The rapid development of autonomous vehicles (AVs) holds vast potential for transportation systems through improved safety, efficiency, and access to mobility. However, due to numerous technical, political, and human factors challenges, new methodologies are needed to design vehicles and transportation systems for these positive outcomes. This article tackles important technical challenges arising from the partial adoption of autonomy (hence termed mixed autonomy, to involve both AVs and human-driven vehicles): partial control, partial observation, complex multi-vehicle interactions, and the sheer variety of traffic settings represented by real-world networks. To enable the study of the full diversity of traffic settings, we first propose to decompose traffic control tasks into modules, which may be configured and composed to create new control tasks of interest. These modules include salient aspects of traffic control tasks: networks, actors, control laws, metrics, initialization, and additional dynamics. Second, we study the potential of modelfree deep Reinforcement Learning (RL) methods to address the complexity of traffic dynamics. The resulting modular learning framework is called Flow. Using Flow, we create and study a variety of mixed-autonomy settings, including single-lane, multilane, and intersection traffic. In all cases, the learned control law exceeds human driving performance (measured by systemlevel velocity) by at least 40% with only 5-10% adoption of AVs. In the case of partially-observed single-lane traffic, we show that a low-parameter neural network control law can eliminate commonly observed stop-and-go traffic. In particular, the control laws surpass all known model-based controllers, achieving nearoptimal performance across a wide spectrum of vehicle densities (even with a memoryless control law) and generalizing to out-ofdistribution vehicle densities.