[Biopython] Volunteers for making Biopython release 1.77

[Daley, Christopher]

I've stood up a Docker container with all of the dependencies and successfully run the full online test suite with the exception of the NCBI_qblast test which seems to be timing out.

I'll make a pull request to update the Docker images once I test them a bit more locally.

Chris


________________________________
From: Peter Cock <p.j.a.cock at googlemail.com>
Sent: Saturday, May 9, 2020 10:47 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

Good news I guess: Bio.PopGen.FDist was deprecated in Release 1.68, removed in Release 1.70. So we don't need to worry about fdist2 anymore.

Perhaps you will have some pull requests to update the Docker images?

Peter

On Sat, May 9, 2020 at 6:40 PM Daley, Christopher <dalchr28 at evergreen.edu<mailto:dalchr28 at evergreen.edu>> wrote:
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<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbiopython%2Fbiopython_docker&data=02%7C01%7Cdalchr28%40evergreen.edu%7Ce9972947678043a59dc508d7f44110dc%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637246432609609976&sdata=bel4oJcIXDukRJ04lh7xRDtCEV4q%2FLP7yJrhktf6ZSI%3D&reserved=0> 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<https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fxxmotif.genzentrum.lmu.de%2Findex.php&data=02%7C01%7Cdalchr28%40evergreen.edu%7Ce9972947678043a59dc508d7f44110dc%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637246432609619967&sdata=anfoX9KQBQf99Vbhle%2BonIg1Uvw4T6nZol5joL2UW%2BI%3D&reserved=0> is down as well. The Bioconda package points to this github repo: https://github.com/soedinglab/xxmotif<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsoedinglab%2Fxxmotif&data=02%7C01%7Cdalchr28%40evergreen.edu%7Ce9972947678043a59dc508d7f44110dc%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637246432609619967&sdata=346MRRlAdxdd6P7ko%2Fl2zC%2BkoA2W%2BftxhDwCb7bSLHg%3D&reserved=0>

Any thoughts on how to proceed?
Chris

________________________________
From: Peter Cock <p.j.a.cock at googlemail.com<mailto:p.j.a.cock at googlemail.com>>
Sent: Friday, May 8, 2020 1:34 PM
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

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%7Ce9972947678043a59dc508d7f44110dc%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637246432609629962&sdata=wYDatOGqtGI3SXjMluMw1hXBcG2C5mrPs3314QwjMZM%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%7Ce9972947678043a59dc508d7f44110dc%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637246432609639958&sdata=huVRxUELB%2Br7P%2FxMjtSGfm0Aoqg9%2BOdmXMaWCU2DCTw%3D&reserved=0>

Peter
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