Hello community,
here is the log from the commit of package python-biopython for
openSUSE:Factory checked in at 2019-07-26 17:33:27
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/python-biopython (Old)
and /work/SRC/openSUSE:Factory/.python-biopython.new.4126 (New)
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Package is "python-biopython"
Fri Jul 26 17:33:27 2019 rev:3 rq:717711 version:1.74
Changes:
--------
--- /work/SRC/openSUSE:Factory/python-biopython/python-biopython.changes
2019-01-21 10:46:35.168295846 +0100
+++
/work/SRC/openSUSE:Factory/.python-biopython.new.4126/python-biopython.changes
2019-07-26 17:33:29.528107070 +0200
@@ -1,0 +2,50 @@
+Tue Jul 23 01:23:01 UTC 2019 - Todd R <[email protected]>
+
+- Update to version 1.74
+ * Our core sequence objects (``Seq``, ``UnknownSeq``, and ``MutableSeq``) now
+ have a string-like ``.join()`` method.
+ * The NCBI now allows longer accessions in the GenBank file LOCUS line,
meaning
+ the fields may not always follow the historical column based positions. We
+ no longer give a warning when parsing these. We now allow writing such
files
+ (although with a warning as support for reading them is not yet
widespread).
+ * Support for the ``mysqlclient`` package, a fork of MySQLdb, has been added.
+ * We now capture the IDcode field from PDB Header records.
+ * ``Bio.pairwise2``'s pretty-print output from ``format_alignment`` has been
+ optimized for local alignments: If they do not consist of the whole
sequences,
+ only the aligned section of the sequences are shown, together with the
start
+ positions of the sequences (in 1-based notation). Alignments of lists will
now
+ also be prettily printed.
+ * ``Bio.SearchIO`` now supports parsing the text output of the HHsuite
protein
+ sequence search tool. The format name is ``hhsuite2-text`` and
+ ``hhsuite3-text``, for versions 2 and 3 of HHsuite, respectively.
+ * ``Bio.SearchIO`` HSP objects has a new attribute called ``output_index``.
This
+ attribute is meant for capturing the order by which the HSP were output in
the
+ parsed file and is set with a default value of -1 for all HSP objects. It
is
+ also used for sorting the output of ``QueryResult.hsps``.
+ * ``Bio.SeqIO.AbiIO`` has been updated to preserve bytes value when parsing.
The
+ goal of this change is make the parser more robust by being able to extract
+ string-values that are not utf-8-encoded. This affects all tag values,
except
+ for ID and description values, where they need to be extracted as strings
+ to conform to the ``SeqRecord`` interface. In this case, the parser will
+ attempt to decode using ``utf-8`` and fall back to the system encoding if
that
+ fails. This change affects Python 3 only.
+ * ``Bio.motifs.mast`` has been updated to parse XML output files from MAST
over
+ the plain-text output file. The goal of this change is to parse a more
+ structured data source with minimal loss of functionality upon future MAST
+ releases. Class structure remains the same plus an additional attribute
+ ``Record.strand_handling`` required for diagram parsing.
+ * ``Bio.Entrez`` now automatically retries HTTP requests on failure. The
+ maximum number of tries and the sleep between them can be configured by
+ changing ``Bio.Entrez.max_tries`` and ``Bio.Entrez.sleep_between_tries``.
+ (The defaults are 3 tries and 15 seconds, respectively.)
+ * All tests using the older print-and-compare approach have been replaced by
+ unittests following Python's standard testing framework.
+ * On the documentation side, all the public modules, classes, methods and
+ functions now have docstrings (built in help strings). Furthermore, the PDF
+ version of the *Biopython Tutorial and Cookbook* now uses syntax coloring
+ for code snippets.
+ * 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.
+
+-------------------------------------------------------------------
Old:
----
biopython-1.73.tar.gz
New:
----
biopython-1.74.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ python-biopython.spec ++++++
--- /var/tmp/diff_new_pack.MYeiZG/_old 2019-07-26 17:33:30.244106777 +0200
+++ /var/tmp/diff_new_pack.MYeiZG/_new 2019-07-26 17:33:30.244106777 +0200
@@ -21,10 +21,10 @@
%{?!python_module:%define python_module() python-%{**} python3-%{**}}
Name: python-biopython
-Version: 1.73
+Version: 1.74
Release: 0
Summary: Python Tools for Computational Molecular Biology
-License: MIT
+License: MIT AND BSD-3-Clause
Group: Development/Libraries/Python
Url: http://www.biopython.org
Source0:
https://files.pythonhosted.org/packages/source/b/biopython/biopython-%{version}.tar.gz
@@ -47,7 +47,6 @@
Recommends: python-pygraphviz
Recommends: python-rdflib
Recommends: python-reportlab
-BuildRoot: %{_tmppath}/%{name}-%{version}-build
%python_subpackages
%description
++++++ biopython-1.73.tar.gz -> biopython-1.74.tar.gz ++++++
/work/SRC/openSUSE:Factory/python-biopython/biopython-1.73.tar.gz
/work/SRC/openSUSE:Factory/.python-biopython.new.4126/biopython-1.74.tar.gz
differ: char 5, line 1
