[Debian-med-packaging] Bug#1009118: python3-biopython: incompatible with muscle >= 5

[Andrius Merkys]

Hello,

Since the bookworm's freeze is getting closer, I would like to attract 
team's attention to bug #1009118 in biopython:

On Thu, 7 Apr 2022 15:44:43 +0300 Andrius Merkys <merkys at debian.org> wrote:
> python3-biopython is incompatible with muscle >= 5.
I tend to think this is serious-ish as biopython integration with muscle 
from Debian package will not work. Upstream has been notified [1] and 
their response was to drop all wrappers at some point. However, it 
becomes clear that this point is beyond the bookworm's freeze (June 
2022, to cite upstream), thus we are at risk of shipping a broken package.

What should we do?

A. Patch biopython to work with muscle >= 5?

B. Patch biopython to detect muscle >= 5 and throw an error?

C. Slap a warning (debian/NEWS) that biopython interface with muscle >=5 
is broken and should only be used with local installations of muscle <5?

Or something else?

[1] https://github.com/biopython/biopython/issues/3902

Best,
Andrius