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

[Andrius Merkys]

Package: python3-biopython
Severity: important
Tags: upstream

Hello,

python3-biopython is incompatible with muscle >= 5. Upstream tests
detect this incompatibility:

======================================================================
ERROR: test_Muscle_profile_simple (test_Muscle_tool.MuscleApplication)
Simple round-trip through app doing a profile alignment.
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Tests/test_Muscle_tool.py",
line 133, in test_Muscle_profile_simple
    output, error = cmdline()
  File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/Application/__init__.py",
line 574, in __call__
    raise ApplicationError(return_code, str(self), stdout_str, stderr_str)
Bio.Application.ApplicationError: Non-zero return code 1 from 'muscle
-out Fasta/temp_align_out3.fa -profile -in1 Fasta/fa01 -in2 Fasta/f001',
message 'Invalid command line'

(only one failing test is shown for brevity)

However, tests with muscle are skipped as the build system is unable to
detect newer muscle. I attach a patch prodding the build system to run
muscle tests. Normally I would push such patch to cause FTBFS for
package, but now I think failures of integration with muscle should not
cause AUTORM for Biopython. Nevertheless, I think this should be fixed
for bookworm.

Andrius
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