[Biopython] Volunteers for making Biopython release 1.77

Mon May 25 09:01:26 UTC 2020

Good catch - that's in the NEWS.rst file too:

https://github.com/biopython/biopython/blob/master/NEWS.rst

We can fix the GitHub copy, but I wouldn't worry about asking Chris to
rebuild the tar-ball and zip file we're planning to use for the release for
this alone:

https://github.com/biopython/DIST/pull/5

Peter

On Mon, May 25, 2020 at 9:53 AM rob miller <rob.miller.gh at gmail.com> wrote:

> Please can you correct typo in the blog post:
>
> > A major contribution by Rob Miller ...  simplifies the analysis and
> manipulation of coordinates of proteins structures.
>
> change last part to:
>
> > simplifies the analysis and manipulation of coordinates of protein
> structures.
>
> (drop the 's' at the end of protein)
>
> Thank you,
>
> Rob.
>
>
> On Mon, May 25, 2020 at 8:40 AM Daley, Christopher <dalchr28 at evergreen.edu>
> wrote:
>
>> Thanks for your patience Peter.
>>
>> I've made a pull request or the tutorial fixes and the tar-ball/zip files
>> to the relevant repos.
>>
>> I'll make a pull request for the post release version bump after I get
>> some sleep myself.
>>
>> The following is a draft of the release blog post:
>>
>> Biopython 1.77 has been released and is available from our website and
>> PyPI.
>>
>> This is the first release since we dropped support for Python 2.7 and
>> 3.5. Focusing on Python 3.6 or later will let us take advantage of new
>> functionality and syntax, and simplify our code base and testing.
>>
>> This release of Biopython supports Python 3.6, 3.7 and 3.8 It has also
>> been tested on PyPy3.6.1 v7.1.1.
>>
>> ``pairwise2`` now allows the input of parameters with keywords and
>> returns the alignments as a list of ``namedtuples``.
>>
>> The codon tables have been updated to NCBI genetic code table version
>> 4.5, which adds Cephalodiscidae mitochondrial as table 33.
>>
>> ``Bio.Restriction`` has been updated to the January 2020 release of
>> REBASE.
>>
>> A major contribution by Rob Miller to ``Bio.PDB`` provides new methods to
>> handle protein structure transformations using dihedral angles (internal
>> coordinates). The new framework supports lossless interconversion between
>> internal and cartesian coordinates, which, among other uses, simplifies the
>> analysis and manipulation of coordinates of proteins structures.
>>
>> As in recent releases, more of our code is now explicitly available under
>> either our original "Biopython License Agreement", or the very similar but
>> more commonly used "3-Clause BSD License".  See the ``LICENSE.rst`` file
>> for more details.
>>
>> Additionally, a number of small bugs and typos have been fixed with
>> further additions to the test suite. There has been further work to follow
>> the Python PEP8, PEP257 and best practice standard coding style, and more
>> of the code style has been reformatted with the ``black`` tool.
>>
>> Many thanks to the Biopython developers and community for making this
>> release possible, especially the following contributors:
>>
>> - Alexander Decurnou (first contribution)
>> - Andrei Istrate (first contribution)
>> - Andrey Raspopov
>> - Austin Varela (first contribution)
>> - Chris Daley
>> - Chris Rands
>> - Deepak Khatri
>> - Hielke Walinga (first contribution)
>> - Kai Blin
>> - Karthikeyan Singaravelan (first contribution)
>> - Markus Piotrowski
>> - Michiel de Hoon
>> - Peter Cock
>> - Rob Miller
>> - Sergio Valqui
>> - Steve Bond
>> - Sujan Dulal (first contribution)
>> - Tianyi Shi (first contribution)
>>
>> ----
>>
>> ------------------------------
>> *From:* Peter Cock <p.j.a.cock at googlemail.com>
>> *Sent:* Sunday, May 24, 2020 4:14 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 Chris, thank you!
>>
>> The wheel updates were not as painless as they can be, but that's done
>> now.
>>
>> We might as well get those tutorial fixes onto the master branch now, and
