> cmd1 = [r'sphinx-apidoc',
> r'-f -F',
This part looks suspicious. Are you sure you don't mean:
'-f', '-F'
here? They need to be separate arguments.
Also, you mention:
> Btw, shell=True is needed here.
Why do you need shell expansion on the arguments? This can be
dangerous unless you know what you're doing. See all the
red-backgrounded warnings the subprocess documentation. For example:
http://docs.python.org/2/library/subprocess.html#frequently-used-arguments
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