[Biopython-dev] Fwd: Biopython 1.68 released

[Peter Cock]

Dear Debian-Med, and Andreas in particular,

This is to let you know we've released Biopython 1.68, and would
be grateful if you could update the Debian Biopython package:

I'm not aware of any changes which will directly affect the
packaging, however minor issues have come to light with
some of the third party binary tests using PAML:

https://github.com/biopython/biopython/issues/923

And PhyML:

https://github.com/biopython/biopython/issues/921
https://github.com/stephaneguindon/phyml/issues/38

As usual, if you do find any other issues, especially from changes
to the tool we test with, we're happy to get your useful feedback.

Thank you,

Peter


---------- Forwarded message ----------
From: Peter Cock <p.j.a.cock at googlemail.com>
Date: Fri, Aug 26, 2016 at 5:32 PM
Subject: Biopython 1.68 released
To: biopython-announce at lists.open-bio.org, Biopython Mailing List
<biopython at lists.open-bio.org>, Biopython-Dev Mailing List
<biopython-dev at lists.open-bio.org>


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).

http://biopython.org/wiki/Download
https://news.open-bio.org/2016/08/26/biopython-1-68-released/

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 (Python 3.5 Windows buildings coming soon)
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):

https://news.open-bio.org/2016/08/26/biopython-1-68-released/

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

Checksums:

$ md5sum biopython-1.68.*
078e915185485a5327937029b7577ddc  biopython-1.68.tar.gz
362e964543a424a2f7585ea4008ea834  biopython-1.68.win32-py2.6.exe
772d07d9a6490d674688d00ede2bdfe9  biopython-1.68.win32-py2.7.exe
fda2d1c8d4a7862f6af85122c86fcd0f  biopython-1.68.win32-py2.7.msi
8de95a90704f15f4c22d5359dbc54b75  biopython-1.68.win32-py3.3.exe
92f40105761520daeeb9128254a8bc94  biopython-1.68.win32-py3.3.msi
b1cd3f6b4ad1096347d5019c68128dac  biopython-1.68.win32-py3.4.exe
9403b9b0d01c22b49edb34e2164c31de  biopython-1.68.win32-py3.4.msi
adb3e8ce60b02b3b46330bbca68f9732  biopython-1.68.zip

$ shasum -a 256 biopython-1.68.*
d1dc09d1ddc8e90833f507cf09f80fa9ee1537d319058d1c44fe9c09be3d0c1f
biopython-1.68.tar.gz
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biopython-1.68.win32-py2.6.exe
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biopython-1.68.win32-py2.7.exe
f92dfefc9a4ee61dda838a61d73a38b55552a1771ce411505009a48702aefd41
biopython-1.68.win32-py2.7.msi
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biopython-1.68.win32-py3.3.exe
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biopython-1.68.win32-py3.3.msi
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biopython-1.68.win32-py3.4.exe
10928347029bc6b0b76567d5f6026a8a002bd3502a7ceeaded7d566938db4bef
biopython-1.68.win32-py3.4.msi
986a0fa6919d2b51959259011dd0674b115383237e109c5a55c37cb18eef999b
biopython-1.68.zip