<div dir="ltr"><div dir="ltr">Hello all,<div><br></div><div>If anyone has tested the current master as requested, I have not</div><div>seen any replies or new reports about the alphabet removal.</div><div><br></div><div>I've now updated our wheel building repository to stage wheels on</div><div>Anaconda (alongside various other scientific python packages) in</div><div>place of the expired Rackspace hosting. That means in principle</div><div>we should be OK to build Biopython 1.78 now.</div><div><br></div><div>There were no comments about where best to put the information</div><div>currently on <a href="https://github.com/biopython/biopython/issues/3156">https://github.com/biopython/biopython/issues/3156</a> -</div><div>I intend to move it to a dedicated page on the website (and update</div><div>the exceptions to point there instead).</div><div><br></div><div>Are there any remaining issues people feel should delay the release,</div><div>or shall I start it in a few days time?</div><div><br></div><div>Thanks,</div><div><br></div><div>Peter</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Aug 16, 2020 at 12:27 PM Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hello all,<div><br></div><div>Michiel and I would like to do the Biopython 1.78 release soon, hopefully in August.</div><div><br></div><div><div>Right now I would encourage all of you familiar with installing from source to try<br></div><div>the latest Biopython from github, and report any issues you find:</div><div><br></div><div><a href="https://github.com/biopython/biopython/issues" target="_blank">https://github.com/biopython/biopython/issues</a><br></div><div><br></div><div></div></div><div>The main change is in the removal of Bio.Alphabet, and I want our documentation</div><div>ready to make this as painless a change as possible. We think the tutorial is ready,</div><div>and I have now updated the code snippets on the website as well (see</div><div><a href="https://github.com/biopython/biopython.github.io" target="_blank">https://github.com/biopython/biopython.github.io</a> for this).</div><div></div><div><br></div><div>Would it help to share a preview of the tutorial on the website? Some time back</div><div>we had the stable release side by side with a manually updated dev version.</div><div><br></div><div><div>We have a few use cases here for sequencing input/ouput where you need to</div><div>specify the kind of sequence (DNA, RNA or protein), which is one of the few</div><div>reasons you might still have been using Bio.Alphabet in your code:</div><div><br></div><div><a href="https://github.com/biopython/biopython/issues/3156" target="_blank">https://github.com/biopython/biopython/issues/3156</a><br></div><div><br></div><div>Any thoughts on where that should be put? Left as an issue; a page on the website;</div><div>a blog post on <a href="http://www.open-bio.org" target="_blank">www.open-bio.org</a>; in the DEPRECATED file, other?</div><div></div></div><div><br></div><div>There is one small stumbling block to the actual release: we need to update</div><div>the temporary staging area used for pre-built wheels before uploading them</div><div>to PyPI. The rackspace storage we and the numpy community were using has</div><div>expired, but the consensus seems to be using <a href="http://anaconda.org" target="_blank">anaconda.org</a> instead:</div><div><br></div><div><a href="https://github.com/biopython/biopython-wheels/issues/6" target="_blank">https://github.com/biopython/biopython-wheels/issues/6</a><br></div><div><br></div><div>Thank you all,</div><div><br></div><div>Peter</div><div><br></div></div>
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