[Biopython-dev] Biopython 1.68 released

[Peter Cock]

Python 3.5 Windows Installers added, thank you to Ben
in what was the first pull request to the DIST repository:

https://github.com/biopython/DIST/pull/1

(I committed the installers from Ben for Biopython 1.67
directly, but with attribution)

Peter


On Fri, Aug 26, 2016 at 5:32 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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
> 09449d7204c65e6010545092f2bc1dc662a0b5f6a873e52a08e19392f935fdb7
> biopython-1.68.win32-py2.6.exe
> a7c2fe52ce8dcf503a492e4ee006dd8bc62faa77078d04c92abdbf7713bf2166
> biopython-1.68.win32-py2.7.exe
> f92dfefc9a4ee61dda838a61d73a38b55552a1771ce411505009a48702aefd41
> biopython-1.68.win32-py2.7.msi
> bce6a4cece7b75650d6a478f4ed9d7d1a5351df42a1820866a0cbd74c254565d
> biopython-1.68.win32-py3.3.exe
> 85bd5d499400e594f77d297966f56c139499711513b9cd24b87fece5a0463fbe
> biopython-1.68.win32-py3.3.msi
> 05c1f59933ef35ecb838649f6fabacb823f2a48c2498ed57ac59a6b3629b5369
> biopython-1.68.win32-py3.4.exe
> 10928347029bc6b0b76567d5f6026a8a002bd3502a7ceeaded7d566938db4bef
> biopython-1.68.win32-py3.4.msi
> 986a0fa6919d2b51959259011dd0674b115383237e109c5a55c37cb18eef999b
> biopython-1.68.zip