[Biopython] Volunteers for making Biopython release 1.77

Sun May 24 15:04:35 UTC 2020

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%7C43377cc97b7e4c3d89d708d7ffc240e9%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637259082084925828&sdata=bmBLHjoNNYplSiX5uzH1dH2sXAULWHiSFBbaSLYtS8A%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%7C43377cc97b7e4c3d89d708d7ffc240e9%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637259082084925828&sdata=QxBtcqJIVch2O%2FC0dNt5sY9MvY4nKBR4rdHB7J8B1H8%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%7C43377cc97b7e4c3d89d708d7ffc240e9%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637259082084925828&sdata=dxxVMA1%2FgG226egjhfgw%2F7B5pJwJUWokAoYvm%2Bh%2BCt8%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%7C43377cc97b7e4c3d89d708d7ffc240e9%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637259082084935814&sdata=ea7lC%2BL1OoJ%2BRIqZ0sP35g8Rl07k4R2ilj8SXsluXy0%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%7C43377cc97b7e4c3d89d708d7ffc240e9%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637259082084935814&sdata=mzPqRdkmkcE7XGRYPVTTFgHRa8nQaEnT1OT9773BOpk%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%7C43377cc97b7e4c3d89d708d7ffc240e9%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637259082084945808&sdata=qrRPXaf4LzV6GkQ8PPP5lPGRr36mBLYxC8vIKBEHHic%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%7C43377cc97b7e4c3d89d708d7ffc240e9%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637259082084945808&sdata=MI2NYUJjzH%2B1VgWfxnol43mUGqpN9Rh0PNxgm3LZtLg%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%7C43377cc97b7e4c3d89d708d7ffc240e9%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637259082084955803&sdata=kBZed0LbFlwUweQL7odWYsWJdlTSdaTNybOVIIejo4I%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%7C43377cc97b7e4c3d89d708d7ffc240e9%7C22adcff7c06f49a68f2050711c40ddaa%7C0%7C0%7C637259082084955803&sdata=v%2Ff15tvWbHp1bfTHAWC2as9G3eOQEpXIsf9uLGnDH5k%3D&reserved=0> WordPress for that - do you want the same username
as your GitHub?

Peter
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