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The code is OK. The problem is that you're using the wrong version of Python. As the 'Installation' chapter of that website says:

Important Note! Be sure to install Python 3, and not Python 2. The programs in this book use Python 3, and you’ll get errors if you try to run them with Python 2. It is so important, I am adding a cartoon penguin telling you to install Python 3 so that you do not miss this message:

You are using Python 2 to run the program.

The result is incorrect because the program depends on a feature that behaves differently in Python 2 than in Python 3. Specifically, dividing two integers in Python 3 produces a floating-point result but in Python 2 it produces a rounded-down integer result. So this expression:

(len(message) / key)

produces 3.75 in Python 3 but produces 3 in Python 2, and therefore this expression:

math.ceil(len(message) / key)

produces 4 (3.75 rounded up is 4) in Python 3 but produces 3 (3 rounded up is 3) in Python 2. This means that your numOfColumns is incorrect and therefore the decryption procedure produces an incorrect result.

You can fix this specific issue by changing (len(message) / key) to (float(len(message)) / key) to force Python 2 to treat that calculation as a floating-point division that will give the desired 3.75 result. But the real solution is to switch to using Python 3, because these differences in behaviour between Python 3 and Python 2 are just going to keep causing trouble as you proceed through the rest of the book.