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

[Étienne Mollier]

Hi all,

Andrius Merkys, on 2022-10-17:
> 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?
> > > 
> > > 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.

I implemented B by checking for "muscle 5" in --version output.
Attempt to make use of such muscle version with biopython would
end up with a RuntimeError, for example:

	Traceback (most recent call last):
	  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_Muscle_tool.py", line 197, in test_simple_msf
	    cmdline = MuscleCommandline(muscle_exe, input=input_file, msf=True)
	              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Align/Applications/_Muscle.py", line 682, in __init__
	    raise RuntimeError("muscle 5 is unsupported in biopython")
	RuntimeError: muscle 5 is unsupported in biopython

I also implemented C with the following NEWS item:

python-biopython (1.80+dfsg-1) experimental; urgency=medium

  Starting with biopython 1.79, command wrappers are being deprecated,
  and may be removed past biopython 1.81.  This has the notable
  implication that support of the muscle command past version 5 has
  never been implemented, and probably will never be[1,2].

  Users of muscle are invited either to use a generic command launcher
  such as the module "subprocess", or to stick to muscle 3.

  [1]: https://github.com/biopython/biopython/issues/3902
  [2]: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1009118

 -- Étienne Mollier <emollier at debian.org>  Wed, 23 Nov 2022 23:19:22 +0100

I tried to keep messages succinct, but if you think this is too
terse, improvements are welcome.

Have a nice day,  :)
-- 
  .''`.  Étienne Mollier <emollier at debian.org>
 : :' :  gpg: 8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
 `. `'   sent from /dev/pts/2, please excuse my verbosity
   `-
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