[Biopython] Biopython 1.78 plans - please help with testing

Wed Sep 2 05:58:52 UTC 2020

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<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<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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