[Biopython] Biopython 1.78 plans - please help with testing

Fri Sep 4 12:15:35 UTC 2020

Hello all,

I took Chris up on his offer of help and after doing the version bump and
triggering the wheel builds, handed over to him. His release PRs are now
merged, wheels uploaded, blog post live:

https://www.open-bio.org/2020/09/04/biopython-1-78-released/
https://twitter.com/Biopython/status/1301855658443255808

I still need to do a little more stuff like the git tab, post release
version bump, and the announcement email. One glitch was the AppVeyor
windows builds did not get stages as expected, but I could get them from
the AppVeyor artifacts cache instead.

Thank you all, especially Chris for helping out on a second release.

Peter

Peter

On Wed, Sep 2, 2020 at 7:07 AM Daley, Christopher <dalchr28 at evergreen.edu>
wrote:

> Hi Peter,
>
> I've run the test suite including online tests without error several
> times, including in an i386 container.
>
> I did a dry run of building a release and took the liberty of drafting
> the blog post already (
> https://www.open-bio.org/wp-admin/post.php?post=5057&action=edit). 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.
>
> Cheers
> Chris D
>
> dalchr28 at evergreen.edu
> +1 360-688-6909
> ------------------------------
> *From:* Biopython <biopython-bounces+dalchr28=
> evergreen.edu at mailman.open-bio.org> on behalf of Markus Piotrowski <
> Markus.Piotrowski at ruhr-uni-bochum.de>
> *Sent:* Tuesday, September 1, 2020 1:49 PM
> *To:* biopython at mailman.open-bio.org <biopython at mailman.open-bio.org>
> *Subject:* Re: [Biopython] Biopython 1.78 plans - please help with testing
>
> 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
> <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>
>  -
> 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>
> 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
> <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>
>
> 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
> <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> 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
> <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>
>
> 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
> <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>;
> 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
> <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>
> instead:
>
> https://github.com/biopython/biopython-wheels/issues/6
> <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>
>
> Thank you all,
>
> Peter
>
>
> _______________________________________________
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> --
> _________________________________
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