[Biopython] Volunteers for making Biopython release 1.77

Thu May 7 13:56:43 UTC 2020

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>
Sent: Wednesday, May 6, 2020 8:40 AM
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

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%7C19fff98a94fd48ec146808d7f1d3c80e%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637243764213082843&sdata=l4wghnNFxk03ZR6a9MgIJXhPEINA0rC%2BEI8Cj5aX634%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%7C19fff98a94fd48ec146808d7f1d3c80e%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637243764213082843&sdata=T%2BRqIl7u6RJE0mOyBt38tv0Xz67A2L0y0DsbqK%2BQrLM%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%7C19fff98a94fd48ec146808d7f1d3c80e%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637243764213092841&sdata=lQfFkK9F9P%2B2k%2Bb89gahILSNx7guZXqU6kBHghsXZjs%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%7C19fff98a94fd48ec146808d7f1d3c80e%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637243764213092841&sdata=aVj2i5yONk%2B3NX2b48X3GPJFktnkEtSbYwb0q%2BEa%2BEg%3D&reserved=0>
(might be resolved already, need triage)

Peter

On Fri, May 1, 2020 at 10:01 AM Michiel de Hoon <mjldehoon at yahoo.com<mailto:mjldehoon at yahoo.com>> wrote:
Hi all,

Recent updates to Biopython have focused on removing the old Python2-specific code and cleaning up the code for Python3.
Since this is now essentially finished, now would be a good time to make the next Biopython release (1.77). Also, this will be the last release before we start removing alphabets from Biopython.

Is anybody (especially junior people) interested in managing this release?
The release process is now well documented:

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%7C19fff98a94fd48ec146808d7f1d3c80e%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637243764213102840&sdata=al5osrGOxCTGxeEUUaojKewYWG09NlOCrYKcB3iwP74%3D&reserved=0>

It also entails looking at recent bug reports and seeing if any of them are sufficiently important that they should be fixed before the release can be made.

If any volunteers could write to the mailing list, then that would be great.

Thanks!

-Michiel
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