[Biopython-dev] Draft Announcement for Biopython 1.54

[David Winter]

Hi all,

Here's a draft announcement for the next release, very happy to take  
corrections and suggestions on how to change it. I'll put a marked up  
version of this on the OBF server soon.

Cheers,
David

--
Biopythn 1.54 Released

The Biopython team is proud to announce Biopython 1.54, a new stable  
release of the Biopython library. Biopython 1.54 comes four months  
after our last release and brings new features, tweaks to some  
established functions and the usual collection of bug fixes.

This is the first stable release to feature the new Bio.Phylo module  
which can be used to read, write and take data from phylogenetic trees  
in Newick, Nexus and PhyloXML formats. The module is the result of  
Erick Talevich's Google Summer of Code project which was supported by  
The National Evolutionary Synthesis Center (NESCent).

Biopython now supports the reading, writing and indexing of Standard Flowgram
Format (SFF) files produced in 454 sequencing. Jose Blanca (the brains  
behind the widely used sff_extract tool) has extended Bio.SeqIO to  
handle these files, making it possible to convert between SFF, FASTQ,  
FASTA and QUAL formats (as trimmed or untrimmed reads).

As well as adding features the new release tweaks and extends some of  
the core modules:

     *Both Bio.SeqIO and Bio.AlignIO will accept filenames as well as  
handles, as detailed here
     *The multiple sequence alignment object that underlies  
Bio.AlignIO has been improved.
     *Bio.SeqIO can read and write EMBL nucleotide files.
     *The dictionary-like object returned Bio.SeqIO.index() has a new  
method "get_raw" that gets unparsed data from a file as a string.
    * Bio.Entrez includes some more DTD files, in particular  
eLink_090910.dtd, needed for our NCBI Entrez Utilities XML parser.

Binaries and source files for Biopython 1.54 are available from the  
downloads page The documentation has been updated to include the  
changes made since our last release.

  A big thanks to every one who tested our beta release or submitted  
bugs since Biopython 1.53. And an especially big thanks to everyone  
who contributed to this release, including four first time contributors:

      * Anne Pajon (first contribution)
     * Brad Chapman
     * Christian Zmasek
     * Eric Talevich
     * Jose Blanca (first contribution)
     * Kevin Jacobs (first contribution)
     * Leighton Pritchard
     * Michiel de Hoon
     * Peter Cock
     * Thomas Holder (first contribution)