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<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
Hi Peter,</div>
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
I've run the test suite including online tests without error several times, including in an i386 container.</div>
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<br>
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
I did a dry run of building a release and<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"> took the liberty of drafting the blog post already (<a href="https://www.open-bio.org/wp-admin/post.php?post=5057&action=edit" id="LPlnk782211">https://www.open-bio.org/wp-admin/post.php?post=5057&action=edit</a>).
Let me know if you want me to take on any more tasks, I'm all set up for building the Tutorial and FAQ after the last release and have a relatively open schedule for the next couple of days.</span></div>
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<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Cheers</span></div>
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<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Chris D</span></div>
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dalchr28@evergreen.edu</div>
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+1 360-688-6909</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Biopython <biopython-bounces+dalchr28=evergreen.edu@mailman.open-bio.org> on behalf of Markus Piotrowski <Markus.Piotrowski@ruhr-uni-bochum.de><br>
<b>Sent:</b> Tuesday, September 1, 2020 1:49 PM<br>
<b>To:</b> biopython@mailman.open-bio.org <biopython@mailman.open-bio.org><br>
<b>Subject:</b> Re: [Biopython] Biopython 1.78 plans - please help with testing</font>
<div> </div>
</div>
<div>Dear Peter,<br>
<br>
Built and tested on Windows 7 64 bit and Windows 10 64 bit. All tests (521 on my systems) passed in offline mode. 524 tests in online mode, of which test_NCBI_qblast failed, most likely due to a timeout.<br>
<br>
Best,<br>
Markus<br>
<br>
<div class="x_moz-cite-prefix">Am 01.09.2020 um 00:14 schrieb Peter Cock:<br>
</div>
<blockquote type="cite">
<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://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbiopython%2Fbiopython%2Fissues%2F3156&data=02%7C01%7Cdalchr28%40evergreen.edu%7C78533a17be5340b4a53f08d84eb8bbfb%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C1%7C637345902635082662&sdata=8KOKyoLTiiIt9jEagYHwSPS79t5DhWjWzTdpdub7jPs%3D&reserved=0" originalsrc="https://github.com/biopython/biopython/issues/3156" shash="ZFnba/AcxtoTLfh44wRMUUG7ZO5ObtPHEjZ9aC1PWyFwtp5WYTFecqslGOSRRBiYJLzB2dtlXg7/zjHIJlUKwMcpmOYeawN3xvtfhbI/F+QiwDUfvbXd3tRto097FKBYlP8bTwrauR+GLSnjEb/R8NeT5B43TphjH2GEOg7XJ0Y=">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="x_gmail_quote">
<div dir="ltr" class="x_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="x_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://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbiopython%2Fbiopython%2Fissues&data=02%7C01%7Cdalchr28%40evergreen.edu%7C78533a17be5340b4a53f08d84eb8bbfb%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C1%7C637345902635092655&sdata=R4%2BGaBpLQ55xN7jdTnDiQZpW%2BQFMSqsThBl%2B%2BnjajUc%3D&reserved=0" originalsrc="https://github.com/biopython/biopython/issues" shash="mCXHObzpsA/1i08XttFacvsvkSYNYicQn5SIcJ86Q5UMZXFn343GBM1iYgUCSse8xm8jby09nJtIng2a+EI9XBqBBIiI2Bk3Plu3ne+fRabCM13g6q6nklpPI/UOpT2qoHUEIfXGlMwSecMuHptDFNNsWqxQWMz5UE3D1e+Bc44=" target="_blank">https://github.com/biopython/biopython/issues</a><br>
