How may I override the compiler (GCC) flags that setup.py uses by default?

Prepend CFLAGS="-O0" before you run setup.py:

% CFLAGS="-O0" python ./setup.py

The -O0 will be appended to CFLAGS while compiling, therefore will override previous -O2 setting.

Another way is add -O0 to extra_compile_args in setup.py:

moduleA = Extension('moduleA', .....,
        include_dirs = ['/usr/include', '/usr/local/include'], 
        extra_compile_args = ["-O0"], 
        )

If you want to remove all default flags, use:

% OPT="" python ./setup.py