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Interesting, I can't reproduce the issue here (when running a python script). I'm still on macOS 12.6.2 and haven't updated to 13 yet - what's your version? It's possible there's some new permission to allow/disallow applications to execute scripts in the terminal (for security reasons). Isn't there some option under "System Preferences"->"Security & Privacy" under the Privacy tab where you could allow Geany to execute scripts in terminal? (There's nothing like that on macOS 12.)
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