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Anaconda is very underrated, I use it both on my linux and mac systems. Also check out: Simple, Clean Python Deploys with Anaconda http://blog.stuart.axelbrooke.com/deployment-with-anaconda

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I love it on Windows but I wonder why you use it on Linux. What does it do better than the alternative (native packages and pip)?

One word - isolation.

One issue with using your system's packaging system is that a lot of system utilities are written in Python which makes it harder to play around with new versions, bleeding edge libs, etc.

Virtualenv is pretty good for isolation.

Not for binary packages, which usually end up requiring libraries installed into /user/local (and let's not get started about the mess that is Python binary deployment on Windows).

I use pyenv on my Mac https://github.com/yyuu/pyenv

infinite8s beat me to it, exactly what he/she said.

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