Malformed Zenodo metadata?

[florisvdh]

Just from observation at Zenodo: it seems that the description is overwritten in a new version, possibly by the content of a commit message. Also the title seems to have changed.

• old version: https://zenodo.org/record/5814814

• new version: https://zenodo.org/record/6533084

[ThierryO]

That repo doesn't have a .zenodo.json yet. I'm planning to write one based on the information in the README.md in case of a project (not a package).

• badges are optional
• version number is optional
• language information taken from default spell check language set in checklist.yml
• CC-BY license (license must be set).

How should we handle the upload type? Here are a few options. Create an test upload at https://sandbox.zenodo.org to see all the options.

• software
• publication / software documentation
• publication / other
• other

Source code of the template

<!-- badges: start -->
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5814813.svg)](https://doi.org/10.5281/zenodo.5814813)
![GitHub](https://img.shields.io/github/license/inbo/patrijs-steekproefkader)
![GitHub release (latest by date)](https://img.shields.io/github/v/release/inbo/patrijs-steekproefkader)
![GitHub Release Date](https://img.shields.io/github/release-date/inbo/patrijs-steekproefkader)
![GitHub Workflow Status](https://img.shields.io/github/workflow/status/inbo/patrijs-steekproefkader/check-source)
![GitHub repo size](https://img.shields.io/github/repo-size/inbo/patrijs-steekproefkader)
<!-- badges: end -->

# Replace this with the title

[Thierry Onkelinx![ORCID logo](https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png)](https://orcid.org/0000-0002-1825-0097)[^INBO][^contact],
[Raïsa Carmen![ORCID logo](https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png)](https://orcid.org/0000-0003-1025-8702)[^INBO],
Thomas Scheppers,
Michiel Stas[^ANB]

[^INBO]: Research Institute for Nature and Forest (INBO)
[^ANB]: Agentschap Natuur en Bos
[^contact]: contactperson

<!-- copyrightholder: Research Institute for Nature and Forest -->
<!-- version: 2023.01 -->
<!-- community: inbo -->
<!-- community: second -->
<!-- abstract: start -->
Place here the abstract. It will be included in the citation metadata.
<!-- abstract: end -->

You can add more information. This will not show in the citation metadata.

Rendered version of the template

---

Replace this with the title

Thierry Onkelinx^INBO, Raïsa Carmen[^INBO], Thomas Scheppers, Michiel Stas[^ANB]

[^INBO]: Research Institute for Nature and Forest (INBO) [^ANB]: Agentschap Natuur en Bos

Place here the abstract. It will be included in the citation metadata.

You can add more information. This will not show in the citation metadata.

[ThierryO]

@inbo/bmk and @inbo/oscibio: can you give me some feedback on this. The main idea is to add a function to writes a .zenodo.json based on the information in the README.md in case of an R project. While parsing the README.md, we can validate the metadata at the same time. The benefits of this:

• more complete and standardised INBO README's.
• all mandatory metadata for Zenodo is present. Making it easy to release new versions to Zenodo. E.g. by adding the repo to zenodo and automatically creating a release when pushing to the main branch. Which triggers a new version in Zenodo.
• generating a CITATION.cff too provides citation information on GitHub. Have a look at the main page of this repository. On the right you'll see "cite this repository".

The example below makes the copyright holder more visible compared to the example above.

---

Replace this with the title

Thierry Onkelinx[^cp][^INBO], Raïsa Carmen[^INBO], Thomas Scheppers, Michiel Stas[^ANB] Research Institute for Nature and Forest[^ch]

[^INBO]: Research Institute for Nature and Forest (INBO) [^ANB]: Agentschap Natuur en Bos [^cp]: contact person [^ch]: copyright holder

Place here the abstract. It will be included in the citation metadata.

You can add more information. This will not show in the citation metadata.

[peterdesmet]

@ThierryO looks cool. Can you clarify what files the function will read and what files the function will (over)write?

If the README is being overwritten, I would follow the output of usethis::use_readme_rmd() as much as possible. E.g. list the badges below the title.

[ThierryO]

@ThierryO looks cool. Can you clarify what files the function will read and what files the function will (over)write?

• The function reads README.md in case of an R project and DESCRIPTION in case of an R package.
• The function overwrites .zenodo.json and CITATION.cff
• The function errors in case mandatory information is missing or malformated.

Should be enforce the same rules on README.md in both projects and packages? The latter would imply that the metadata in README.md matches with DESCRIPTION.

[peterdesmet]

Thanks! No, I would not enforce README.md and DESCRIPTION to match, so the formatting rules would only be there for projects. But I would try to have those formatting rules play nice with output of usethis::use_readme_md()

Other notes:

1. I would opt to have:

[author](orcid_url)[^affiliation]
author[^affiliation]
author

And not try to add ORCID logos.

2. I would opt for <!-- description --> rather than abstract, since that is the term used in Zenodo.

[ThierryO]

We recommend to use checklist::create_project() and checklist::create_package(). Those functions will create an RStudio project with templates. The user chooses interactively which items to add (and check) in case of a project. In case of a package we activate the entire set of templates and checks. Use the setup_*() variants on existing projects and packages.

[ThierryO]

94 now has a new citation_meta class. Running citation_meta$new() at the project root will first extract the citation meta and then write the citation files.

In case of a project it reads README.md . Have a look at this README.md to see the required format. citation_meta$new() will overwrite .zenodo.json and CITATION.cff.

In case of an R package it reads DESCRIPTION. Unfortunately we can't store keywords nor the Zenodo community information in that file. Currently we store in README.md using the same format as with projects. Another option would be to store that information in checklist.yml. citation_meta$new() will overwrite .zenodo.json, CITATION.cff and inst/CITATION.