[Biopython] Volunteers for making Biopython release 1.77

Thu May 14 12:15:19 UTC 2020

The UniProt/SwissProt parser issue #2417 is closed now.

Also we should include this tiny fix:

https://github.com/biopython/biopython/pull/2891

Peter

On Thu, May 14, 2020 at 12:10 PM Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> Excellent news, thank you Chris.
>
> Two passes of LaTex is the norm when using labels and references, three
> passes if you use references to page numbers. The Makefile should do that.
> Hevea includes its own loop which is a littles easier to use.
>
> As to the outstanding issues, the BLAST DB v5 test update seems easy
> enough - could you review this pull request Chris?
>
> https://github.com/biopython/biopython/issues/2863
> https://github.com/biopython/biopython/pull/2890
>
> Updating the BLAST wrappers would be nice, but it seems we might just skip
> that (and silence the test warnings about the BLAST wrappers being out of
> date) if we're serious about dropping the Bio.Application framework:
>
> https://github.com/biopython/biopython/issues/2184
> https://github.com/biopython/biopython/issues/2877
>
> Oh, and can we close the UniProt/SwissProt parser issue or not?:
>
> https://github.com/biopython/biopython/issues/2417
>
> Other suggestions are https://github.com/biopython/biopython/pull/2399 which
> has some merge conflicts and needs a review.
>
> Also if I can finish the documentation
> https://github.com/biopython/biopython/pull/2334 would be nice to include
> too.
>
> Right now I still think only #2863/#2890 for the BLAST test, and #2417 for
> UniProt/SwissProt are blockers.
>
> Peter
>
> On Thu, May 14, 2020 at 8:16 AM Daley, Christopher <dalchr28 at evergreen.edu>
> wrote:
>
>> 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> 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%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>
>> *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%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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