I can't reproduce the issue, neither on Windows nor on Linux (Windows: Python 3.6; Linux: Python 3.5).

I support @elextr's observation about the newlines but the docs for input() tell that trailing newlines are stripped (https://docs.python.org/3/library/functions.html#input).
Not sure what's happening on your system but since it happens on a usual command prompt as well on your system, it seems unrelated to Geany.

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