Issue with SV matrix generation

[sfhart33]

I am getting " AttributeError: 'DataFrame' object has no attribute 'append' " when I try to run the latest version of SigProferMatrixGenerator on SV data. I think this may because the latest version (v1.3.0) requires Pandas and Numpy >= 2.0.0, where the append function was removed.

error with current version

conda create --name sigprofiler_env python=3.9 numpy pandas -y
conda activate sigprofiler_env
pip install SigProfilerMatrixGenerator
SigProfilerMatrixGenerator sv_matrix_generator ./data/SV_indiv_bedpe/ test_SVs ./outputs/test_SVs/

works with the previous version

conda create --name sigprofiler_env2 python=3.9 numpy pandas -y
conda activate sigprofiler_env2
pip install SigProfilerMatrixGenerator==1.2.31
SigProfilerMatrixGenerator sv_matrix_generator ./data/SV_indiv_bedpe/ test_SVs ./outputs/test_SVs/

[GACGAMA]

I am getting the same error, and I installed the program in a similar fashion.

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/ggama1/.local/lib/python3.11/site-packages/Sig                                                                                                                         ProfilerMatrixGenerator/scripts/SVMatrixGenerator.py", line                                                                                                                          1016, in generateSVMatrix
    result = annotateBedpe(data)
             ^^^^^^^^^^^^^^^^^^^
  File "/home/ggama1/.local/lib/python3.11/site-packages/Sig                                                                                                                         ProfilerMatrixGenerator/scripts/SVMatrixGenerator.py", line                                                                                                                          818, in annotateBedpe
    sample_bps = sample_bps.append(
                 ^^^^^^^^^^^^^^^^^
  File "/home/ggama1/.local/lib/python3.11/site-packages/pan                                                                                                                         das/core/generic.py", line 6299, in __getattr__
    return object.__getattribute__(self, name)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'DataFrame' object has no attribute 'append'                                                                                                                         . Did you mean: '_append'?

[mdbarnesUCSD]

Thanks, we will be looking into releasing a patch for this.