[Biopython-dev] Biopython 1.70 release

Peter Cock p.j.a.cock at googlemail.com
Mon Jul 10 16:30:39 UTC 2017

On Mon, Jul 10, 2017 at 4:43 PM, Peter Cock <p.j.a.cock at googlemail.com>

> Hello all,
> I'd like to delay the PyPI upload and official release announcement until
> someone else has confirmed they could install this - any volunteers?
> http://biopython.org/DIST/biopython-1.70.tar.gz
> http://biopython.org/DIST/biopython-1.70.zip

Also, here's a draft of the release annoucmenet blog post for comment.
As usual, this is based heavily on the NEWS file entry.



Dear Biopythoneers,

Source distributions of Biopython 1.70are now available from the downloads
page <http://biopython.org/wiki/Download> on the official Biopython website
<http://biopython.org/>, and the release is also on the Python Package
Index (PyPI) <https://pypi.python.org/pypi/biopython/1.68>. Windows
installers and/or wheels should be available later.

This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6 (we have
now dropped support for Python 3.3). It has also been tested on PyPy v5.7,
PyPy3.5 v5.8 beta, and Jython 2.7 (although we are deprecating support for

*New Logo*

Biopython now has a new logo <http://biopython.org/wiki/Logo>, contributed
by Patrick Kunzmann. Drawing on our original logo (with two yellow snakes)
and the current Python logo, this shows a yellow and blue snake forming a
double helix.

[image: [Biopython Logo]]

*Setup changes*

We now explicitly recommend installation using pip, rather than the classic
“python setup.py install” approach. In a related change, we now depend on
the Python package setuptools (rather than the older package distutils in
the Python standard library) and have made the dependency on NumPy explicit
and automatic (except on Jython).

*License changes*

As of Biopython 1.69, we have started to dual-license Biopython under both
our original liberal “Biopython License Agreement”, and the very similar
but more commonly used “3-Clause BSD License”. A growing number of the
Python files are explicitly available under either license, but most of the
code remains under the “Biopython License Agreement” only. See the LICENSE
<https://github.com/biopython/biopython/blob/master/LICENSE.rst> file for
more details.

*Code changes*

Bio.AlignIO now supports Mauve’s eXtended Multi-FastA (XMFA) file
format under the format name “mauve” (contributed by Eric Rasche).

Bio.ExPASy was updated to fix fetching PROSITE and PRODOC records, and
return text-mode handles for use under Python 3.

Two new arguments for reading and writing blast-xml files have been
added to the Bio.SearchIO functions (read/parse and write, respectively).
They are use_raw_hit_idsand use_raw_query_ids. Check out the
relevant SearchIO.BlastIO documentation for a complete description of what
these arguments do.

Bio.motifs was updated to support changes in MEME v4.11.4 output.

The Bio.Seq sequence objects now have a .count_overlap() method
to supplement the Python string like non-overlap based .count() method.

The Bio.SeqFeature location objects can now be compared for equality.

In Bio.Phylo.TreeConstruction, the DistanceMatrix class (previously
_DistanceMatrix) has a new method .format_phylip() to write
Phylip-compatible distance matrix files (contributed by Jordan Willis).

Additionally, a number of small bugs 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.


Many thanks to the Biopython developers and community for making this
release possible, especially the following contributors:

   - Aaron Kitzmiller (first contribution)
   - Adil Iqbal (first contribution)
   - Allis Tauri
   - Andrew Guy
   - Ariel Aptekmann (first contribution)
   - Bertrand Caron (first contribution)
   - Chris Rands
   - Connor T. Skennerton
   - Eric Rasche
   - Eric Talevich
   - Francesco Gastaldello
   - François Coste (first contribution)
   - Frederic Sapet (first contribution)
   - Jimmy O’Donnell (first contribution)
   - Jared Andrews (first contribution)
   - John Kern (first contribution)
   - Jordan Willis (first contribution)
   - João Rodrigues
   - Kai Blin
   - Markus Piotrowski
   - Mateusz Korycinski (first contribution)
   - Maximilian Greil
   - Michiel de Hoon
   - morrme (first contribution)
   - Noam Kremen (first contribution)
   - Patrick Kunzmann
   - Peter Cock
   - Rasmus Fonseca (first contribution)
   - Rodrigo Dorantes-Gilardi (first contribution)
   - Sacha Laurent (first contribution)
   - Sourav Singh
   - Ted Cybulski (first contribution)
   - Tiago Antao
   - Wibowo ‘Bow’ Arindrarto
   - Zheng Ruan
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