Literate Program Execution for Reproducible Research and Executable Papers

Lepton is an automaton for literate executable papers. It enables researchers to publish their work in the form of a script or program that can generate the research paper along with the corresponding source code, input data and output results. Lepton files do not contain pre-computed results, but the full set of instructions for reproducing the results presented in the manuscript. Taking inspiration from literate programming for code review and code re-use, we have written Lepton to facilitate the review and re-use of computational methods. Lepton is designed to provide strong guarantees for the reproducibil-ity of the results, many features for easily applying the methods to new data while remaining unobtrusive and easy to deploy in any environment. Lepton is designed for writing reproducible technical reports during method development, and journal manuscripts when the research is polished. Developped independently from the Elsevier Executable Paper Grand Challenge, it addresses similar issues and objectives. This manuscript was written with Lepton.