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There are far more simplify methods. expr.simplify? gives a hint:

See also: "simplify_full()", "simplify_trig()", "simplify_rational()", "simplify_rectform()", "simplify_factorial()", "simplify_log()", "simplify_real()", "simplify_hypergeometric()", "canonicalize_radical()"

In this case simplify_trig will do the job.

var('u')
expr = 1-cos(u)^2
expr.simplify_trig()