I've never bothered with virtualenvwrapper - I create virtualenvs alongside my projects, and call `$virtualenv/bin/python` or `$virtualenv/bin/pip` etc. directly. Sometimes I activate the virtualenv, sometimes I don't.
That's what I do too. I mostly activate them by hand nowadays, just to avoid calling python. Fish is smart enough that it knows that, if I type a period in a directory that contains a virtualenv, I want to activate it.