Sometimes Vim's Python binary can't find a package you've installed.
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in vim
:py3 import sys; print(sys.path)
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navigate to that location and find the python binary, in my case:
cd /usr/local/opt/python@3.8/Frameworks/Python.framework/Versions/3.8/bin
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install isort using this binary
./python3.8 -m pip install isort