[Biopython-dev] Draft announcement for Biopython 1.68

[Peter Cock]

Hello all,

Other than perhaps rebuilding the tar and zip files to include a
tiny update to the NEWS file (adding release date, plus we
should thank Ben for building Windows binaries), I think we're
almost ready to announce Biopython 1.68.

Lluís Revilla has kindly tested building from the tar-ball on
Linux with Python 2.7,

http://mailman.open-bio.org/pipermail/biopython-dev/2016-August/021538.html

It would be nice have an independent test of a Windows
MSI and EXE installer as well...

Draft announcement copy-and-pasted from the NEWS file:

--

Dear Biopythoneers,

Source distributions and Windows installers for Biopython 1.68 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
this will be our final release to run on Python 2.6. It has also been tested
on PyPy 5.0, PyPy3 version 2.4, and Jython 2.7.

Bio.PDB has been extended to parse the RSSB's new binary Macromolecular
Transmission Format (MMTF, see http://mmtf.rcsb.org), in addition to the
mmCIF and PDB file formats (contributed by Anthony Bradley). This requires
an optional external dependency on the mmtf-python library.

Module Bio.pairwise2 has been re-written (contributed by Markus Piotrowski).
It is now faster, addresses some problems with local alignments, and also
now allows gap insertions after deletions, and vice versa, inspired by the
http://dx.doi.org/10.1101/031500 preprint from Flouri et al.

The two sample graphical tools SeqGui (Sequence Graphical User Interface)
and xbbtools were rewritten (SeqGui) or updated (xbbtools) using the tkinter
library (contributed by Markus Piotrowski). SeqGui allows simple nucleotide
transcription, back-transcription and translation into amino acids using
Bio.Seq internally, offering of the NCBI genetic codes supported in Biopython.
xbbtools is able to open Fasta formatted files, does simple nucleotide
operations and translations in any reading frame using one of the NCBI genetic
codes. In addition, it supports standalone Blast installations to do local
Blast searches.

New NCBI genetic code table 26 (Pachysolen tannophilus Nuclear Code)
has been added to Bio.Data (and the translation functionality), and table 11
is now also available under the alias Archaeal.

In line with NCBI website changes, Biopython now uses HTTPS rather than
HTTP to connect to the NCBI Entrez and QBLAST API.

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
and best practice standard coding style.

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

Anthony Bradley (first contribution)
Ben Fulton
Carlos Pena
Connor T. Skennerton
Iddo Friedberg
Kai Blin
Kristian Davidsen (first contribution)
Markus Piotrowski
Olivier Morelle (first contribution)
Peter Cock
Tiago Antao
Travis Wrightsman
Uwe Schmitt (first contribution)
Xiaoyu Zhuo (first contribution)

Thank you all.

Release announcement here (RSS feed available):
http://news.open-bio.org/news/...

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



On Thu, Aug 25, 2016 at 9:21 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Thu, Aug 25, 2016 at 5:57 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> On Thu, Aug 25, 2016 at 12:08 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>>
>>> I'll keep you posted - but hope to finish the release this afternoon.
>>>
>>> Peter
>>
>> This will probably be the tagged commit for Biopython 1.68,
>>
>> https://github.com/biopython/biopython/commit/914d7ecef2cbc5c550cba311a5f56e47c0abc3ce
>>
>
> Or possibly with this tiny update to the NEWS file to add the
> Biopython 1.68 release date:
>
> https://github.com/biopython/biopython/commit/2314205f50bd805136faeb83207c57c2f843b0f9
>
> That won't alter the epydoc API output, the Tutorial, nor as far
> as I know the Windows installers. It might be worth me re-doing
> the tar and zip but I'm inclined to leave them as is.
>
> Peter