Open File -> Settings, go to Install, find atom-runner and install it:

atom-runner for python

To specify the python version you want to use go File -> Config and add runner section (use your path to python):

    userId: ...
      python: "c:\\Python36-32\\python.exe"

Note: 2 spaces indent are important! Just copy runner section from snippet above and paste to your config

Go to your py file and press Alt+R on Windows or Ctrl+R on Linux