[Biopython] Biopython 1.78 plans - please help with testing

[Markus Piotrowski]

Dear Peter,

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.

Best,
Markus

Am 01.09.2020 um 00:14 schrieb Peter Cock:
> Hello all,
>
> If anyone has tested the current master as requested, I have not
> seen any replies or new reports about the alphabet removal.
>
> I've now updated our wheel building repository to stage wheels on
> Anaconda (alongside various other scientific python packages) in
> place of the expired Rackspace hosting. That means in principle
> we should be OK to build Biopython 1.78 now.
>
> There were no comments about where best to put the information
> currently on https://github.com/biopython/biopython/issues/3156 -
> I intend to move it to a dedicated page on the website (and update
> the exceptions to point there instead).
>
> Are there any remaining issues people feel should delay the release,
> or shall I start it in a few days time?
>
> Thanks,
>
> Peter
>
> On Sun, Aug 16, 2020 at 12:27 PM Peter Cock <p.j.a.cock at googlemail.com 
> <mailto:p.j.a.cock at googlemail.com>> wrote:
>
>     Hello all,
>
>     Michiel and I would like to do the Biopython 1.78 release soon,
>     hopefully in August.
>
>     Right now I would encourage all of you familiar with installing
>     from source to try
>     the latest Biopython from github, and report any issues you find:
>
>     https://github.com/biopython/biopython/issues
>
>     The main change is in the removal of Bio.Alphabet, and I want our
>     documentation
>     ready to make this as painless a change as possible. We think the
>     tutorial is ready,
>     and I have now updated the code snippets on the website as well (see
>     https://github.com/biopython/biopython.github.io for this).
>
>     Would it help to share a preview of the tutorial on the website?
>     Some time back
>     we had the stable release side by side with a manually updated dev
>     version.
>
>     We have a few use cases here for sequencing input/ouput where you
>     need to
>     specify the kind of sequence (DNA, RNA or protein), which is one
>     of the few
>     reasons you might still have been using Bio.Alphabet in your code:
>
>     https://github.com/biopython/biopython/issues/3156
>
>     Any thoughts on where that should be put? Left as an issue; a page
>     on the website;
>     a blog post on www.open-bio.org <http://www.open-bio.org>; in the
>     DEPRECATED file, other?
>
>     There is one small stumbling block to the actual release: we need
>     to update
>     the temporary staging area used for pre-built wheels before
>     uploading them
>     to PyPI. The rackspace storage we and the numpy community were
>     using has
>     expired, but the consensus seems to be using anaconda.org
>     <http://anaconda.org> instead:
>
>     https://github.com/biopython/biopython-wheels/issues/6
>
>     Thank you all,
>
>     Peter
>
>
> _______________________________________________
> Biopython mailing list  -Biopython at mailman.open-bio.org
> https://mailman.open-bio.org/mailman/listinfo/biopython

-- 
_________________________________
Dr. Markus Piotrowski
Privatdozent/Akademischer Rat
Lehrstuhl für Molekulargenetik und Physiologie der Pflanzen
ND 3/49
Universitätsstr. 150
44801 Bochum

Tel. xx49-(0)234-3224290
Fax. xx49-(0)234-3214187

http://www.ruhr-uni-bochum.de/pflaphy/Seiten_dt/Piotrowski_d.html
http://homepage.ruhr-uni-bochum.de/Markus.Piotrowski/Index.html

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20200901/06b7c51f/attachment.htm>