if you are going to open python files on pycharm you should open the project from pythonCode folder not the root folder (this one). pycharm seem to have issues when there are nootbook files because it will actually run the server for notebook and send all output to notebook instead of console. opening in pythonCode folder solves everything!
Installation Instructions:
##Mac OS X install homebrew
brew install python3
pip3 install numpy ipython
pip3 install theano
pip3 install requests
pip3 install jinja2
pip3 install tornado
pip3 install jsonschema
pip3 install matplotlib
##Linux (Ubuntu)
sudo apt-get intall python3 [I'm not sure if this is 100% needed]
sudo apt-get install python3-pip
sudo pip3 install numpy ipython
sudo pip3 install theano
sudo pip3 install requests
sudo pip3 install jinja2
sudo pip3 install tornado
sudo pip3 install jsonschema
sudo pip3 install matplotlib
##Will open in a web browser:
ipython3 notebook