The following two reproducible papers (in astronomy) were recently published:
They both follow the “reproducible paper template”: http://akhlaghi.org/pdf/reproducible-paper.pdf . The full source of the project is uploaded to arXiv with the paper’s LaTeX source and is also version controlled in Git and software tarballs are backed up in Zenodo.
You can see the Git commit checksum of the version that was published at the end of their abstracts. The full list of used/built software and (their citations, when they have one) are also published in the last page of the paper’s PDF (to see the PDF, click on the “PDF” link on the top-right side of the page).
The project’s source can be run automatically (infrastructure primarily written in Bash and Make), and contains instructions on where to download the data and software tarballs (of pre-defined versions), commands on how to unpack, configure, build and install the software, commands to run the software on the data to do all the analysis and finally, the LaTeX source of the paper that will also be automatically built (the slides above should be a good introduction to the system).
This reproducible paper template is under heavy development, so any feedback would be very welcome.