You will want to include a repetitive square wave and give it at least a few cycles to work with. Also, make it an integer number of cycles as best you can. Otherwise, windowing becomes more of an issue. Also, center it around 0, without a DC offset. And if you want more accurate peaks (ones that better reflect the actual magnitude at each frequency then perhaps use the "flat top" window. It's a little better at that goal. Not much else to add.
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