[Biopython] Volunteers for making Biopython release 1.77

Sat May 9 17:40:16 UTC 2020

Glad it was a simple fix.

I started building a Docker container to run the full tests locally based on the https://github.com/biopython/biopython_docker repo, updated to Ubuntu 18.04 and Python 3.6. In doing so, I discovered that the download link for fdist2 is dead and there doesn't seem to be any other source for it online. Checking the other links it also seems like http://xxmotif.genzentrum.lmu.de<http://xxmotif.genzentrum.lmu.de/index.php> is down as well. The Bioconda package points to this github repo: https://github.com/soedinglab/xxmotif

Any thoughts on how to proceed?
Chris

________________________________
From: Peter Cock <p.j.a.cock at googlemail.com>
Sent: Friday, May 8, 2020 1:34 PM
To: Daley, Christopher <dalchr28 at evergreen.edu>
Cc: Michiel de Hoon <mjldehoon at yahoo.com>; biopython at biopython.org <biopython at biopython.org>
Subject: Re: [Biopython] Volunteers for making Biopython release 1.77

Good work on this documentation fix Chris - something I was hoping we'd fixed for the next release:

https://github.com/biopython/biopython/issues/2502<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbiopython%2Fbiopython%2Fissues%2F2502&data=02%7C01%7Cdalchr28%40evergreen.edu%7C7b4f8ecaf310434a3ef708d7f38f3ab5%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637245668819672472&sdata=vURpurv9OtDscqOlvhwzLAJRpTkXIL8kBBdThBPixb4%3D&reserved=0>

Another important task (which on re-reading might be made even more explicit) is running all the tests locally, including the online tests (since we skip those on TravisCI and AppVeyor). This occasionally throws up nasty surprises:

https://biopython.org/wiki/Building_a_release<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbiopython.org%2Fwiki%2FBuilding_a_release&data=02%7C01%7Cdalchr28%40evergreen.edu%7C7b4f8ecaf310434a3ef708d7f38f3ab5%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637245668819672472&sdata=lrcab79xhC4o2iSgzIe%2Bcy%2FGmqcPlVB4cgzdqzk9HSw%3D&reserved=0>

Peter

On Thu, May 7, 2020 at 5:03 PM Peter Cock <p.j.a.cock at googlemail.com<mailto:p.j.a.cock at googlemail.com>> wrote:
Sounds good Chris,

Let's start with putting together a list of any blocking issues or pull requests. Community suggestions are welcome too, that's why we're discussing it openly on the mailing list.

Also to all our regular contributors - please say now if have something nearly ready which you are hoping to get included.

Thanks all,

Peter

On Thu, May 7, 2020 at 2:56 PM Daley, Christopher <dalchr28 at evergreen.edu<mailto:dalchr28 at evergreen.edu>> wrote:
Hi Peter,
Yes, that's me. I've been wanting to contribute more but this year hasn't exactly gone to plan...
I'm happy to start today and go through the issues and pull requests and we can set up a workflow that you feel is the most manageable.
Cheers
Chris

________________________________
From: Peter Cock <p.j.a.cock at googlemail.com<mailto:p.j.a.cock at googlemail.com>>
Sent: Wednesday, May 6, 2020 8:40 AM
To: Daley, Christopher <dalchr28 at evergreen.edu<mailto:dalchr28 at evergreen.edu>>
Cc: Michiel de Hoon <mjldehoon at yahoo.com<mailto:mjldehoon at yahoo.com>>; biopython at biopython.org<mailto:biopython at biopython.org> <biopython at biopython.org<mailto:biopython at biopython.org>>
Subject: Re: [Biopython] Volunteers for making Biopython release 1.77

Hi Christopher, is this you on GitHub with one pull request to Biopython already?

https://github.com/chebizarro<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fchebizarro&data=02%7C01%7Cdalchr28%40evergreen.edu%7C7b4f8ecaf310434a3ef708d7f38f3ab5%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637245668819682467&sdata=bgHgMzJhAkw1ZqCIxRtb1HPlmAxlNnBMJPSEVGClb2Q%3D&reserved=0>
https://github.com/biopython/biopython/pull/2349<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbiopython%2Fbiopython%2Fpull%2F2349&data=02%7C01%7Cdalchr28%40evergreen.edu%7C7b4f8ecaf310434a3ef708d7f38f3ab5%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637245668819692466&sdata=bjE6INbsHfTiQMFZy9f9GxsGqOg8m4w0GSCVeMjhbqM%3D&reserved=0>

Some of the release steps need accounts or write permissions, but we could do most of it via pull requests so that doesn't stop you taking a very active role.

First is working out what if any blocking issues remain to be addressed before calling a commit freeze and doing the release. Do you have any thoughts on this? Even additional eyes on the open issues and pull requests would be helpful there.

Thank you,

Peter

On Wed, May 6, 2020 at 3:37 PM Daley, Christopher <dalchr28 at evergreen.edu<mailto:dalchr28 at evergreen.edu>> wrote:
I missed the original message due to aggressive spam filtering by our IT dept.
I'd be very much interested in managing a release, especially now the mid quarter rush is over. I've looked at the process and can pretty much get started straight away.
Chris Daley

Sent from my Verizon, Samsung Galaxy smartphone

________________________________
From: Biopython <biopython-bounces+dalchr28=evergreen.edu at mailman.open-bio.org<mailto:evergreen.edu at mailman.open-bio.org>> on behalf of Peter Cock <p.j.a.cock at googlemail.com<mailto:p.j.a.cock at googlemail.com>>
Sent: Wednesday, May 6, 2020 7:11:32 AM
To: Michiel de Hoon <mjldehoon at yahoo.com<mailto:mjldehoon at yahoo.com>>
Cc: biopython at biopython.org<mailto:biopython at biopython.org> <biopython at biopython.org<mailto:biopython at biopython.org>>
Subject: Re: [Biopython] Volunteers for making Biopython release 1.77

Perhaps I will have to do it again? Anyway - are there any open issues you all think need to be fixed before the release? My initial thoughts are just these two:

NCBI BLAST v2.10.0 updates with arguments and DB changes:
https://github.com/biopython/biopython/issues/2863<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbiopython%2Fbiopython%2Fissues%2F2863&data=02%7C01%7Cdalchr28%40evergreen.edu%7C7b4f8ecaf310434a3ef708d7f38f3ab5%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637245668819692466&sdata=QgXOSZ%2FZk5coJ7YQsg2e67fLtPVtI7m1W4ag2fGOieY%3D&reserved=0>

UniProt release 2019_11 changes FT and CC lines
https://github.com/biopython/biopython/issues/2417<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbiopython%2Fbiopython%2Fissues%2F2417&data=02%7C01%7Cdalchr28%40evergreen.edu%7C7b4f8ecaf310434a3ef708d7f38f3ab5%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637245668819702461&sdata=viSIr82O49db7anmX09dwo5V2D49jTUB62HCx8lHSlQ%3D&reserved=0>
(might be resolved already, need triage)

Peter

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