Beta release, docs, and an API

Moving from the alpha to the beta version with an API design. The alpha releases were focused on defining the functionality of the CLI. In the beta version, the CLI remains unchanged; however, a full internal design has been applied to create a coherent API. The controller, optimizers, and maker modules have been fully replaced by run, api, and filters. See the new full API documentation for details on using these modules outside of the CLI. Additionally, pytest has been removed from the install requirements since it is an assumption of the default test runner but not an API requirement.