Python is the py in pywikipedia. It's a programming language that runs on many different platforms, and is at the heart of all the pywikipedia scripts. Python files are immediately obvious by their extension: .py.
Because all pywikipedia scripts are written in Python, the first word you must type in the command line to use a bot is "python". Hence:
python replace.py -fix:spell -start:!
Although it is not at all necessary to know how to program in Python in order to effectively use pywikipedia scripts, it is necessary to understand the basics of using the so-called "python shell"