Resolving problems with PIP after Upgrading to OS X El Capitan

After I upgraded my Mac to El Capitan, I was having some problems installing new packages. I was getting access denied errors when some packages tried to upgrade (and hence remove) existing packages.

For those not in virtualenvs, I had package installed to the default Python site packages directory (/Library/Python/2.7/site-packages in my case). This was causing problems because El Capitan included a new feature called System Integrity Protection (also called rootless) that prevents you (even as root via sudo) from modifying files in a number of system directories, which seemed to be affecting this.

Below are the steps I took to resolve the issue, which is a general outline for how you can resolve this issue for yourself:

  1. Capture a list of all packages you have installed. Use pip freeze > some-file-to-keep-results
  2. Disable System Integrity Protection, which involves rebooting into recovery mode (hold Command+R), launch a terminal, use the command csrutil disable and reboot back into normal mode.
  3. Uninstall all packages from pip. Use pip freeze | xargs sudo pip uninstall -y or uninstall the package manually.
  4. Ensure that all the packages in the system site-packages directory are gone (/Library/Python/2.7/site-packages), remove any remaining packages manually.
  5. Re-enable System Integrity Protection using the same procedure as #2, with the csrutil enable command
  6. Once again rebooted in normal mode again, install a version of python that’s not the one that comes with OS X. brew install python will do that if you have the Homebrew package manager installed. This is better for development uses for Python anyway.
  7. Install pip manually by downloading the file from the link, and running it with python You can also install pip via Homebrew, but there are some reasons to do it the manual way.
  8. Finally, and this might not be required in your case, pip still wasn’t available via the shell, so I needed to manually create a command to invoke it. I created a script pip in /usr/local/bin and made it invoke the pip package:
    python /usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip/ $@

    Finally, I modified the script to executable with chmod uga+x pip.

  9. After pip is back in place and working, I re-installed the packages I previously had with pip install -r some-file-to-keep-results

    That’s it. Hopefully its at least that easy for you.

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