This can be easily solved by editing the /home/.atom/packages/script/lib/grammars.coffee file (note that the atom folder is hidden so you might have to press ctrl+H to view hidden files and folders)
Inside grammars.coffee find:
Python:"Selection Based": command: "python" args: (context) -> ['-u', '-c', context.getCode()]"File Based": command: "python" args: (context) -> ['-u', context.filepath]and replace with:
Python:"Selection Based": command: "python3" args: (context) -> ['-u', '-c', context.getCode()]"File Based": command: "python3" args: (context) -> ['-u', context.filepath]Save changes, restart Atom and enjoy running your scripts with python 3
EDIT: On Windows I believe the grammars.coffee file is located in C:/Users/Your_Username/AppData/Local/atom/packagesAgain, the AppData folder is hidden so you might have to change your settings to view hidden files and folders.
