I had the same problem with Aptana and just solved it. In my case I had configured another interpreter (IronPython) for running another script. When I got back to a previous script I got the same error message as you "Unable to get project for the run" because it was trying to run it with IronPython instead of Python.
I would therefore recommand the following:
1) Check your interpreter configuration.
-> Window -> Preferences -> Pydev -> Interpreter Python
If you have no interpreter there try autoconfig. If it doesn't work you will have to browse it yourself by clicking New (then it should be somewhere like C:\Python27\python.exe)
2) If you have an interpreter, it means that Aptana is trying to run your script with another interpreter. In that case right click on your script file in Aptana -> Run as -> Python run.
That worked for me.
Good luck !