Archive releases on Zenodo and update citation instructions

[namurphy]

An emerging best practice is to openly archive scientific software on the Zenodo online repository, or another online repository that can provide a particular version of a code with a persistent identifier such as a DOI. If you were to create a community on Zenodo for the Dedalus Project, this could also be a place where people applying Dedalus would be able to upload their scripts (which in turn would give prospective new users access to sample problems that they could expand and/or modify) and their simulation results (which would help with reproducibility).

Another possibility would be the Journal of Open Source Software which would be an opportunity for the code itself to undergo peer review. Going this route would let authors cite the source code in exactly the same way as a journal article.

After doing this, I'd also suggest updating the citation instructions to request that authors cite both the Dedalus paper and the specific version of Dedalus that was used for the project they are publishing using the DOI from the Zenodo record. The article by Bouquin et al. 2020 goes into a lot more detail about why do do this, and there's also a video that goes over this article.

[jsoishi]

Hi Nick,

Thanks for this. We have been thinking about creating a hub for dedalus-related content from our userbase, and the Zenodo communties seem like a really good option for that. Do you know of any simulation code examples of that? My quick perusal turned up datasets, but no scripts or other simulation input type communities.

[namurphy]

I don't know of any simulation codes that make extensive use of the community feature on Zenodo, but here are a few peripheral examples that might give a better idea of what a Zenodo community for Dedalus could include, both as records and as metadata for the community itself.

• Astropy community
• PlasmaPy community
• Gkeyll community

[kburns]

With the release of v3.0.0, I've setup a zenodo record for the code here: http://doi.org/10.5281/zenodo.10445656

[afraser3]

FYI Keaton: looks like there's an incomplete section on the zenodo page, see screenshot below. Doesn't look like a big deal, just thought I'd notify you in case you're worried about it.

Might be worth listing this on the "citations" page on the dedalus webpage.

[kburns]

Thanks, we also have a zenodo community here: https://zenodo.org/communities/dedalus