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Pytmosph3R computes transmission and emission spectra based on 3D atmospheric simulations, for example, performed with the LMDZ generic global climate model. It produces transmittance maps of the atmospheric limb at all wavelengths that can then be spatially integrated to yield the transmission spectrum. Pytmosph3R can use 3D time-varying atmospheric structures from a GCM as well as simpler, parameterized 1D or 2D structures, and can be used in notebooks or on the command line.