[Biopython] Biopython 1.67 released

[Peter Cock]

Dear Biopythoneers,

This was long over-due, but Biopython 1.67 was released earlier today.
The most recent delay was due to migrating our website from MediaWiki
to GitHub Pages earlier this year, following an OBF server failure.

See: https://news.open-bio.org/2016/06/08/biopython-1-67-released/

Source distributions and Windows installers for Biopython 1.66 are now
available from the downloads page on the official Biopython website,
and the release is also on the Python Package Index (PyPI).

This release of Biopython supports Python 2.6, 2.7, 3.3, 3.4 and 3.5,
but support for Python 2.6 is considered to be deprecated. It has also
been tested on PyPy 5.0, PyPy3 version 2.4, and Jython 2.7.

Comparison of SeqRecord objects until now has used the default Python
object comparison (are they the same instance in memory?). This can be
surprising, but comparing all of the attributes would be too complex.
As of this release attempting to compare SeqRecord objects should
raise an exception instead. If you want the old behaviour, use
id(record1) == id(record2) instead.

New experimental module Bio.phenotype is for working with Phenotype
Microarray plates in JSON and the machine vendor's CSV format
(contributed by Marco Galardini).

Following the convention used elsewhere in Biopython, there is a new
function Bio.KEGG.read(...) for parsing KEGG files expected to contain
a single record only - the existing function Bio.KEGG.parse(...) is
intended to be used to iterate over multi-record files.

When a gap character is defined, Bio.Seq will now translate gap codons
(e.g. "---") into a single gap ("-") in the protein sequence. The gap
character is inferred from the Seq object's alphabet, but it can also
be passed as an argument to the translate method.

The new NCBI genetic code table 25, covering Candidate Division SR1
and Gracilibacteria, has been added to Bio.Data (and the translation
functionality).

The Bio.Entrez interface will automatically use an HTTP POST rather
than HTTP GET if the URL would exceed 1000 characters. This is based
on NCBI guidelines and the fact that very long queries like complex
searches can otherwise trigger an HTTP Error 414 Request URI too long.

Foreign keys are now used when creating BioSQL databases with SQLite3
(this was not possible until SQLite version 3.6.19). The BioSQL
taxonomy code now updates the taxon table left/right keys when
updating the taxonomy.

There have been some fixes to the MMCIF structure parser which now
uses identifiers which better match results from the PDB structure
parse.

The restriction enzyme list in Bio.Restriction has been updated to the
May 2016 release of REBASE.

The mmCIF parser in Bio.PDB.MMCIFParser has been joined by a second
version which only looks at the ATOM and HETATM lines and can be much
faster.

The Bio.KEGG.REST will now return unicode text-based handles, except
for images which remain as binary bytes-based handles, making it
easier to use with the mostly text-based parsers in Biopython.

Note that the BioSQL test configuration information is now in a new
file Tests/biosql.ini rather than directly in Tests/test_BioSQL_*.py
as before. You can make a copy of the provided example file
Tests/biosql.ini.sample as Tests/biosql.ini and edit this if you wish
to run the BioSQL tests.

Additionally, a number of small bugs have been fixed with further
additions to the test suite, and there has been further work to follow
the Python PEP8 standard coding style, and in converting our docstring
documentation to use the reStructuredText markup style.

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

Aaron Rosenfeld (first contribution)
Anders Pitman (first contribution)
Barbara Mühlemann (first contribution)
Ben Fulton
Ben Woodcroft (first contribution)
Brandon Invergo
Brian Osborne (first contribution)
Carlos Pena
Chaitanya Gupta (first contribution)
Chris Warth (first contribution)
Christiam Camacho (first contribution)
Connor T. Skennerton
David Koppstein (first contribution)
Eric Talevich
Jacek Śmietański (first contribution)
João D Ferreira (first contribution)
João Rodrigues
Joe Cora (first contribution)
Kai Blin
Leighton Pritchard
Lenna Peterson
Marco Galardini (first contribution)
Markus Piotrowski
Matt Ruffalo (first contribution)
Matteo Sticco (first contribution)
Nader Morshed (first contribution)
Owen Solberg (first contribution)
Peter Cock
Steve Bond (first contribution)
Terry Jones (first contribution)
Vincent Davis
Zheng Ruan

Again this list of contributors is longer than usual, which is good,
but partly reflects the delay since our last release. My apologies.

Peter

--

Dr. Peter Cock,
Bioinformatician at The James Hutton Institute;
Open Bioinformatics Foundation, board of directors, secretary;
Co-chair for BOSC 2016;
Biopython developer.