</div>
<div><br>
</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://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbiopython%2Fbiopython.github.io&data=02%7C01%7Cdalchr28%40evergreen.edu%7C78533a17be5340b4a53f08d84eb8bbfb%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C1%7C637345902635092655&sdata=Q4plSXLjqyyJ6NgZvPb306AxDmE8sbg8sluJ%2FSQg%2Baw%3D&reserved=0" originalsrc="https://github.com/biopython/biopython.github.io" shash="QytWrnsuLlM8iAvtW/PasjpHnwcCAzSZdqGKkjGjmzKD+1VqihiXoQSstrx318JBM+OqSRs1IiGOMR4fQikkf80y54yUlNcM+97Q0V+aA/BAN3jxQpAGrXYxS1ss08eh3ggUgFw3nDNzR0qk69xpwRxFw7Gt/z2JPyvPpOJXzZc=" target="_blank">https://github.com/biopython/biopython.github.io</a> for
this).</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://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbiopython%2Fbiopython%2Fissues%2F3156&data=02%7C01%7Cdalchr28%40evergreen.edu%7C78533a17be5340b4a53f08d84eb8bbfb%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C1%7C637345902635092655&sdata=32eu6HvYbPgWjQ4iflDMw79xTKBPVYrUauomP3R22jI%3D&reserved=0" originalsrc="https://github.com/biopython/biopython/issues/3156" shash="xagyc5La1MaOXfNoSBFkOgdbSlJq6HdYQqUbLO+dKskgI2YMIj0HmG1SzrkTqKplq+grXZE+7hRs9i5QRPt0ahqLf1LlhXTcPjwkwdJPbB7THpET/IbsgkTNm5zopBaIhaidAI8JLdYDc2xpq5Xjz6VYGal8WY8PuoyDotkRkqc=" 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="https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.open-bio.org%2F&data=02%7C01%7Cdalchr28%40evergreen.edu%7C78533a17be5340b4a53f08d84eb8bbfb%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C1%7C637345902635102654&sdata=%2F1vIXznY1th1lS57kM0dwz55KCxhxz68jLr6fBh%2BvCw%3D&reserved=0" originalsrc="http://www.open-bio.org/" shash="h+eG1SuENeIR6dmdjsqq+5BEfDsVYPMuQLts7/Okk8UCJL2AtXe8LUPP0zMdcACZpidqvBcDoziM2HV9zZSLf/nwS/v65wQbGJbPkuXtUfBsYpZFsdn4KWTw9qWZhEqbZRTHQ96UKc7YcXNfHJrZddIIQALLdBfYxWd5h9OZQ8I=" target="_blank">
www.open-bio.org</a>; in the DEPRECATED file, other?</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="https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fanaconda.org%2F&data=02%7C01%7Cdalchr28%40evergreen.edu%7C78533a17be5340b4a53f08d84eb8bbfb%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C1%7C637345902635102654&sdata=FoTs8rHrl7XtAJVf6T%2FzDDm%2B6RtbDuun55XwBm%2F63Yc%3D&reserved=0" originalsrc="http://anaconda.org/" shash="mNZyRPeaHKB1jdiUocq4ry/Pv4o3e4ZlrhMvzu7pHaigtcuEvcN4t2KHQG2mtlT+Mt9AzvAFcfP5hshvwl/OomZlmba3zh5muZvrT0LkmaGuRE0bg4L1SIOeYExU2B+XAYqbBUieRBWqXFIv8D9UV26i57d+3NKl+vsorsXh6r0=" target="_blank">
anaconda.org</a> instead:</div>
<div><br>
</div>
<div><a href="https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbiopython%2Fbiopython-wheels%2Fissues%2F6&data=02%7C01%7Cdalchr28%40evergreen.edu%7C78533a17be5340b4a53f08d84eb8bbfb%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C1%7C637345902635112644&sdata=%2BPzpJsH%2FbzV2h%2Bzq%2BG1Ovvt4cgUJ%2BHZfA8Y1BmTm8wg%3D&reserved=0" originalsrc="https://github.com/biopython/biopython-wheels/issues/6" shash="Hl0eckpnOHJ5SYjka9UfaUK+fFFEUxXsyN5bpizu1AcxXuJ44rEzzpc4w7eMfoUxsCKRjn3fWD4mdhAOcVFEhSsk7yklumaCh45XjUvbBp6JCbvzlL2AUS0pk7hupRKyHCnnyBZpFIcfOOuVMGUvkGE5nG19agLdqpELjsLUgdU=" 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>
</blockquote>
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Dr. Markus Piotrowski
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Lehrstuhl für Molekulargenetik und Physiologie der Pflanzen
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