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I found it hard to make scons build outside my source directory (instead of polluting it). This is important for example when you don't want random files showing up in your git clone.

With waf, this is easy.

Subjectively, waf code looks more Pythonic than scons, though both are supposedly Python.

Waf is also much nicer for end-users, if you're the sort who distributes source packages. It mimics the "./configure; make; make install" sequence as "./waf configure; ./waf; ./waf install".

I haven't used Waf either, but some information is here:

www.scons.org/wiki/SconsVsOtherBuildTools