[Debian-med-packaging] Bug#1131072: python-biopython: autopkgtest regression with NumPy 2.4

[roehling at debian.org]

Source: python-biopython
Version: 1.86+dfsg-1
Severity: important
User: debian-python at lists.debian.org
Usertags: numpy2.4

Dear maintainer,

According to https://ci.debian.net data, your package python-biopython has an
autopkgtest regression with numpy.

The following architectures failed: amd64, arm64.

Hopefully relevant excerpt from
https://ci.debian.net/packages/p/python-biopython/unstable/amd64/69506848/
follows:

129s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0
152s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack)
152s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python)
152s FAIL
220s ERROR: test_coord_space (test_PDB_vectors.VectorTests.test_coord_space)
220s TypeError: only 0-dimensional arrays can be converted to Python scalars
220s ValueError: setting an array element with a sequence.
220s FAILED (failures = 1)
258s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0
282s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack)
282s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python)
282s FAIL
337s ERROR: test_coord_space (test_PDB_vectors.VectorTests.test_coord_space)
337s TypeError: only 0-dimensional arrays can be converted to Python scalars
337s ValueError: setting an array element with a sequence.
337s FAILED (failures = 1)
338s dependencies         FAIL non-zero exit status 1
561s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0
584s FAIL
688s ERROR: test_coord_space (test_PDB_vectors.VectorTests.test_coord_space)
688s TypeError: only 0-dimensional arrays can be converted to Python scalars
688s ValueError: setting an array element with a sequence.
688s FAILED (failures = 1)
724s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0
753s FAIL
853s ERROR: test_coord_space (test_PDB_vectors.VectorTests.test_coord_space)
853s TypeError: only 0-dimensional arrays can be converted to Python scalars
853s ValueError: setting an array element with a sequence.
853s FAILED (failures = 1)
855s full_suite           FAIL non-zero exit status 1
855s dependencies         FAIL non-zero exit status 1
855s full_suite           FAIL non-zero exit status 1