Bio/Entrez/DTDs/modules.ent | 7 0 + 7 - 0 !
1 file changed, 7 deletions(-)

 remove non dfsg free dtd

Tests/Blast/html_msgid_29_blastx_001.html | 5 2 + 3 - 0 !
1 file changed, 2 insertions(+), 3 deletions(-)

 do not use privacy-breach-logo

Doc/cookbook/Restriction/Restriction.html | 3 0 + 3 - 0 !
1 file changed, 3 deletions(-)

 fix privacy breach with html5shiv

Bio/Align/Applications/_Muscle.py | 5 5 + 0 - 0 !
1 file changed, 5 insertions(+)

 raise runtime error when trying to use wrapper on muscle 5.
Bug: https://github.com/biopython/biopython/issues/3902
Bug-Debian: https://bugs.debian.org/1009118

Bio/Align/Applications/_Muscle.py | 10 9 + 1 - 0 !
Tests/test_Muscle_tool.py | 12 9 + 3 - 0 !
2 files changed, 18 insertions(+), 4 deletions(-)

 expect muscle3 as executable instead of muscle.
Bug-Debian: https://bugs.debian.org/1009118

Tests/test_Align_codonalign.py | 6 6 + 0 - 0 !
Tests/test_codonalign.py | 6 6 + 0 - 0 !
2 files changed, 12 insertions(+)

 skip scipy tests within test_align_codonalign.
 Note that this patch may be related to #1086108.  Chances are it will
 be removable once the bug is resolved.

Bug-Debian: https://bugs.debian.org/1079439

Bio/PDB/binary_cif.py | 10 9 + 1 - 0 !
1 file changed, 9 insertions(+), 1 deletion(-)

 fix test failure on 32-bit platforms.
 This fixes the following symptom while running the test suite of
 Biopython on 32-bit processors:
 .
           File "/builds/med-team/python-biopython/debian/output/source_dir/.pybuild/cpython3_3.12/build/Bio/PDB/binary_cif.py", line 85, in _run_length_decoder
             decoded_data = np.repeat(data[::2].astype(dtype), data[1::2])
                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
           File "/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py", line 466, in repeat
             return _wrapfunc(a, 'repeat', repeats, axis=axis)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
           File "/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py", line 68, in _wrapfunc
             return _wrapit(obj, method, *args, **kwds)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
           File "/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py", line 45, in _wrapit
             result = getattr(asarray(obj), method)(*args, **kwds)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
         TypeError: Cannot cast array data from dtype('uint32') to dtype('int32') according to the rule 'safe'