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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="moz-cite-prefix">Am 01.09.2020 um 00:14 schrieb Peter
Cock:<br>
</div>
<blockquote type="cite"
cite="mid:CAKVJ-_4GUrS6V8TX-YV13XRbvbApuCGPttfr8DxaOTxz-pB_sQ@mail.gmail.com">
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<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"
moz-do-not-send="true">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"
moz-do-not-send="true">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" moz-do-not-send="true">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://github.com/biopython/biopython.github.io"
target="_blank" moz-do-not-send="true">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://github.com/biopython/biopython/issues/3156"
target="_blank" moz-do-not-send="true">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" moz-do-not-send="true">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="http://anaconda.org" target="_blank"
moz-do-not-send="true">anaconda.org</a> instead:</div>
<div><br>
</div>
<div><a
href="https://github.com/biopython/biopython-wheels/issues/6"
target="_blank" moz-do-not-send="true">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>
</div>
</div>
<br>
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</blockquote>
<br>
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