Hi Andreas, On 2022-10-13 14:31, Andreas Tille wrote:
On Thu, 7 Apr 2022 15:44:43 +0300 Andrius Merkys <merkys@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