The system Python (in /usr/bin/) may end up in your PATH environment variable before your installed version (in /usr/local/bin/). Homebrew and the official Python installer will both symlink executables to /usr/local/bin/python3 depending on which one was installed last. The /usr/bin/python3 is the system Python, and the one you want to avoid using. You can use where python3 or where idle3 to see which executables you have available in your path. They can all co-exist if you know what you are doing, but I recommend choosing either the Homebrew method or the official installer and not both. It can get confusing and you may accidently install a package to one version of Python while your IDE is using a different version. In addition to the system Python 2 and Python 3, you can also have Python 3 installed from the official installer as well as Homebrew's Python 3 all at once. It is possible to have multiple versions of Python installed.
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