I have a fairly straightforward Ubuntu (13.04) desktop installation, which comes complete with several Ubuntu-packaged Python utilities — these live in /usr/lib/python2.7 and are owned by root. I call these "system" Python packages.

I also do a lot of scientific work with Python and so I have installed tools like numpy, matplotlib, etc. using pip — these live in /usr/local/lib/python2.7 and are owned by me (I chowned /usr/local because I'm the only user on this machine). I call these "local" Python packages. I put the local path in front of the system one in my PYTHONPATH so that I load local packages preferentially.

Now, I'm trying to upgrade one of the local packages that I installed using pip, and pip is failing because it wants to uninstall a dependent system package as part of the upgrade process.

I have two questions about this, addressing the problem from each end :

One way to fix this problem is to get pip to upgrade my local packages and ignore the system-installed ones (if possible). Can I prevent pip from trying to uninstall a system package during a local package upgrade, but only for one dependency ?

Another way would be to have pip install a newer version of the package, and then use that version to satisfy dependencies in apt related tools. Is there a way to tell Ubuntu that a pip-installed package will satisfy an apt dependency ?

(I am familiar with virtualenv, but on this machine I only ever use this one environment, so I'd really like to avoid keeping track of whether I'm working in the correct virtualenv.)