[Biopython] Volunteers for making Biopython release 1.77

Thu May 14 07:16:33 UTC 2020

I fetched the latest commits just now and ran the full tests, including the tar-ball and documentation and it all seems to be in order. I do a lot of Latex work, so pretty well set up in that area although I had to install Hevea from APT. The version in the Ubuntu 18.04 repos is 2.30 which is pretty recent and seems to output the Tutorial nicely enough although it took two passes of the latex compiler.
It looks all set from this end, barring the pull requests - are there any blocking issues or PRs?
Chris
________________________________
From: Peter Cock <p.j.a.cock at googlemail.com>
Sent: Tuesday, May 12, 2020 7:52 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

Excellent - Markus said on GitHub that the NCBI tests did complete recently but sometimes took up to 2 hours. This is something we will probably have to reduce as that is not practical.

If you haven't already, I suggest you next try building the tar-ball and wheels locally, installing them, and running the tests from an unzipped tar-ball. The reason we do this is to catch problems with the manifest (e.g. new test files not being included in the tar-ball).

Also are you setup to build the Tutorial? Latex is easy to install (just a large download), but Hevea can be a pain. I did spend some effort trying to get that into conda, but didn't succeed.

Peter

On Mon, May 11, 2020 at 3:20 PM Daley, Christopher <dalchr28 at evergreen.edu<mailto:dalchr28 at evergreen.edu>> wrote:
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<mailto:p.j.a.cock at googlemail.com>>
Sent: Saturday, May 9, 2020 10:47 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

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%7C0f2d9d6e9164401aa66e08d7f684241d%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637248919720142489&sdata=Bxr5BeYAh7J8wj8VUy6bLwBcwz4Cne3j5nnkmGe0RwI%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%7C0f2d9d6e9164401aa66e08d7f684241d%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637248919720142489&sdata=Is7cTyw%2BAieycEyj5VWm8cDoZaUziCrGG8OvYGfmTKg%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%7C0f2d9d6e9164401aa66e08d7f684241d%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637248919720152483&sdata=%2BntvyTrH3Drw0DeZLhCksmBkRURRwcWWgqF7fz5%2BwyU%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%7C0f2d9d6e9164401aa66e08d7f684241d%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637248919720162478&sdata=OwY6vorDjyNvrN3Lhm1OXe5ECBeqVfhEaiYugyREXcs%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%7C0f2d9d6e9164401aa66e08d7f684241d%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637248919720162478&sdata=stgShVLrb%2BuUsjXenxp2PQeFaWFQa4OKqX67Y6CzQQI%3D&reserved=0>

Peter
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