[Biopython-dev] Biopython 1.70 released

[Peter Cock]

Dear Biopythoneers,

We now have pre-compiled wheels for Linux, Mac OS X and
Windows ready for use:

https://pypi.python.org/pypi/biopython/1.70

This should make it possible to quickly install Biopython on Linux,
Mac OS X or Windows, *without* needing a compiler, e.g.

$ pip install biopython==1.70

For example, this ought to work on Windows Python 2.7:

C:\Python27\Scripts\pip install biopython==1.70

We would welcome feedback (e.g. do you still want the traditional
point-and-click Windows graphical installers?) and will gradually
be improving the instructions on our download page:

http://biopython.org/wiki/Download

Special thanks to Matthew Brett and the MacPython/NumPy/sklearn
community who have developed an automated system for building
Python Wheels - plus RackSpace, TravisCI and AppVeyor, for
providing the resources to do this.

And once again, thank you to everyone who contributed to this
release of Biopython.

Thank you all,

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