Stop pip installing dependancies already installed using apt-get

Question

How do I make sure packages installed using pip don't install dependancies already installed using apt-get?

For example, on Ubuntu you can install the package Numpy using apt-get install python-numpy. Which gets installed to:

usr/local/lib/python2.7/dist-packages 

I've noticed that when I install a package that requires numpy using pip for example, pip install scipy instead of skipping the numpy dependancy it installs again to a different location.

/usr/lib/python2.7/dist-packages

What pip should do is skip any python packages installed globally, right?

Answer 1

In key here is to prevent multiple package managers to install into the same directories.

One strategy is to create a virtualenv that is aware of the package of its parent interpreter. This can be done by using the --system-site-packages option.

virtualenv -p /usr/bin/python --system-site-packages py27
source py27/bin/activate

This environment will not be empty by default. You may want to compare /usr/bin/python -m pip list and python -m pip list.

See also this question

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For many (scientific) packages there are also wheels available on pypi. Wheels are already binary and thus need no further compilation.