<div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Jul 10, 2017 at 4:43 PM, Peter Cock <span dir="ltr"><<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hello all,<br>
<br>
I'd like to delay the PyPI upload and official release announcement until<br>
someone else has confirmed they could install this - any volunteers?<br>
<br>
<a href="http://biopython.org/DIST/biopython-1.70.tar.gz" rel="noreferrer" target="_blank">http://biopython.org/DIST/<wbr>biopython-1.70.tar.gz</a><br>
<a href="http://biopython.org/DIST/biopython-1.70.zip" rel="noreferrer" target="_blank">http://biopython.org/DIST/<wbr>biopython-1.70.zip</a></blockquote><div><br></div><div>Also, here's a draft of the release annoucmenet blog post for comment.</div><div>As usual, this is based heavily on the NEWS file entry.</div><div><br></div><div>Peter</div><div><br></div><div>--</div><div><br></div><div><p style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;border:0px;margin:0px 0px 24px;padding:0px;vertical-align:baseline;color:rgb(51,51,51);font-family:Georgia,"Bitstream Charter",serif;font-size:16px">Dear Biopythoneers,</p><p style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;border:0px;margin:0px 0px 24px;padding:0px;vertical-align:baseline;color:rgb(51,51,51);font-family:Georgia,"Bitstream Charter",serif;font-size:16px">Source distributions of Biopython 1.70are now available from the <a href="http://biopython.org/wiki/Download" style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline;color:rgb(116,51,153)">downloads page</a> on the official <a href="http://biopython.org/" style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline;color:rgb(116,51,153)">Biopython website</a>, and the release is also <a href="https://pypi.python.org/pypi/biopython/1.68" style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline;color:rgb(116,51,153)">on the Python Package Index (PyPI)</a>. Windows installers and/or wheels should be available later.</p><p style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;border:0px;margin:0px 0px 24px;padding:0px;vertical-align:baseline;color:rgb(51,51,51);font-family:Georgia,"Bitstream Charter",serif;font-size:16px"><span id="gmail-more-1602" style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline"></span>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).</p><p style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;border:0px;margin:0px 0px 24px;padding:0px;vertical-align:baseline;color:rgb(51,51,51);font-family:Georgia,"Bitstream Charter",serif;font-size:16px"><em style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline"><strong style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">New Logo</strong></em></p><p class="gmail-p1" style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;border:0px;margin:0px 0px 24px;padding:0px;vertical-align:baseline;color:rgb(51,51,51);font-family:Georgia,"Bitstream Charter",serif;font-size:16px"><span class="gmail-s1" style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Biopython now has a new <a href="http://biopython.org/wiki/Logo" style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline;color:rgb(116,51,153)">logo</a>, contributed by Patrick Kunzmann. Drawing on our </span><span class="gmail-s1" style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">original logo (with two yellow snakes) and the current Python logo, this shows a yellow and blue snake </span><span class="gmail-s1" style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">forming a double helix.</span></p><p style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;border:0px;margin:0px 0px 24px;padding:0px;vertical-align:baseline;color:rgb(51,51,51);font-family:Georgia,"Bitstream Charter",serif;font-size:16px"><img class="gmail-size-medium gmail-wp-image-1684 gmail-aligncenter" src="https://news.open-bio.org/wp-content/uploads/2017/07/biopython_logo_l-300x200.png" alt="" width="300" height="200" style="background: transparent; border: 0px; margin: 0px auto 12px; padding: 0px; vertical-align: baseline; clear: both; display: block; max-width: 100%; height: auto;"><img class="gmail-size-medium gmail-wp-image-1166 gmail-aligncenter" src="https://news.open-bio.org/wp-content/uploads/2013/12/biopython-300x84.jpg" alt="[Biopython Logo]" width="300" height="84" style="background: transparent; border: 0px; margin: 0px auto 12px; padding: 0px; vertical-align: baseline; clear: both; display: block; max-width: 100%; height: auto;"></p><p style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;border:0px;margin:0px 0px 24px;padding:0px;vertical-align:baseline;color:rgb(51,51,51);font-family:Georgia,"Bitstream Charter",serif;font-size:16px"><em style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline"><strong style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Setup changes</strong></em></p><p style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;border:0px;margin:0px 0px 24px;padding:0px;vertical-align:baseline;color:rgb(51,51,51);font-family:Georgia,"Bitstream Charter",serif;font-size:16px">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).</p><p style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;border:0px;margin:0px 0px 24px;padding:0px;vertical-align:baseline;color:rgb(51,51,51);font-family:Georgia,"Bitstream Charter",serif;font-size:16px"><em style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline"><strong style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">License changes</strong></em></p><p style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;border:0px;margin:0px 0px 24px;padding:0px;vertical-align:baseline;color:rgb(51,51,51);font-family:Georgia,"Bitstream Charter",serif;font-size:16px">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 <a href="https://github.com/biopython/biopython/blob/master/LICENSE.rst" style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline;color:rgb(116,51,153)">LICENSE</a> file for more details.</p><p style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;border:0px;margin:0px 0px 24px;padding:0px;vertical-align:baseline;color:rgb(51,51,51);font-family:Georgia,"Bitstream Charter",serif;font-size:16px"><em style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline"><strong style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Code changes</strong></em></p><p style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;border:0px;margin:0px 0px 24px;padding:0px;vertical-align:baseline;color:rgb(51,51,51);font-family:Georgia,"Bitstream Charter",serif;font-size:16px"><tt style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline;font-size:15px;line-height:21px">Bio.AlignIO</tt> now supports Mauve’s eXtended Multi-FastA (XMFA) file format under the format name “mauve” (contributed by Eric Rasche).</p><p style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;border:0px;margin:0px 0px 24px;padding:0px;vertical-align:baseline;color:rgb(51,51,51);font-family:Georgia,"Bitstream Charter",serif;font-size:16px"><tt style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline;font-size:15px;line-height:21px">Bio.ExPASy</tt> was updated to fix fetching PROSITE and PRODOC records, and return text-mode handles for use under Python 3.