[Debichem-devel] Bug#1053865: prody: incompatible with python3-biopython > 1.79

[Andrius Merkys]

Source: prody
Version: 2.3.1+dfsg-3
Severity: serious
Justification: FTBFS
Tags: sid ftbfs
Forwarded: https://github.com/prody/ProDy/issues/1723

Hello,

prody FTBFS with python3-biopython > 1.79:

======================================================================
FAIL: testBuildMSAlocal 
(prody.tests.sequence.test_analysis.TestBuildMSA.testBuildMSAlocal)
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence/test_analysis.py", 
line 1210, in testBuildMSAlocal
     assert_array_equal(expect, result)
   File 
"/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line 
985, in assert_array_equal
     assert_array_compare(operator.__eq__, x, y, err_msg=err_msg,
   File "/usr/lib/python3.11/contextlib.py", line 81, in inner
     return func(*args, **kwds)
            ^^^^^^^^^^^^^^^^^^^
   File 
"/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line 
862, in assert_array_compare
     raise AssertionError(msg)
AssertionError:
Arrays are not equal

Mismatched elements: 2 / 2 (100%)
  x: array([<Sequence: 1 (msa_3hsyA_3o21A[0]; length 380; 354 residues 
and 26 gaps)>,
        <Sequence: 2 (msa_3hsyA_3o21A[1]; length 380; 374 residues and 6 
gaps)>],
       dtype=object)
  y: array([<Sequence: 1 (Unknown[0]; length 80; 59 residues and 21 gaps)>,
        <Sequence: 2 (Unknown[1]; length 80; 64 residues and 16 gaps)>],
       dtype=object)

The upstream knows about the issue.

Best,
Andrius