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Apparently re-installing or adding the empy is not enough.

If you used another interpreter (e.g. Anaconda, virtualenv) etc. they may leave links to cache inside your catkin workspace if you accidentally used them before. This messes up the $PYTHONPATH which was prepending python3 libs from anaconda in my case, even though I wasn't sourcing anaconda anywhere afterwards.

What made it work was the following:

1. source ros from /opt/ros/kinetic/setup.zsh

2. clean up your catkin workspace (except src)

   cd ~/catkin_ws
   unlink src/CMakeLists.txt
   rm -rf build
   rm -rf devel
   rm .catkin_workspace
   

3. re-initialize the workspace with catkin_init_workspace from inside src

4. catkin_make

Apparently re-installing or adding the empy is not enough.

If you used another interpreter (e.g. Anaconda, virtualenv) etc. they may leave links to cache inside your catkin workspace if you accidentally used them before. This messes up the $PYTHONPATH which was prepending python3 libs from anaconda in my case, even though I wasn't sourcing anaconda anywhere afterwards.

What made it work was the following:

1. source ros from /opt/ros/kinetic/setup.zsh

2. clean up your catkin workspace (except src)

   cd ~/catkin_ws
   unlink src/CMakeLists.txt
   rm -rf build
   rm -rf devel
   rm .catkin_workspace
   

3. re-initialize the workspace with catkin_init_workspace from inside src

4. catkin_make