ReScience

[agitter]

The ReScience journal could be a potential use case for manubot-rootstock. From https://arxiv.org/abs/1707.04393:

The main inconvenience of the GitHub platform is its almost complete lack of support for the publishing steps, once a submission has successfully passed the reviewing process. At this point, the submission consists of an article text in Markdown format plus a set of code and data files in a git repository. The desired archival form is an article in PDF format plus a permanent archive of the submitted code and data, with a Digital Object Identifier (DOI) providing a permanent reference. The Zenodo platform allows straightforward archiving of snapshots of a repository hosted on GitHub, and issues a DOI for the archive. This leaves the task of producing a PDF version of the article, which is currently handled by the managing editor of the submission, in order to ease the technical burden on our authors

[vsmalladi]

Looks like an excellent use case.

[dhimmel]

@rougier (lead contributor of ReScience/ReScience): check out the manubot project. It's a method for manuscript publishing via GitHub using continuous integration. You can see it in action at https://greenelab.github.io/scihub-manuscript/ and https://greenelab.github.io/deep-review/.

While the project is still under heavy development, you may be interested in using it in the future for ReScience. If so, your contribution helping build this system would be much appreciated!

[rougier]

That's fantastic ! This is precisely the kind of automation we were looking for. Currently, we (manually) produce a PDF via pandoc but we were also interested in producing the HTML (and xml as well if possible). Do you have some documentation on your project ? (I did not yet dig into it).

[dhimmel]

Do you have some documentation on your project ? (I did not yet dig into it).

The documentation is not great right now (work in progress), but is spread between:

• https://github.com/greenelab/manubot-rootstock/tree/master/references
• https://github.com/greenelab/manubot-rootstock/blob/master/CONTRIBUTING.md#markdown
• actual content markdown files like https://github.com/greenelab/manubot-rootstock/blob/master/content/03.figures.md

[agitter]

@rougier We used an early version of this build system for a review article, and the methods section there also provides a nice introduction to this project.