[Biopython-dev] Biopython 1.62 release in progress

Wibowo Arindrarto w.arindrarto at gmail.com
Wed Aug 28 21:17:57 UTC 2013

Hi everyone,

I've written a draft of our 1.62 release (below). I'd appreciate it if
somebody gives it another look (for typos, etc.). Also, if I miss
somebody in the contributors list, please let me know :).


Biopython 1.62 released

Source distributions and Windows installers for **Biopython** 1.62 are
now available from the [downloads
page](http://biopython.org/wiki/Download) on the [official Biopython
website](http://biopython.org/wiki/Main_Page) and from the [Python
Package Index (PyPI)](https://pypi.python.org/pypi/biopython).

# Python support

This is our first official release that supports Python 3.
Specifically, we tested under Python 3.3. Other versions of Python 3
may still work albeit with some issues.

We still fully support Python 2.5, 2.6, and 2.7. Support under
[Jython](http://www.jython.org/) is available for versions 2.5 and 2.7
and under [PyPy](http://pypy.org/) for versions 1.9 and 2.0. However,
unlike CPython, Jython and PyPy support is partial: NumPy and our C
extensions are not covered.

Please note that this release marks our last official support Python
2.5. Beginning from Biopython 1.63, the minimum supported Python
version will be 2.6.

# Highlights

* The translation functions will give a warning on any partial codons
(and this will probably become an error in a future release). If you
know you are dealing with partial sequences, either pad with N to
extend the sequence length to a multiple of three, or explicitly trim
the sequence.

* The handling of joins and related complex features in Genbank/EMBL
files has been changed with the introduction of a CompoundLocation
object. Previously a SeqFeature for something like a multi-exon CDS
would have a child SeqFeature (under the sub_features attribute) for
each exon. The sub_features property will still be populated for now,
but is deprecated and will in future be removed. Please consult the
examples in the help (docstrings) and Tutorial.

* Thanks to the efforts of Ben Morris, the Phylo module now supports
the file formats NeXML and CDAO. The Newick parser is also
significantly faster, and can now optionally extract bootstrap values
from the Newick comment field (like Molphy and Archaeopteryx do). Nate
Sutton added a wrapper for FastTree to Bio.Phylo.Applications.

* New module Bio.UniProt adds parsers for the GAF, GPA and GPI formats
from UniProt-GOA.

* The BioSQL module is now supported in Jython. MySQL and PostgreSQL
databases can be used. The relevant JDBC driver should be available in

* Feature labels on circular GenomeDiagram figures now support the
label_position argument (start, middle or end) in addition to the
current default placement, and in a change to prior releases these
labels are outside the features which is now consistent with the
linear diagrams.

* The code for parsing 3D structures in mmCIF files was updated to use
the Python standard library's shlex module instead of C code using

* The Bio.Sequencing.Applications module now includes a BWA command
line wrapper.

* Bio.motifs supports JASPAR format files with multiple
position-frequence matrices.

Additionally there have been other minor bug fixes and more unit tests.

# Contributors

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

Alexander Campbell (first contribution)
Andrea Rizzi (first contribution)
Anthony Mathelier (first contribution)
Ben Morris (first contribution)
Brad Chapman
Christian Brueffer
David Arenillas (first contribution)
David Martin (first contribution)
Eric Talevich
Iddo Friedberg
Jian-Long Huang (first contribution)
Joao Rodrigues
Kai Blin
Michiel de Hoon
Nate Sutton (first contribution)
Peter Cock
Petra Kubincová (first contribution)
Phillip Garland
Saket Choudhary (first contribution)
Tiago Antao
Wibowo 'Bow' Arindrarto
Xabier Bello (first contribution)



On Wed, Aug 28, 2013 at 8:28 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Wed, Aug 28, 2013 at 6:31 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> Hello all,
>> I'm starting the release 1.62 process now, getting the new DSSP
>> test working cross platform was more work than I expected -
>> thank goodness for the BuildBot server yet again :)
>> Please don't commit anything to the master branch until further
>> notice,
>> Thanks,
>> Peter
> While I finish off the Windows installers etc, and have dinner,
> would anyone like to volunteer to write a draft for the release
> announcement to go out on the mailing lists and news blog?
> http://news.open-bio.org/news/category/obf-projects/biopython/
> These are usually based on the rather dry NEWS file information,
> and the previous announcement for style/links/etc.
> Thanks,
> Peter
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython-dev

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