>> use that for the official git-tag and tar-ball for PyPI (and zip file which
>> currently we still put on the website along with it, but PyPI no longer
>> takes both). Could you make a pull request for that please?
>>
>> Note the wheels don't have the tutorial included, so it doesn't matter if
>> we include those fixes or not.
>>
>> Things you'll need me or someone else with the permissions to do include
>> the git tag, upload to PyPI (I can get the wheels from rackspace, and the
>> tar-ball from our website as per pull request (D) discussed earlier), and
>> publishing the blog post.
>>
>> The final (trivial) pull request is the post release version bump, after
>> which we can start merging things for the next release.
>>
>> VOLUNTEERS: Now would be the perfect time to test the proposed wheel
>> files currently on rackspace, see link on
>> 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%7C132edb990b7047c1185308d8003844ee%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637259588979262947&sdata=C%2B01eajlnmm0ISUDuG0p8jrIbS%2F60rhhfTuw0k2Mgy8%3D&reserved=0>
>>
>> Good night everyone, I'm turning in now.
>>
>> Peter
>>
>> On Sun, May 24, 2020 at 4:04 PM Daley, Christopher <
>> dalchr28 at evergreen.edu> wrote:
>>
>> I noticed that there are several references to the old epydoc api urls in
>> other tutorial files. I've updated them in my fork and the Tutorial files
>> in the DIST pull request I just made were generated with the new api links.
>> I checked them all manually but I could have missed something.
>>
>> I'll submit a pull request to update the main repo after the release.
>> Checking these also highlighted that almost all of the links to the
>> biopython site in both the code and docs are using http:// instead of
>> https:// - probably not a high priority with the redirects in place, but
>> I'll file and issue for future reference.
>>
>> Chris
>> ------------------------------
>> *From:* Peter Cock <p.j.a.cock at googlemail.com>
>> *Sent:* Sunday, May 24, 2020 2:09 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
>>
>> Just an FYI, the docstring automatic update worked perfectly,
>>
>> https://biopython.org/docs/1.77/api/index.html
>> <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbiopython.org%2Fdocs%2F1.77%2Fapi%2Findex.html&data=02%7C01%7Cdalchr28%40evergreen.edu%7C132edb990b7047c1185308d8003844ee%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637259588979272945&sdata=eKZpPEOBzori1sziD25cX3VUEV8yoqAAz4To6uwrUZ8%3D&reserved=0>
>>
>>
>> Look for the "Deploying application" expandable entry at the end of the
>> TravisCI API job:
>>
>> https://travis-ci.org/github/biopython/biopython/jobs/690561073
>> <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftravis-ci.org%2Fgithub%2Fbiopython%2Fbiopython%2Fjobs%2F690561073&data=02%7C01%7Cdalchr28%40evergreen.edu%7C132edb990b7047c1185308d8003844ee%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637259588979282941&sdata=60ejqflQ4gkYAFK1lF%2FuaMhO7X2ZQ%2F3AsPrpS1AsqsA%3D&reserved=0>
>>
>> (Travis will update either dev or the current version automatically, the
>> script here deliberately does not care about git tags to allow tweaks to be
>> made if there are any last minute fixes needed in the docstrings).
>>
>> This has drawn my attention to the API links in the Tutorial - the
>> reference in Doc/Tutorial/chapter_quick_start.tex is just to
>> http://biopython.org/DIST/docs/api/
>> <https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiopython.org%2FDIST%2Fdocs%2Fapi%2F&data=02%7C01%7Cdalchr28%40evergreen.edu%7C132edb990b7047c1185308d8003844ee%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637259588979282941&sdata=1SppCmiqXhSjN%2FQ3bhTVcWxLQLZ0ctJE%2BUzlzc%2FpqNA%3D&reserved=0>
>> which is the old epydoc pages, and we could add an FAQ entry too?
>>
>> Chris - If you have already started building the Tutorial, don't worry -
