[Biopython-dev] Time for Biopython 1.65?

Peter Cock p.j.a.cock at googlemail.com
Wed Dec 17 20:45:31 UTC 2014

On Wed, Dec 17, 2014 at 7:19 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> The 1.65 tar.gz and zip are now live on the DIST folder
> for a test, plus the updated Tutorial and API docs are live.

I will reupload the tar-gz and zip file shortly with this
tiny change (not relevant for the Windows installers):


> I will work on the news announcement (and dinner).
> In a few hours time - assuming none of you find a
> last minute problem in the uploaded files - I will tag
> the commit for github, publish the announcement,
> and push this to PyPI.

How does this draft look?



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).

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.

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