use the Open Journals GitHub Action to automatically compile your paper each time you update your repository.

[matteodelucchi]

This relates to #33

[j-i-l]

GitHub actions to build the paper mentioned in the joss submission process:

https://github.com/marketplace/actions/open-journals-pdf-generator

[j-i-l]

@matteodelucchi Is it imperative that we use .Rmd and not just common markdown for the paper?

It seems pandoc in the suggested action has some issues with the codeblocks:

https://github.com/furrer-lab/abn/actions/runs/8324704687/artifacts/1334612738

[matteodelucchi]

@matteodelucchi Is it imperative that we use .Rmd and not just common markdown for the paper?

It seems pandoc in the suggested action has some issues with the codeblocks:

https://github.com/furrer-lab/abn/actions/runs/8324704687/artifacts/1334612738

md might cause troubles with pkgdown to build the site. But it is not strictly required to include the paper in the page as seperate article.
I would change it to md format and then potentially make the required changes for pkgdown.

[j-i-l]

There is also a bug in the *.Rmd (and so in the *.md) file:

https://github.com/furrer-lab/abn/actions/runs/8327692324/job/22785964650#step:4:28

should be fixed with 83d3b78

[j-i-l]

paper build is ok.

@matteodelucchi suggestion:
We keep the JOSSpaper branch and do all edits on the paper there, once a first version is ready we squash/merge it into main. In that way we do not clutter up the repo history with edits for the paper.
If we need to do code changes in the context of the paper, we push them to main and merge main into JOSSpaper.

We can already create a draft pull request for JOSSpaper > main, which allows to view and comment in the timeline of the paper.