>> we can fix that for the next release, and separately if it might be time to
>> start replacing the epydoc pages with redirects.
>>
>> Peter
>>
>> On Sat, May 23, 2020 at 6:31 PM Peter Cock <p.j.a.cock at googlemail.com>
>> wrote:
>>
>> Excellent - let's hope there are no surprises,
>>
>> Peter
>>
>> On Sat, May 23, 2020 at 6:28 PM Daley, Christopher <
>> dalchr28 at evergreen.edu> wrote:
>>
>> I've got time this weekend and already have a branch with most of (A)
>> ready to go.  I'll work through the rest of the steps today with a Monday
>> release date in mind.
>>
>> I've got an i386 container building at the moment to see if there's an
>> obvious cause/fix for 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%7C132edb990b7047c1185308d8003844ee%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637259588979292939&sdata=iVo2Z6fIE46TFnKj%2BcQegx%2B94gsEDMJlYHbuvR3awMk%3D&reserved=0>
>>
>> My github username is as good as any I figure.
>>
>> Chris
>> ------------------------------
>> *From:* Peter Cock <p.j.a.cock at googlemail.com>
>> *Sent:* Saturday, May 23, 2020 8:19 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
>>
>> Looks ready to go - no other last minute issues have been raised, have
>> they?
>>
>> I'd like to include this, but won't hold it up to wait:
>>
>> https://github.com/biopython/biopython/pull/2334
>> <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbiopython%2Fbiopython%2Fpull%2F2334&data=02%7C01%7Cdalchr28%40evergreen.edu%7C132edb990b7047c1185308d8003844ee%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637259588979292939&sdata=vJDgi%2BdJU3VsKemYbVkkTMR9Ytvk6rTGX464hQGZP8g%3D&reserved=0>
>>
>> Also any ideas on the remaining Debian / BLAST+ issue welcome:
>>
>> 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%7C132edb990b7047c1185308d8003844ee%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637259588979302935&sdata=J4kFhs%2FwpXF1tswtXzmwor2EfalvlB1QTVnsnmOZiSI%3D&reserved=0>
>>
>> Chris - against the background instructions
>> 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%7C132edb990b7047c1185308d8003844ee%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637259588979312924&sdata=awuYY5Z0ATI6O3Lii86tEmmQ470o55CmQHx8J7Le0GU%3D&reserved=0>
>> do you want to start with:
>>
>> (A) pull request to the main repository update the version in __init__.py
>> and the tutorial,
>> and NEWS.rst - perhaps dated Monday if you're going to be able to work on
>> it this weekend?
>> Otherwise give yourself a couple of days leeway as some of these steps
>> will need me
>> or another core developer to merge on your behalf.
>>
>> (B) pull request to the DIST repository with updated Tutorial built with
>> that
>>
>> The next steps must wait on those pull requests being merged. Note once
>> (A) is merged,
>> TravisCI should update the API docs for 1.77 automatically:
>> https://github.com/biopython/docs
>> <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbiopython%2Fdocs&data=02%7C01%7Cdalchr28%40evergreen.edu%7C132edb990b7047c1185308d8003844ee%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637259588979312924&sdata=%2FBUD8964JuQ%2FuZMizzbfqh4BS1o6M4utmR%2FiqossnFI%3D&reserved=0>
>>
>> (C) Once (A) is merged, pull request the wheel repository to build the
>> wheels
>>
>> (D) Once (A) is merged, pull request to the website with the new tar-ball
>> and zip
>>
>> (E) Draft a release announcement based on the NEWS.rst file, I can set
>> you up with
>> an account on the open-bio.org
>> <https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fopen-bio.org%2F&data=02%7C01%7Cdalchr28%40evergreen.edu%7C132edb990b7047c1185308d8003844ee%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637259588979322922&sdata=MU%2Bjmvjr4dmMRgMS3McMuflI3c246oL0v9ibpGNNhY4%3D&reserved=0>
>> WordPress for that - do you want the same username
>> as your GitHub?
>>
>> Peter
>>
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