The Lepton project
Introduction
What is Lepton ?
Lepton is a tool for the literate execution of programs that I have developped for reproducible research, software engineering and teaching computational science. As in literate programming, source code and documentation can be encapsulated in the same file. In addition, Lepton files can contain executable instructions.
Why use Lepton ?
Lepton is intended for producing documents / technical reports that are self-contained:
- source code is embedded inside the document, not in external files,
- figures and graphics are generated by scripts that are embedded inside the document, rather than external scripts,
- rather than copy-and-paste results, the output of executable instructions is automatically inserted in the document,
- even input data can be embedded inside a document,
- these elements can be divided into meaningful entities, re-used in several places, and documented by the author.
This has several consequences:
- when generating scientific results, all the relevant information is available: source code, instructions, parameters, and the documentation for the methods
- when programming, a single instruction compiles the project, runs the test cases, inserts the figures, and produces an execution report,
- when teaching, randomized exercises can be written, with full solutions, and mass-produced,
- the document is executable for easy reproduction and sharing with co-workers
News
- [2012-04-05] Lepton at a workshop on Reproducible Research in Orléans. http://www.fdpoisson.fr/cascimodot/RRRR.php
- [2012-06-04] I will talk about Lepton at ICCS 2012 http://www.iccs-meeting.org/
- [2012-06-25] This page has been split into several pages (see links on the left menu). A new example with minimal LaTeX requirements is available for download below.
- [2012-10-09] Lepton at the Image Analysis Seminar (University Paris 13)
- [2012-12-10] Lepton at the ICERM Workshop "Reproducibility in Computational and Experimental Mathematics" http://icerm.brown.edu/tw12-5-rcem
- [2013-05-26] Proposed mini-symposium on Reproducible Research at the SMAI2013 Congress, currently under review http://smai.emath.fr/smai2013/
Downloads
Support for other platforms is work in progress
A MD5 hash is used to verify the integrity of the downloaded file.
The LaTeX style file is available here : lepton.sty
Applications
N.B. Some of the applications below were written in Sweave when only the R language is used.
Small examples
Reproducible research and papers published using Lepton
- S. Li-Thiao-Té, J.J. Daudin and S. Robin. Bayesian model averaging for estimating the number of classes. Applications to the total number of species in metagenomics. To appear in Journal of Applied Statistics
- S. Li-Thiao-Té, Literate Program Execution for Reproducible Research and Executable Papers, Proceedings of the International Conference on Computational Science, ICCS 2012, http://dx.doi.org/10.1016/j.procs.2012.04.047
- S. Li-Thiao-Té, Literate Program Execution for Teaching Computational Science, Proceedings of the International Conference on Computational Science, ICCS 2012, http://dx.doi.org/10.1016/j.procs.2012.04.190
Literate programming
- Image analysis methods: belief propagation, detection of significant orientations
Report generation
- Comparing the cost of printing solutions.
- Analysing the answers from a survey.
Teaching
- Introduction to statistics (in French Beamer slides Δ, source file Δ)
- Lecture notes
- Random exercises with solutions
- Random exams with solutions
- Statistical tables (PDF Δ, source file Δ). With random exams, we can generate a specific statistical table for each subject.
Miscellaneous
- Code for publishing this website (Wiki system on local web server + static export + additional files)
- Code certification
