Comment #4 on issue 1840 by [email protected]: atoms is non-greedy
http://code.google.com/p/sympy/issues/detail?id=1840

This now gives:

In [111]: (1+(1+log(x))**2).atoms(Function, Pow)
Out[111]:
   ⎛            2        ⎞
set⎝(log(x) + 1) , log(x)⎠

In [112]: (log(x**2)**2).atoms(Function, Pow)
Out[112]:
   ⎛                2    ⎞
   ⎜ 2     ⎛ 2⎞      ⎛ 2⎞⎟
set⎝x , log⎝x ⎠, log ⎝x ⎠⎠

So I think it was actually fixed.

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