To set up a clean and easy to manage Python development environment on Mac OS X (or more generally - a Linux-like working environment), I try to obey the following guidelines:
Use Homebrew as the package management tool. General tools or system wide packages are installed through Homebrew.
Install Python 2 and 3 (including pip) from Homebrew. Though Python 2 comes with OS X by default, but the version might be lower and may be changed due to OS X upgrade in the future.