[Biopython] Volunteers for making Biopython release 1.77

Mon May 25 08:34:20 UTC 2020

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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