Hello community,
here is the log from the commit of package python-biopython for
openSUSE:Factory checked in at 2019-11-21 12:59:22
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/python-biopython (Old)
and /work/SRC/openSUSE:Factory/.python-biopython.new.26869 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "python-biopython"
Thu Nov 21 12:59:22 2019 rev:4 rq:750003 version:1.75
Changes:
--------
--- /work/SRC/openSUSE:Factory/python-biopython/python-biopython.changes
2019-07-26 17:33:29.528107070 +0200
+++
/work/SRC/openSUSE:Factory/.python-biopython.new.26869/python-biopython.changes
2019-11-21 12:59:23.782514399 +0100
@@ -1,0 +2,52 @@
+Wed Nov 20 20:17:31 UTC 2019 - Todd R <[email protected]>
+
+- Update to version 1.75
+ * The restriction enzyme list in Bio.Restriction has been updated to the
August
+ 2019 release of REBASE.
+ * ``Bio.SeqIO`` now supports reading and writing files in the native format
of
+ Christian Marck's DNA Strider program ("xdna" format, also used by Serial
+ Cloner), as well as reading files in the native formats of GSL Biotech's
+ SnapGene ("snapgene") and Textco Biosoftware's Gene Construction Kit
("gck").
+ * ``Bio.AlignIO`` now supports GCG MSF multiple sequence alignments as the
"msf"
+ format (work funded by the National Marrow Donor Program).
+ * The main ``Seq`` object now has string-like ``.index()`` and ``.rindex()``
+ methods, matching the existing ``.find()`` and ``.rfind()``
implementations.
+ The ``MutableSeq`` object retains its more list-like ``.index()``
behaviour.
+ * The ``MMTFIO`` class has been added that allows writing of MMTF file format
+ files from a Biopython structure object. ``MMTFIO`` has a similar
interface to
+ ``PDBIO`` and ``MMCIFIO``, including the use of a ``Select`` class to write
+ out a specified selection. This final addition to read/write support for
+ PDB/mmCIF/MMTF in Biopython allows conversion between all three file
formats.
+ * Values from mmCIF files are now read in as a list even when they consist
of a
+ single value. This change improves consistency and reduces the likelihood
of
+ making an error, but will require user code to be updated accordingly.
+ * ``Bio.PDB`` has been updated to support parsing REMARK 99 header entries
from
+ PDB-style Astral files.
+ * A new keyword parameter ``full_sequences`` was added to ``Bio.pairwise2``'s
+ pretty print method ``format_alignment`` to restore the output of local
+ alignments to the 'old' format (showing the whole sequences including the
+ un-aligned parts instead of only showing the aligned parts).
+ * A new function ``charge_at_pH(pH)`` has been added to ``ProtParam`` and
+ ``IsoelectricPoint`` in ``Bio.SeqUtils``.
+ * The ``PairwiseAligner`` in ``Bio.Align`` was extended to allow generalized
+ pairwise alignments, i.e. alignments of any Python object, for example
+ three-letter amino acid sequences, three-nucleotide codons, and arrays of
+ integers.
+ * A new module ``substitution_matrices`` was added to ``Bio.Align``, which
+ includes an ``Array`` class that can be used as a substitution matrix. As
+ the ``Array`` class is a subclass of a numpy array, mathematical operations
+ can be applied to it directly, and C code that makes use of substitution
+ matrices can directly access the numerical values stored in the
substitution
+ matrices. This module is intended as a replacement of ``Bio.SubsMat``,
+ which is currently unmaintained.
+ * 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 further
+ additions to the test suite, and there has been further work to follow the
+ Python PEP8, PEP257 and best practice standard coding style. We have also
+ started to use the ``black`` Python code formatting tool.
+
+
+-------------------------------------------------------------------
Old:
----
biopython-1.74.tar.gz
New:
----
biopython-1.75.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ python-biopython.spec ++++++
--- /var/tmp/diff_new_pack.g2nlyD/_old 2019-11-21 12:59:24.626514140 +0100
+++ /var/tmp/diff_new_pack.g2nlyD/_new 2019-11-21 12:59:24.626514140 +0100
@@ -16,17 +16,15 @@
#
+%{?!python_module:%define python_module() python-%{**} python3-%{**}}
# Tests require a network connection
%bcond_with test
-
-%{?!python_module:%define python_module() python-%{**} python3-%{**}}
Name: python-biopython
-Version: 1.74
+Version: 1.75
Release: 0
Summary: Python Tools for Computational Molecular Biology
License: MIT AND BSD-3-Clause
-Group: Development/Libraries/Python
-Url: http://www.biopython.org
+URL: http://www.biopython.org
Source0:
https://files.pythonhosted.org/packages/source/b/biopython/biopython-%{version}.tar.gz
Source100: python-biopython-rpmlintrc
BuildRequires: %{python_module devel}
@@ -54,7 +52,7 @@
available Python tools for computational molecular biology.
%prep
-%setup -n biopython-%{version}
+%setup -q -n biopython-%{version}
# remove all execute bits from documentation and fix line endings
find -type f -exec chmod -x {} 2>/dev/null ';'
find -type f -exec sed -i 's/\r//' {} 2>/dev/null ';'
@@ -74,7 +72,7 @@
%if %{with test}
%check
export LANG=en_US.UTF-8
-%python_exec setup.py test
+%pytest
%endif
%files %{python_files}
++++++ biopython-1.74.tar.gz -> biopython-1.75.tar.gz ++++++
/work/SRC/openSUSE:Factory/python-biopython/biopython-1.74.tar.gz
/work/SRC/openSUSE:Factory/.python-biopython.new.26869/biopython-1.75.tar.gz
differ: char 5, line 1
