[Biopython-dev] 1.64 mock release announcement

Tiago Antao tra at popgen.net
Wed May 28 10:42:09 UTC 2014

Comments and corrections appreciated. I have reduced the number of
items from the NEWS page. If you disagree with this, please say
(especially because I do not have a real grasp of which paragraphs are
really more/less work).

I will also make some corrections to http://biopython.org/wiki/Download
while we are at it (e.g add postgres reference, mysql-connector, ...)

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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.

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) 2013.

Bio.Phylo now has tree construction and consensus modules, from on the
Google Summer of Code (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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