[Biopython-dev] Biopython 1.70 released

[Peter Cock]

You must all be using git or PyPI via pip, since no one spotted this:

https://github.com/biopython/biopython.github.io/commit/2ca7da29933e1ffa4e82e918bd73a4d077fd61a2

Ah well, the download page has the Biopython 1.70 links now.

I'm still working on pre-compiled wheels though, see this thread:
http://mailman.open-bio.org/pipermail/biopython-dev/2017-July/021817.html

Peter

On Tue, Jul 11, 2017 at 11:54 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Dear Biopythoneers,
>
> Source distributions of Biopython 1.70 are now available from the
> downloads page on the official Biopython website, and the release is
> also on the Python Package Index (PyPI). Windows installers and/or
> wheels should be available later.
>
> http://biopython.org/wiki/Download
> https://pypi.python.org/pypi/biopython/1.70
>
> This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6 (we
> have now dropped support for Python 3.3). It has also been tested on
> PyPy v5.7, PyPy3.5 v5.8 beta, and Jython 2.7 (although we are
> deprecating support for Jython).
>
> New Logo:
>
> Biopython now has a new logo, contributed by Patrick Kunzmann. Drawing
> on our original logo (with two yellow snakes) and the current Python
> logo, this shows a yellow and blue snake forming a double helix.
>
> Setup changes:
>
> We now explicitly recommend installation using pip, rather than the
> classic “python setup.py install” approach. In a related change, we
> now depend on the Python package setuptools (rather than the older
> package distutils in the Python standard library) and have made the
> dependency on NumPy explicit and automatic (except on Jython).
>
> License changes:
>
> As of Biopython 1.69, we have started to dual-license Biopython under
> both our original liberal “Biopython License Agreement”, and the very
> similar but more commonly used “3-Clause BSD License”. A growing
> number of the Python files are explicitly available under either
> license, but most of the code remains under the “Biopython License
> Agreement” only. See the LICENSE file for more details.
>
> Code changes:
>
> Bio.AlignIO now supports Mauve’s eXtended Multi-FastA (XMFA) file
> format under the format name “mauve” (contributed by Eric Rasche).
>
> Bio.ExPASy was updated to fix fetching PROSITE and PRODOC records, and
> return text-mode handles for use under Python 3.
>
> Two new arguments for reading and writing blast-xml files have been
> added to the Bio.SearchIO functions (read/parse and write,
> respectively). They are use_raw_hit_idsand use_raw_query_ids. Check
> out the relevant SearchIO.BlastIO documentation for a complete
> description of what these arguments do.
>
> Bio.motifs was updated to support changes in MEME v4.11.4 output.
>
> The Bio.Seq sequence objects now have a .count_overlap() method to
> supplement the Python string like non-overlap based .count() method.
>
> The Bio.SeqFeature location objects can now be compared for equality.
>
> In Bio.Phylo.TreeConstruction, the DistanceMatrix class (previously
> _DistanceMatrix) has a new method .format_phylip() to write
> Phylip-compatible distance matrix files (contributed by Jordan
> Willis).
>
> 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, PEP257 and best practice standard coding style.
>
> Acknowledgements:
>
> Many thanks to the Biopython developers and community for making this
> release possible, especially the following contributors:
>
> - Aaron Kitzmiller (first contribution)
> - Adil Iqbal (first contribution)
> - Allis Tauri
> - Andrew Guy
> - Ariel Aptekmann (first contribution)
> - Ben Fulton
> - Bertrand Caron (first contribution)
> - Chris Rands
> - Connor T. Skennerton
> - Eric Rasche
> - Eric Talevich
> - Francesco Gastaldello
> - François Coste (first contribution)
> - Frederic Sapet (first contribution)
> - Jimmy O'Donnell (first contribution)
> - Jared Andrews (first contribution)
> - John Kern (first contribution)
> - Jordan Willis (first contribution)
> - João Rodrigues
> - Kai Blin
> - Markus Piotrowski
> - Mateusz Korycinski (first contribution)
> - Maximilian Greil
> - Michiel de Hoon
> - morrme (first contribution)
> - Noam Kremen (first contribution)
> - Patrick Kunzmann
> - Peter Cock
> - Rasmus Fonseca (first contribution)
> - Rodrigo Dorantes-Gilardi (first contribution)
> - Sacha Laurent (first contribution)
> - Sourav Singh
> - Ted Cybulski (first contribution)
> - Tiago Antao
> - Wibowo 'Bow' Arindrarto
> - Zheng Ruan
>
> Thank you all.
>
> P.S. You can follow @Biopython on Twitter
>
> https://twitter.com/biopython
>
> Checksums:
>
> $ md5sum biopython-1.70.*
> feff7a3e2777e43f9b13039b344e06ff  biopython-1.70.tar.gz
> 6307ab27c257fe69b9dae4bfc3052f49  biopython-1.70.zip
>
> $ shasum -a 256 biopython-1.70.*
> 4a7c5298f03d1a45523f32bae1fffcff323ea9dce007fb1241af092f5ab2e45b
> biopython-1.70.tar.gz
> 34312ce899f6c3fc9dea77ca997f9a8c228043d05284a0653577594aeb119d4f
> biopython-1.70.zip