Joss: Explain how to preview papers in the JOSS format

[mhucka]

In trying to prepare a paper submission, I got stumped by formatting: the submission guidelines give a sample paper in Markdown format with YAML metadata and Bibtex for bibliography, but there doesn't seem to be an explanation of how an author can generate a preview of the paper in the JOSS format.

Where can I find information about the software pipeline and command arguments to be used?

To be clear, I know multiple ways of generating HTML from Markdown files – I just don't know what JOSS does in particular. I'd like to preview my paper while preparing a submission.

[arfon]

@mhucka - this is the command that we run when processing the submissions. It's also the same command that is run by the @whedon bot in review issues (e.g. https://github.com/openjournals/joss-reviews/issues/501#issuecomment-351157004)

For now there's some documentation available on the Whedon Gem repository which is the best way to replicate the PDF papers. Sorry this isn't easier :-\

[mhucka]

@arfon Thank you very much for that pointer – that was exactly what I needed. This allowed me to create a simple Makefile that encapsulates the process of running pandoc to generate a PDF using the Whedon latex template. I put it in a gist if you would like to see it. The makefile can certainly be improved (e.g., by making it get title and author from the .md file), but perhaps this can be the start of something that can be made available to other people too.

[vsoch]

Hey @cMadan @mhucka I'm following the issue here, as well as a few other boards - apologies for cross posting, I'm not sure if there's a better way!

The reason I'm poking is because I hit this (and similar issues with Docker / building pdfs) myself! So the last few days I am working on a "whedon paper builder" (actual branding TBD after discussion with @arfon) that is going to serve as a tool for a new organization openbases that is going to provide templates intended for open journals submissions. For this particular issue, the whedon docker container that generates papers (still under development, just fyi!) I think could be a strong start! Specifically, it can:

• locally take a paper.md (and other inputs) and generate the paper (here it is) and this table.
• be customized for the metadata, logo, etc.
• be used as a template if you fork the repo! It will generate an updated table of paper manifests on Github pages so you can come back in the future, find old papers.

My next plans are to:

1. Create an equivalent Github repo template with the circle config that does everything except build the whedon container (it will just use it from Docker Hub) so that a user can just fork the repo to preview their paper (as an artifact on Circle or back to Github pages).
2. Create journal specific testing for the paper submission, so you can fail that before getting your pdf and submitting it. That will be provided by this library.

So for example we can have a repo like openbases/submission-joss that will use this container with additional tests for a joss submission, openbases/submission-jose, etc., along with a vanilla openbases/paper-whedon (or something like that, apologies I'm a bit tired!)

There is still a few weeks development before a complete open base template (basically a circle config that will take you from raw stuffs to submission without a huge hassle) but in the meantime I/we would love feedback! The primary question I want to know:

• Does this fit your use case, why or why not?
• Suggestions for features or differences in usability?

Thanks everyone! I'm off to :zzz:

@arfon @FelixHenninger @tylerburleigh @jodeleeuw

[vsoch]

Quick update - @arfon and I chat and the container helper previously (not well chosen) named "whedon" is now builder-whedon! He builds. Here are new links:

• https://github.com/openbases/builder-whedon
• https://openbases.github.io/builder-whedon/

[mhucka]

Thanks for this work and the ping. I haven't had a chance to write a new joss article, but when I do, I'll take a look at this!

[CameronDevine]

I recently wanted to preview a JOSE paper, and ended up writing a bash script to compile both JOSS and JOSE papers. The script is based off of the pandoc options in lib/whedon/processor.rb. This script automatically downloads the LaTeX template, CSL file, and appropriate logo from the wheadon repository then compiles the paper using the included metadata. Other information can be included using command line arguments.

[vsoch]

@CameronDevine did you try the paper builder? --> https://github.com/openbases/builder-pdf