The next generation of spacecraft technology is anticipated to enable novel applications, including onboard processing, machine learning, and decentralized operational scenarios. Although several of these applications have been previously investigated, the real-world operational limitations associated with actual mission scenarios have been only superficially addressed. Here, we present an open-source Python module called PASEOS, capable of modeling operational scenarios involving one or multiple spacecraft. It considers several physical phenomena, including thermal, power, bandwidth, and communications constraints, and the impact of radiation on spacecraft. PASEOS can be run as a high-performance-oriented numerical simulation and/or in a real-time mode on edge hardware. We demonstrate these capabilities in three scenarios: one in real-time simulation on a Unibap iX-10 100 satellite processor, another in a simulation modeling an entire constellation performing tasks over several hours, and one training a machine learning model in a decentralized setting. While we demonstrate tasks in Earth orbit, PASEOS also allows deep space scenarios. Our results show that PASEOS can model the described scenarios efficiently and thus provide insight into operational considerations. We show this by measuring runtime and overhead as well as by investigating the constellation's modeled temperature, battery status, and communication windows. By running PASEOS on an actual satellite processor, we showcase how PASEOS can be directly included in hardware demonstrators for future missions. Overall, we provide the first solution to holistically model the physical constraints spacecraft encounter in space. The PASEOS module is available online with extensive documentation, enabling researchers to incorporate it into their studies quickly.