This PyCharm issue occurs because of changes the the iPython api with iPython version 5. Until Jetbrains fix this, reverting to an earlier version of iPython (version 4) will correct this. As @chenfei has discovered, this can be done through pip:
$ pip uninstall ipython
$ pip install ipython==4.2.0
Edit
And if you can’t wait that long, Jetbrains have released a patch
https://youtrack.jetbrains.com/issue/PY-20013#comment=27-1512407
Final Edit
This issue has been fixed in PyCharm 2016.2