[Biopython] Biopython 1.72 has been released

Wed Jun 27 23:29:35 UTC 2018

Just in time for the Biopython update!  \o/

On June 27, 2018 at 4:08:01 PM, Peter Cock (p.j.a.cock at googlemail.com<mailto:p.j.a.cock at googlemail.com>) wrote:

Dear Biopythoneers,

I'm writing this in Portland at the GCC BOSC 2018 conference, where I
will present the Biopython Project Update 2018 talk tomorrow.
Yesterday during my airport layover in Iceland, I published the
Biopython 1.72 release to our website and PyPI:

https://biopython.org/wiki/Download
https://pypi.python.org/pypi/biopython/1.72

This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6. It
has also been tested on PyPy2.7 v6.0.0 and PyPy3.5 v6.0.0.

Internal changes to Bio.SeqIO have sped up the SeqRecord .format
method and SeqIO.write (especially when used in a for loop).

The MAF alignment indexing in Bio.AlignIO.MafIO has been updated to
use inclusive end co-ordindates to better handle searches at end
points. This will require you to rebuild any existing MAF index files.

In this release more of our code is now explicitly available under
either our original "Biopython License Agreement", or the very similar
but more commonly used "3-Clause BSD License". See the LICENSE.rst
file for more details.

The Entrez module now supports the NCBI API key. Also you can now set
a custom directory for DTD and XSD files. This allows Entrez to be
used in environments like AWS Lambda, which restricts write access to
specific directories. Improved support for parsing NCBI Entrez XML
files that use XSD schemas.

Internal changes to our C code mean that NumPy is no longer required
at compile time - only at run time (and only for those modules which
use NumPy).

Seq, UnknownSeq, MutableSeq and derived classes now support integer
multiplication methods, matching native Python string methods.

A translate method has been added to Bio.SeqFeature that will extract
a feature and translate it using the codon_start and transl_table
qualifiers of the feature if they are present.

Bio.SearchIO is no longer considered experimental, and so it does not
raise warnings anymore when imported.

A new pairwise sequence aligner is available in Bio.Align, as an
alternative to the existing pairwise sequence aligner in
Bio.pairwise2.

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

Benjamin Vaisvil (first contribution)
Blaise Li
Chad Parmet
Chris Rands
Connor T. Skennerton
Francesco Gastaldello
Michiel de Hoon
Pamela Russell (first contribution)
Peter Cock
Spencer Bliven
Wibowo 'Bow' Arindrarto

Thank you all.

Peter

P.S. You can follow @Biopython on Twitter

--

Checksums for interest/public record:

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