.gz deleted file mode 100644 index aa5fa08..0000000 --- a/biopython-1.71.tar.gz +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:4f1770a29a5b18fcaca759bbc888083cdde2b301f073439ff640570d4a93e033 -size 16031832 diff --git a/biopython-1.73.tar.gz b/biopython-1.73.tar.gz new file mode 100644 index 0000000..c633614 --- /dev/null +++ b/biopython-1.73.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:70c5cc27dc61c23d18bb33b6d38d70edc4b926033aea3b7434737c731c94a5e0 +size 15715102 diff --git a/python-biopython-rpmlintrc b/python-biopython-rpmlintrc new file mode 100644 index 0000000..04dad7f --- /dev/null +++ b/python-biopython-rpmlintrc @@ -0,0 +1,2 @@ +addFilter("devel-file-in-non-devel-package .*\.c") +addFilter("devel-file-in-non-devel-package .*\.h") diff --git a/python-biopython.changes b/python-biopython.changes index 1faf983..22a45ef 100644 --- a/python-biopython.changes +++ b/python-biopython.changes @@ -1,3 +1,55 @@ +------------------------------------------------------------------- +Fri Jan 4 17:31:38 UTC 2019 - Todd R + +- 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 diff --git a/python-biopython.spec b/python-biopython.spec index 907df32..f770f45 100644 --- a/python-biopython.spec +++ b/python-biopython.spec @@ -1,7 +1,7 @@ # # 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 # 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) # 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-%{**}} Name: python-biopython -Version: 1.71 +Version: 1.73 Release: 0 Summary: Python Tools for Computational Molecular Biology License: MIT Group: Development/Libraries/Python Url: http://www.biopython.org -Source: https://files.pythonhosted.org/packages/source/b/biopython/biopython-%{version}.tar.gz -BuildRequires: flex +Source0: https://files.pythonhosted.org/packages/source/b/biopython/biopython-%{version}.tar.gz +Source100: python-biopython-rpmlintrc +BuildRequires: %{python_module devel} +BuildRequires: %{python_module numpy-devel} +BuildRequires: %{python_module setuptools} +BuildRequires: %{python_module xml} BuildRequires: fdupes +BuildRequires: flex BuildRequires: python-rpm-macros 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-xml Recommends: python-matplotlib @@ -69,7 +70,7 @@ export LANG=en_US.UTF-8 %install export LANG=en_US.UTF-8 %python_install -%python_expand %fdupes %{buildroot}%{$python_sitelib} +%python_expand %fdupes %{buildroot}%{$python_sitearch} %if %{with test} %check @@ -78,7 +79,6 @@ export LANG=en_US.UTF-8 %endif %files %{python_files} -%defattr(-,root,root) %doc CONTRIB.rst DEPRECATED.rst NEWS.rst README.rst %doc Doc/ %license LICENSE.rst