[Biopython] Volunteers for making Biopython release 1.77

Daley, Christopher dalchr28 at evergreen.edu
Mon May 25 07:40:16 UTC 2020 

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<mailto: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<mailto:p.j.a.cock at googlemail.com>>
Sent: Sunday, May 24, 2020 2:09 AM
To: Daley, Christopher <dalchr28 at evergreen.edu<mailto:dalchr28 at evergreen.edu>>
Cc: Michiel de Hoon <mjldehoon at yahoo.com<mailto:mjldehoon at yahoo.com>>; biopython at biopython.org<mailto:biopython at biopython.org> <biopython at biopython.org<mailto: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<mailto: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<mailto: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<mailto:p.j.a.cock at googlemail.com>>
Sent: Saturday, May 23, 2020 8:19 AM
To: Daley, Christopher <dalchr28 at evergreen.edu<mailto:dalchr28 at evergreen.edu>>
Cc: Michiel de Hoon <mjldehoon at yahoo.com<mailto:mjldehoon at yahoo.com>>; biopython at biopython.org<mailto:biopython at biopython.org> <biopython at biopython.org<mailto: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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