Most likely via chemical spectra; determining the chemicals in the atmosphere and finding ones that have chemical signatures that run counter to a natural process.
An atmosphere with oxygen and methane at habitable zone temperatures means something has to be replenishing those gasses otherwise the oxygen would react with the methane (or almost anything else, oxygen is super reactive).
Or directly imaging the planet and finding the planet (or parts of the planet if we ever get that kind of detail) the exact colour optimal for photosynthesis on that planet (combination of star and atmosphere etc).
Or I guess a surface feature clearly artificial, Alistair Reynolds did that in one of his series, a clearly artificial feature was carved into the face of a planet to get the attention of anyone looking.
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Uncertainty is an uncomfortable position.
But certainty is an absurd one.
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