[Biopython] Biopython 1.65 released

[Peter Cock]

Dear Biopythoneers,

Source distributions and Windows installers for Biopython 1.65 are
now available from the downloads page on the official Biopython
website and from the Python Package Index (PyPI).

See: http://biopython.org/wiki/Download

This release of Biopython supports Python 2.6, 2.7, 3.3 and 3.4. It is
also tested on PyPy 2.0 to 2.4, PyPy3 version 2,4, and Jython 2.7b2.

The most visible change is that the Biopython sequence objects now
use string comparison, rather than Python’s object comparison. This
has been planned for a long time with warning messages in place
(under Python 2, the warnings were sadly missing under Python 3).

The Bio.KEGG and Bio.Graphics modules have been expanded with
support for the online KEGG REST API, and parsing, representing
and drawing KGML pathways.

The Pterobranchia Mitochondrial genetic code has been added to
Bio.Data (and the translation functionality), which is the new NCBI
genetic code table 24.

The Bio.SeqIO parser for the ABI capillary file format now exposes
all the raw data in the SeqRecord’s annotation as a dictionary. This
allows further in-depth analysis by advanced users.

Bio.SearchIO QueryResult objects now allow Hit retrieval using its
alternative IDs (any IDs listed after the first one, for example as
used with the NCBI BLAST NR database).

Bio.SeqUtils.MeltingTemp has been rewritten with new functionality.

The new experimental module Bio.CodonAlign has been renamed
Bio.codonalign (and similar lower case PEP8 style module names
have been used for the sub-modules within this).

Bio.SeqIO.index_db(…) and Bio.SearchIO.index_db(…) now store
any relative filenames relative to the index file, rather than (as
before) relative to the current directory at the time the index was
built. This makes the indexes less fragile, so that they can be used
from other working directories. NOTE: This change is backward
compatible (old index files work as before), however relative paths
in new indexes will not work on older versions of Biopython!

Behind the scenes, we have done a lot of work applying PEP8
coding styles to Biopython, and improving the formatting of the
source code documentation (PEP257 docstrings).

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

Alan Du (first contribution)
Carlos Pena (first contribution)
Colin Lappala (first contribution)
Christian Brueffer
David Bulger (first contribution)
Eric Talevich
Evan Parker (first contribution)
Hongbo Zhu
Kai Blin
Kevin Wu (first contribution)
Leighton Pritchard
Leszek Pryszcz (first contribution)
Markus Piotrowski
Matt Shirley (first contribution)
Mike Cariaso (first contribution)
Peter Cock
Seth Sims (first contribution)
Tiago Antao
Travis Wrightsman (first contribution)
Tyghe Vallard (first contribution)
Vincent Davis
Wibowo ‘Bow’ Arindrarto
Zheng Ruan

This is a longer list of contributors and changes than usual, but
it was also a longer gap since our last release.

Thank you all.

Release announcement here (RSS feed available):
http://news.open-bio.org/news/2014/12/biopython-1-65-released/

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