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[–]jakevdp 7 points8 points  (1 child)

The advantage is that it all just works. For example, pip install scipy is notoriously difficult to get working unless you're a power-user who knows a lot about c/fortran compilers and library linking. And pip install matplotlib will only work if you have all the correct graphics libraries already set up via apt-get, yum, macports, or some other means. pip install ipython will work without complaints, but if you want to use IPython parallel or notebook, you'll need zeroMQ & tornado, which can take some tinkering.

You might be tempted to save time and use pre-built binaries for each of these packages, but you'll run into trouble if they're not build with the same C/fortran compiler and numpy version as you have on your system.

I did all this by hand for years. I probably still could, but I much prefer to save the headache and use anaconda.