Hi, 

We have currently

sage: x, y = var('x y')
sage: fyx = function('f')(y, x)
sage: fyx.arguments()
(x, y)

which is just the reverse of the expected output. 

Similarly, we have

sage: atan2(y,x).arguments()
(x, y)

Taking a look at the code, one sees that fyx.arguments() calls 
fyx.variables(), which returns a "sorted tuple of variables that occur in 
this expression" (according to the documentation). The "sorted" action 
explains the result. But the latter remains plain false. 

Note that SymPy provides the correct result:

sage: fyx._sympy_().args
(y, x)
sage: atan2(y,x)._sympy_().args
(y, x)

Eric.

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