How can I make homebrew’s python and pyenv live together?

You can install pyenv in your home directory (as described in pyenv’s installation guide), and then create a symlink at ~/.pyenv/versions to $(brew --cellar)/python:

ln -s $(brew --cellar python)/* ~/.pyenv/versions/

The way Homebrew works nowadays, this will pick up both 2.x and 3.x.

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