[Debian-med-packaging] Bug#1022307: python3-biopython: incompatible with muscle >= 5

[Étienne Mollier]

Control: severity 1022307 normal

Hi Andreas,

Andreas Tille, on 2022-11-25:
> Am Thu, Nov 24, 2022 at 10:35:06PM +0100 schrieb Étienne Mollier:
> > 
> > python-biopython 1.80 is uploaded to experimental and should
> > build soon[1], if this is not the case already.  I haven't had a
> > lot of opportunities to extensively test interactions between
> > muscle3 and 5; I guess the situation will be clearer when
> > muscle3 makes it through NEW.  It would be nice that people
> > using biopython and muscle give this a try as early as possible.
> 
> Thanks a lot for this.
> 
> I've just reverted the version of t-coffee and have uploaded
> t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 - not proud about
> this name, but well, it should do the trick without an epoch. 
> 
> Hope this will settle the situation with biopython soonish.

Thanks, this should reduce the noise on the t_coffee front.
Since python-biopython 1.79 doesn't fail to build from source
anymore, I reduce the severity already.  I don't close just yet
to avoid forgetting to bring back t-coffee in the build time
test dependencies when migrating biopython 1.80 to unstable.
There is also a FIXME item related to muscle3 support, that can
be brought back once muscle3 passes through the NEW queue.

Speaking of biopython 1.80, pseudo-excuses are looking good[1].
I fixed the autopkgtest regression in python-faidx yesterday.
When trying to rebuild reverse dependencies, I also noted an
issue in python-pauvre[2], which I forwarded upstream, since it
didn't look easy to fix on first sight.  Once sorted, I suppose
it would be feasible to upgrade biopython 1.80 in unstable.

[1]: https://qa.debian.org/excuses.php?experimental=1&package=python-biopython
[2]: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1024835

Have a nice day,  :)
-- 
Étienne Mollier <emollier at emlwks999.eu>
Fingerprint:  8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/pts/3, please excuse my verbosity.
On air: Chicago - Make Me Smile
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