Hi guys,

Not really an issue, but a tool that may be worth mentioning here. For a while I've been working on a Python module, called academicmarkdown, with basically the same aim as you guys appear to have. You can find it here:

• https://github.com/smathot/academicmarkdown

Essentially, academicmarkdown is a Markdown pre-processor that adds some functionality necessary for serious academic writing. For example, you can easily include figures and refer to them by ID in the text. It also integrates with Zotero, through pyzotero. Under the hood, it relies mostly on pandoc and wkhtmltopdf.

It works quite well, and I've written two manuscript using it. The PDF export function is nearly perfect, I think, but pandoc's export to other formats is less good. Usable for sharing the manuscript with co-authors, but not submission-ready stuff.

This is an example of a manuscript made with academicmarkdown:

• Mathôt S, Dalmaijer ES, Grainger J, Van der Stigchel S. (2014) The pupillary light response reflects exogenous attention and inhibition of return. PeerJ PrePrints 2:e422v1 http://dx.doi.org/10.7287/peerj.preprints.422v1

I've written it mostly for personal use (the module, not the paper!), and I probably won't have time to turn this into a major project, accepting feature requests, etc. But I'd be more than happy to accept contributions, and maybe it can at least serve as an example of one possible way (of many) to write academic manuscripts in Markdown.

Cheers!
Sebastiaan