[Biopython-dev] Biopython 1.66 released

[Peter Cock]

Dear Biopythoneers,

Source distributions and Windows installers for Biopython 1.66 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
and: https://pypi.python.org/pypi/biopython/1.66

This release of Biopython supports Python 2.6, 2.7, 3.3, 3.4 and 3.5, although
support for Python 2.6 is now deprecated. It has also been tested on PyPy 2.4
to 2.6, PyPy3 version 2.4, and Jython 2.7.

Further work on the Bio.KEGG and Bio.Graphics modules now allows drawing KGML
pathways with transparency.

The Bio.SeqIO "abi" parser now decodes almost all the documented fields used
by the ABIF instruments – including the individual color channels.

Bio.PDB now has a QCPSuperimposer module using the Quaternion Characteristic
Polynomial algorithm for superimposing structures. This is a fast alternative
to the existing SVDSuperimposer code using singular value decomposition.

Bio.Entrez now implements the NCBI Entrez Citation Matching function
(ECitMatch), which retrieves PubMed IDs (PMIDs) that correspond to a set of
input citation strings. Bio.Entrez.parse(...) now supports NCBI XML files
using XSD schemas, which will be downloaded and cached like NCBI DTD files.

A subtle bug in how multi-part GenBank/EMBL locations on the reverse strand
were parsed into CompoundLocations was fixed: complement(join(...)) as used
by the NCBI worked, but join(complement(...),complement(...),...) as used by
EMBL/ENSEMBL gave the CompoundLocation parts in the wrong order. A related bug
when taking the reverse complement of a SeqRecord containing features with
CompoundLocations was also fixed.

Additionally, a number of small bugs have been fixed with further additions to
the test suite, and there has been further work on conforming to the Python
PEP8 standard coding style.

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

Alan Medlar (first contribution)
Anthony Mathelier (first contribution)
Antony Lee (first contribution)
Anuj Sharma (first contribution)
Ben Fulton (first contribution)
Bertrand Néron (first contribution)
Brandon Invergo
Carlos Pena
Christian Brueffer
Connor T. Skennerton (first contribution)
David Arenillas (first contribution)
David Nicholson (first contribution)
Emmanuel Noutahi (first contribution)
Eric Rasche (first contribution)
Fabio Madeira (first contribution)
Franco Caramia (first contribution)
Gert Hulselmans (first contribution)
Gleb Kuznetsov (first contribution)
João Rodrigues
John Bradley (first contribution)
Kai Blin
Kian Ho (first contribution)
Kozo Nishida (first contribution)
Kuan-Yi Li (first contribution)
Leighton Pritchard
Lucas Sinclair
Michiel de Hoon
Peter Cock
Saket Choudhary
Sunhwan Jo (first contribution)
Tarcisio Fedrizzi (first contribution)
Tiago Antao
Vincent Davis

This is a longer list than usual, which is good, but in part this reflects the
fact that this release is long overdue. Sorry, that was my fault.

Thank you all.

Release announcement here (RSS feed available):
http://news.open-bio.org/news/2015/10/biopython-1-66-released/

P.S. You can follow @Biopython on Twitter
https://twitter.com/Biopython