I believe that the main difference between running an application from 
macOS’s terminal and via clicking on it is that clicking on it runs the 
application in a very bare environment with almost no environment variables 
so that your application can’t find the home directory or the current 
encoding/locale and any application which it is supposed to find in $PATH 
will be invisible to it. I’m afraid the best I can offer for debugging is 
to wrap your code in something like the block below then inspect 
/tmp/error-message.txt to see what the problem really is.

import traceback
try:
    # Your code here.except BaseException as ex:
     with open("/tmp/error-message.txt", "w") as f:
         traceback.print_exc(file=f)
     raise

If you find that that file never gets written, it’s probably macOS’s 
gatekeeper blocking your application from running.
​

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