Thermal dominated X-ray spectra of neutron stars in quiescent transient X-ray binaries and neutron stars that undergo thermonuclear bursts are sensitive to mass and radius. The mass-radius relation of neutron stars depends on the equation of state that governs their interior. Constraining this relation accurately is thus of fundamental importance to understand the nature of dense matter. In this context we introduce a pipeline to calculate realistic model spectra of rotating neutron stars with hydrogen and helium atmospheres. An arbitrarily fast rotating neutron star with a given equation of state generates the spacetime in which the atmosphere emits radiation. We use the Lorene/nrotstar code to compute the spacetime numerically and the ATM24 code to solve the radiative transfer equations self-consistently. Emerging specific intensity spectra are then ray-traced through the neutron stars spacetime from the atmosphere to a distant observer with the Gyoto code. Here, we present and test our fully relativistic numerical pipeline. To discuss and illustrate the importance of realistic atmosphere models we compare our model spectra to simpler models like the commonly used isotropic color-corrected blackbody emission. We highlight the importance of considering realistic model-atmosphere spectra together with relativistic ray tracing to obtain accurate predictions. We also insist on the crucial impact of the stars rotation on the observables. Finally, we close a controversy that has been appearing in the literature in the recent years regarding the validity of the ATM24 code.