How to get rid of specific warning messages in python while keeping all other warnings as normal?

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If Scipy is using the warnings module, then you can suppress specific warnings. Try this at the beginning of your program:

import warnings
warnings.filterwarnings("ignore", message="divide by zero encountered in divide")

If you want this to apply to only one section of code, then use the warnings context manager:

import warnings
with warnings.catch_warnings():
    warnings.filterwarnings("ignore", message="divide by zero encountered in divide")
    # .. your divide-by-zero code ..

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