</p><p style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;border:0px;margin:0px 0px 24px;padding:0px;vertical-align:baseline;color:rgb(51,51,51);font-family:Georgia,"Bitstream Charter",serif;font-size:16px">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 <tt style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline;font-size:15px;line-height:21px">use_raw_hit_ids</tt>and <tt style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline;font-size:15px;line-height:21px">use_raw_query_ids</tt>. Check out the relevant SearchIO.BlastIO documentation for a complete description of what these arguments do.</p><p style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;border:0px;margin:0px 0px 24px;padding:0px;vertical-align:baseline;color:rgb(51,51,51);font-family:Georgia,"Bitstream Charter",serif;font-size:16px"><tt style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline;font-size:15px;line-height:21px">Bio.motifs</tt> was updated to support changes in MEME v4.11.4 output.</p><p style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;border:0px;margin:0px 0px 24px;padding:0px;vertical-align:baseline;color:rgb(51,51,51);font-family:Georgia,"Bitstream Charter",serif;font-size:16px">The <tt style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline;font-size:15px;line-height:21px">Bio.Seq</tt> sequence objects now have a <tt style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline;font-size:15px;line-height:21px">.count_overlap()</tt> method to supplement the Python string like non-overlap based <tt style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline;font-size:15px;line-height:21px">.count()</tt> method.</p><p style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;border:0px;margin:0px 0px 24px;padding:0px;vertical-align:baseline;color:rgb(51,51,51);font-family:Georgia,"Bitstream Charter",serif;font-size:16px">The <tt style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline;font-size:15px;line-height:21px">Bio.SeqFeature</tt> location objects can now be compared for equality.</p><p style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;border:0px;margin:0px 0px 24px;padding:0px;vertical-align:baseline;color:rgb(51,51,51);font-family:Georgia,"Bitstream Charter",serif;font-size:16px">In <tt style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline;font-size:15px;line-height:21px">Bio.Phylo.TreeConstruction</tt>, the <tt style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline;font-size:15px;line-height:21px">DistanceMatrix</tt> class (previously <tt style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline;font-size:15px;line-height:21px">_DistanceMatrix</tt>) has a new method <tt style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline;font-size:15px;line-height:21px">.format_phylip()</tt> to write Phylip-compatible distance matrix files (contributed by Jordan Willis).</p><p style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;border:0px;margin:0px 0px 24px;padding:0px;vertical-align:baseline;color:rgb(51,51,51);font-family:Georgia,"Bitstream Charter",serif;font-size:16px">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.</p><p style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;border:0px;margin:0px 0px 24px;padding:0px;vertical-align:baseline;color:rgb(51,51,51);font-family:Georgia,"Bitstream Charter",serif;font-size:16px"><em style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline"><strong style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Acknowledgements</strong></em></p><p style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;border:0px;margin:0px 0px 24px;padding:0px;vertical-align:baseline;color:rgb(51,51,51);font-family:Georgia,"Bitstream Charter",serif;font-size:16px">Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:</p><ul style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;border:0px;margin:0px 0px 24px 1.5em;padding:0px;vertical-align:baseline;list-style:square;color:rgb(51,51,51);font-family:Georgia,"Bitstream Charter",serif;font-size:16px"><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Aaron Kitzmiller (first contribution)</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Adil Iqbal (first contribution)</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Allis Tauri</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Andrew Guy</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Ariel Aptekmann (first contribution)</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Bertrand Caron (first contribution)</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Chris Rands</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Connor T. Skennerton</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Eric Rasche</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Eric Talevich</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Francesco Gastaldello</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">François Coste (first contribution)</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Frederic Sapet (first contribution)</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Jimmy O’Donnell (first contribution)</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Jared Andrews (first contribution)</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">John Kern (first contribution)</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Jordan Willis (first contribution)</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">João Rodrigues</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Kai Blin</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Markus Piotrowski</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Mateusz Korycinski (first contribution)</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Maximilian Greil</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Michiel de Hoon</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">morrme (first contribution)</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Noam Kremen (first contribution)</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Patrick Kunzmann</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Peter Cock</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Rasmus Fonseca (first contribution)</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Rodrigo Dorantes-Gilardi (first contribution)</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Sacha Laurent (first contribution)</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Sourav Singh</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Ted Cybulski (first contribution)</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Tiago Antao</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Wibowo ‘Bow’ Arindrarto</li><li style="background:transparent;border:0px;margin:0px;padding:0px;vertical-align:baseline">Zheng Ruan</li></ul></div></div></div></div>