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

[Andrius Merkys]

Hi Andreas,

On 2022-10-13 14:31, Andreas Tille wrote:
>> 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?
> 
> Well, I guess if it would be that simple upstream would have stepped in.
> While it would be the optimal solution I'm afraid we will fail in this
> (and I would love a lot if someone would prove me wrong here!)

Right, this is most likely too much work.

>> 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?
> 
> I think both B+C is a sensible way to simply set bug #1009118 wishlist
> to give room for A anyway.

I agree this would make biopython fit to release in bookworm.

>> Or something else?
> 
> Maintaining a muscle4 package?  May be quite some users have scripts
> adapted to muslce 4 and there might be some use for this as well?

This might work, if it is not too much effort to maintain both muscle 
versions in bookworm. I would prefer B+C for simplicity.

Best,
Andrius