[Biopython] Volunteers for making Biopython release 1.77

[Peter Cock]

Thank you Chris,

You did a great job yesterday - things look ready to release today.

I've just merged the Tutorial update, that means this is probably going to
be the commit we tag as Biopython 1.77, as it should match the tutorial you
built:

https://github.com/biopython/biopython/commit/a353d84221f8381b6853a7562b048853d91aae8e

VOLUNTEERS: I'd like to heard at least one independent test of any of the
wheels (available for now on RackSpace), plus the tar-ball or zip file
available here:

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

Chris - did you get an email from WordPress about your account on
open-bio.org, or do I need to reset the password and email it to you
manually?

Peter


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
>
>
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