plotProfile error on matrix created with --maxThreshold set

[vojtace]

When I run plotProfile on matrix created with the --maxThreshold set I get an error. When I don't use --maxThreshold with computeMatrix or when I downgrade numpy to 1.22.0 everything works fine.

Software version causing the error: deeptools 3.5.5, python 3.12.7 and numpy 1.26.4 (i.e. what I get from "conda install deeptools" at this moment)

The error: Traceback (most recent call last): File "/home/user/miniforge3/envs/genomics/bin/plotProfile", line 10, in sys.exit(main()) ^^^^^^ File "/home/user/miniforge3/envs/genomics/lib/python3.12/site-packages/deeptools/plotProfile.py", line 919, in main filterHeatmapValues(hm, hm.parameters['min threshold'], hm.parameters['max threshold']) File "/home/user/miniforge3/envs/genomics/lib/python3.12/site-packages/deeptools/computeMatrixOperations.py", line 430, in filterHeatmapValues np.warnings.filterwarnings('ignore') ^^^^^^^^^^^ File "/home/user/miniforge3/envs/genomics/lib/python3.12/site-packages/numpy/init.py", line 333, in getattr raise AttributeError("module {!r} has no attribute " AttributeError: module 'numpy' has no attribute 'warnings'. Did you mean: 'hanning'? Traceback (most recent call last): File "/usr/lib/python3.12/urllib/request.py", line 1506, in open_local_file stats = os.stat(localfile)

[emattei]

I want to confirm that this is reproducible because I am getting the exact same error when --maxThreshold is set

[rysterzhu]

I am reproducing the error using computeMatrix --maxThreshold. According to online comments, np.warnings has been removed from numpy. It is recommended to manually remove or comment line 433 of computeMatrixOperations.py to skip the bug.