Excitation energy transfer is a ubiquitous process of fundamental importance for understanding natural phenomena, such as photosynthesis, as well as advancing technologies ranging from photovoltaics to development of photosensitizers and fluorescent labels. This work provides an overview of recent advancements in excitation energy transfer modeling with the PyFREC software package. Computational methods currently implemented in PyFREC include molecular fragmentation techniques, as well as methods for electronic coupling computations, analysis of coupled electronic excited states, and quantum dynamics simulations. Advanced functionality and possible vectors for future development of the package are also explored.