[Biopython-dev] 1.64 mock release announcement

[Tiago Antao]

On Wed, 28 May 2014 11:51:59 +0100
Peter Cock <p.j.a.cock at googlemail.com> wrote:

> Good plan. I think I put this in the README file but could you check
> that too?

The README is fine (I will patch the wiki page in a similar fashion).

New proposed version:

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Source distributions and Windows installers for Biopython 1.64 are now
available from the downloads page on the official Biopython website and
(soon) from the Python Package Index (PyPI).

This release of Biopython supports Python 2.6 and 2.7, 3.3 and also the
new 3.4 version. Biopython is also tested on PyPy 2.0 to 2.3, and
Jython 2.7b2.

The module Bio.CodonAlign is now in the master branch. It facilitates
building codon alignment and further analysis upon it. This work is
from the Google Summer of Code (GSoC) project by Zheng Ruan.

Bio.Phylo now has tree construction and consensus modules, from on the
GSoC work by Yanbo Ye.

Bio.Entrez will now automatically download and cache new NCBI DTD files
for XML parsing under the user's home directory (using ``~/.biopython``
on Unix like systems, and ``$APPDATA/biopython`` on Windows).

Bio.Sequencing.Applications now includes a wrapper for the samtools
command line tool.

Bio.PopGen.SimCoal now also supports fastsimcoal.

SearchIO hmmer3-text, hmmer3-tab, and hmmer3-domtab now support output
from hmmer3.1b1.

BioSQL can now use the mysql-connector package (available for Python 2,
3 and PyPy) as an alternative to MySQLdb (Python 2 only) to connect to
a MySQL database.

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

Chunlei Wu (first contribution)
Edward Liaw (first contribution)
Eric Talevich
Leighton Pritchard
Manlio Calvi (first contribution)
Markus Piotrowski (first contribution)
Melissa Gymrek (first contribution)
Michiel de Hoon
Nigel Delaney (first contribution)
Peter Cock
Saket Choudhary
Tiago Antao
Vincent Davis (first contribution)
Wibowo 'Bow' Arindrarto
Yanbo Ye (first contribution)
Zheng Ruan (first contribution)

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