[Debian-med-packaging] Bug#1022307: status on t_coffee causing biopython ftbfs

[Étienne Mollier]

Hi Nilesh,

Nilesh Patra, on 2022-11-23:
> On Wed, 23 Nov 2022 15:07:32 +0200 Andrius Merkys <merkys at debian.org> wrote:
> > On Tue, 22 Nov 2022 23:54:48 +0100 =?utf-8?Q?=C3=89tienne?= Mollier 
> > <emollier at debian.org> wrote:
> > > Hi, mostly retitling the open entry against biopython for the
> > > sake of clarity, and also pinging both bugs to reset auto-
> > > removal counters.  We don't have much news from t_coffee
> > > upstream to day unfortunately.  Maybe it will be necessary to
> > > revert the t-coffee version bump for the upcoming Debian release
> > > or do people see other options?
> > 
> > This issue is blocking Python 3.11-add transition, but we surely do not 
> > want biopython to be dropped from testing. However, the problem is not 
> > with biopython, but with t-coffee which biopython merely uses for tests. 
> > Would it be acceptable to skip t-coffee tests for now thus unblocking 
> > Python 3.11-add transition?
> > This bug report should remain open to remind 
> > us bring t-coffee tests back once #1022570 is solved.
> 
> That sounds quite a reasonable thing to do, but we probably should also
> decrese the severity of this bug to "important" to let biopython be in testing
> once the corresponding tests are skipped.
> 
> Étienne, what do you think?

I removed the build-dependency on t-coffee for the experimental
upload of biopython 1.80 in order to get tests to go through.
This skips the faulty test in biopython.  t-coffee merely
enhances biopython, and I don't believe it would impede the
overall usability of the module.

It will be possible to reduce the severity of the bug once one
migrates python-biopython to sid.  If in the meantime t-coffee
gets fixed or reverted, then we could even restore the tests and
close the bug.

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/2, please excuse my verbosity.
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