Hi Andrius,
Am Thu, Oct 13, 2022 at 12:14:01PM +0300 schrieb Andrius Merkys:
> Since the bookworm's freeze is getting closer, I would like to attract
> team's attention to bug #1009118 in biopython:
Thanks a lot for the reminder!
> On Thu, 7 Apr 2022 15:44:43 +0300 Andrius Merkys <mer...@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!)
> 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.
> 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?
Kind regards
Andreas.
> [1] https://github.com/biopython/biopython/issues/3902
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