In recent years there has been a great interest in topological materials and in their intriguing properties. Here, we present a first principles method to compute topological invariants of three-dimensional gapless phases. Our approach allows to calculate the topological charges of Weyl points through the efficient numerical computation of gap Chern numbers, which relies solely on the photonic Green's function of the system. Typically, the topological numbers of a material system are written in terms of the Bloch eigenmodes, and their calculation can be a rather challenging computational problem. We particularize the framework to the Weyl points that are found to emerge in a magnetized plasma due to the breaking of time reversal symmetry. We discuss the relevance of modelling nonlocality when considering the topological properties of continuous media such as the magnetized plasma. Our theory may be extended to other three-dimensional topological phases, or to Floquet systems.