[Biopython] Volunteers for making Biopython release 1.77

[Peter Cock]

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>
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>
> *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>
> 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>
> *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%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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