AbstractDevelopment of models and dedicated numerical methods for dynamics in fractured rocks is an active research field, with research moving towards increasingly advanced process couplings and complex fracture networks. The inclusion of coupled processes in simulation models is challenged by the high aspect ratio of the fractures, the complex geometry of fracture networks, and the crucial impact of processes that completely change characteristics on the fracture-rock interface. This paper provides a general discussion of design principles for introducing fractures in simulators, and defines a framework for integrated modeling, discretization, and computer implementation. The framework is implemented in the open-source simulation software PorePy, which can serve as a flexible prototyping tool for multiphysics problems in fractured rocks. Based on a representation of the fractures and their intersections as lower-dimensional objects, we discuss data structures for mixed-dimensional grids, formulation of multiphysics problems, and discretizations that utilize existing software. We further present a Python implementation of these concepts in the PorePy open-source software tool, which is aimed at coupled simulation of flow and transport in three-dimensional fractured reservoirs as well as deformation of fractures and the reservoir in general. We present validation by benchmarks for flow, poroelasticity, and fracture deformation in porous media. The flexibility of the framework is then illustrated by simulations of non-linearly coupled flow and transport and of injection-driven deformation of fractures. All results can be reproduced by openly available simulation scripts.