Mac OS X 10.11.5 pip install getting Operation Not Permitted error

The new versions of Mac Os come with high restrictions on what you can do and is called: System Integrity Protection.

There is unfortunately not much we can do about that, and anyway the reason for System Integrity Protections seem to be reasonable.

Plus usually you do not want to install things systemwide, there is no reason to use sudo in front ofpip. If you don't have the permissions, there is likely a good reason.

You should be able to install any packages as user by using the --user:

pip install ipython --user

Which will have the advantage of installing in your home, where you have ~0 chance of breaking your system. Moreover it will not require you to use sudo that you shouldn't have to use anyway.

I would also encourage you to not use system-python on a mac:
1) It's never up to date, and is linked weirdly with some binary libraries
2) It's Python2.7, which will not be supported anymore soon

Prefer brew install python/brew install python3 that have complete separate Python installation that do not require sudo either. Or, anaconda that does the same, support multiple environment, and have binary of many python packages that Homebrew lacks.