Hello community,
here is the log from the commit of package python-biopython for
openSUSE:Factory checked in at 2019-01-21 10:46:29
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/python-biopython (Old)
and /work/SRC/openSUSE:Factory/.python-biopython.new.28833 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "python-biopython"
Mon Jan 21 10:46:29 2019 rev:2 rq:662924 version:1.73
Changes:
--------
--- /work/SRC/openSUSE:Factory/python-biopython/python-biopython.changes
2018-05-29 16:47:33.454233309 +0200
+++
/work/SRC/openSUSE:Factory/.python-biopython.new.28833/python-biopython.changes
2019-01-21 10:46:35.168295846 +0100
@@ -1,0 +2,52 @@
+Fri Jan 4 17:31:38 UTC 2019 - Todd R <[email protected]>
+
+- 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.
+
+-------------------------------------------------------------------
Old:
----
biopython-1.71.tar.gz
New:
----
biopython-1.73.tar.gz
python-biopython-rpmlintrc
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ python-biopython.spec ++++++
--- /var/tmp/diff_new_pack.5jImyh/_old 2019-01-21 10:46:36.292294465 +0100
+++ /var/tmp/diff_new_pack.5jImyh/_new 2019-01-21 10:46:36.292294465 +0100
@@ -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
-BuildRequires: fdupes
-BuildRequires: python-rpm-macros
-BuildRequires: python3-2to3
+Source0:
https://files.pythonhosted.org/packages/source/b/biopython/biopython-%{version}.tar.gz
+Source100: python-biopython-rpmlintrc
BuildRequires: %{python_module devel}
-BuildRequires: %{python_module setuptools}
BuildRequires: %{python_module numpy-devel}
+BuildRequires: %{python_module setuptools}
BuildRequires: %{python_module xml}
+BuildRequires: fdupes
+BuildRequires: flex
+BuildRequires: python-rpm-macros
+BuildRequires: python3-2to3
Requires: python-numpy
Requires: python-xml
Recommends: python-matplotlib
@@ -69,7 +70,7 @@
%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 @@
%endif
%files %{python_files}
-%defattr(-,root,root)
%doc CONTRIB.rst DEPRECATED.rst NEWS.rst README.rst
%doc Doc/
%license LICENSE.rst
++++++ biopython-1.71.tar.gz -> biopython-1.73.tar.gz ++++++
/work/SRC/openSUSE:Factory/python-biopython/biopython-1.71.tar.gz
/work/SRC/openSUSE:Factory/.python-biopython.new.28833/biopython-1.73.tar.gz
differ: char 5, line 1
++++++ python-biopython-rpmlintrc ++++++
addFilter("devel-file-in-non-devel-package .*\.c")
addFilter("devel-file-in-non-devel-package .*\.h")
