In Autumn 2021 we have started to work on making our lessons and other material we have created over the years, citable. At the same time we wish to assign a digital object identifier (DOI) to each lesson so that the material becomes persistent and remains findable. However, the main motivation for this work is to get some metrics about the use of our material and also to give contributors better credit and to make it possible for them to get and display metrics about their contributions.
This effort is work in progress and in this document we will summarize our discussions, decisions, findings, and observations so that we can then use these later when we conclude this effort lesson by lesson.
- We will use Zenodo because it is a well-established service which we know and which integrates nicely with the repositories hosting the lessons and because we will need to be able to update metadata (author information) without changing the DOI record.
- We will convert the 3 remaining Jekyll lessons to Sphinx to simplify pdf export.
- We will not start with https://allcontributors.org/ because it requires each contributor to have a GitHub account which we have found a too strict limitation.
- We start with tracking authorship in CITATION.cff since GitHub presents a "cite as" button when this file is present.
- If we find that CITATION.cff is not enough or does not provide the right categories, we will try to track this in the .zenodo.json which Zenodo understands and we could generate CITATION.cff from this file. It seems that if a .zenodo.json is present in a repo, it has on Zenodo precedence over a CITATION.cff.
Distinguishing authors and contributors
- Removed "code" (lesson material) does not mean removing authorship unless the author prefers to be removed.
- Example for how Carpentries do it (unix shell lesson):
- Definitions of the roles:
- "creator": significant contributions
- "contributor"/Editor: reviewing/approving contributions
- "contributor"/Other: smaller contributions
- On Zenodo we start with "creator" (author) and "contributor" (other).
- See also categories that Zenodo understands: https://developers.zenodo.org/#representation (search for "creators" and "contributors")
- We are a bit unsure whether one person can assume more than one role on Zenodo. probably yes. If so, maybe one occurence for the highest contribution is best.
- We still need to verify whether CITATION.cff and/or .zenodo.json can map to the definitions of roles (above).
How we will reach out to creators and contributors
- We will do this on a per-lesson basis and we will start with the lessons which we teach the most often.
- Contributors are not only people who have contributed with Git commits, but could also be people that contributed with input and ideas in other form.
- We reach out to everybody and ask whether they want to be contributor or author.
- If a person cannot be reached, we do not add the person without consent and rather add the person later once we reach them.
- Reaching out to creators and contributors will happen via GitHub issues close to the lesson repository but those who do not respond or may not be on GitHub will be reached via email.
- On the GitHub issue we will ask authors for their ORCID.
Archiving lessons as pdf
- When archiving lessons on Zenodo we have the choice of archiving the repository as is (the sources) or to generate a pdf version of the lesson and archiving the pdf.
- We have concluded that we wish to attempt depositing pdf versions unless this turns out too difficult.
- The pdf versions will be generated automatically as part of a "release" workflow.
- The automatic pdf generation is relatively straightforward with Sphinx lessons but less trivial with Jekyll-based lessons.
- We will focus on Sphinx lessons and prefer converting Jekyll-based lessons to Sphinx lessons rather than investing time in generating pdfs from Jekyll lessons.
- But we have also concluded that cite-ability is more important than preserving a pdf version of the lessons since we expect the lessons to evolve and be continuously improved and the credit aspect is found more important than the preservation aspect.
ORCID vs. Zenodo community
- We have decided against introducing a project ORCID for CodeRefinery and rather collect related records in a CodeRefinery Zenodo community.
How we wish to test the workflow
- For one or two example lessons we will create a fork and test the release deployment and DOI generation on Zenodo sandbox.
Suggested workflow to make lessons citable via Zenodo
- Add a .zenodo.json to the lesson repo, for example:
"affiliation": "Feline research institute",
"name": "Field, Gar"
"affiliation": "Feline research institute",
"name": "Cat, Felix"
- Generate pdfs from Sphinx sources via LaTeX:
latex_engine = 'xelatex'(makes emojis work), then
make clean ; make latexpdf.
- This will become part of GitHub Actions, it will not be a manual step.
- Create a release of the lesson on GitHub.
- On Zenodo, check syncing with GitHub.
- About Zenodo https://about.zenodo.org/
- Zenodo policies https://about.zenodo.org/policies/
- Zenodo FAQ https://help.zenodo.org/
- Zenodo REST API https://developers.zenodo.org/
- Zenodo .zenodo.json and GitHub https://developers.zenodo.org/#github
- GitHub-Zenodo tutorial https://guides.github.com/activities/citable-code/
- The https://allcontributors.org/ specification and GitHub bot
- The CITATION.cff format https://citation-file-format.github.io/
- The CITATION.cff format keywords https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md
- SPDX ID short-form identifiers for FOSS license information https://spdx.dev/ids/