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Scholarly citation, archival DOI, preprint and software-paper workflow

Document status: verified. Canonical source.

Summary

CITATION.cff provides machine-readable software and preferred-publication metadata on GitHub. Zenodo can archive public GitHub releases and assign a DOI to each release. Quarto renders one manuscript source to citeable HTML and PDF. arXiv accepts topical, refereeable scientific contributions. The Journal of Open Source Software (JOSS) reviews research software only after demonstrated research use, sustained public development and feature completeness.

Evidence

  • GitHub parses CITATION.cff from the repository root and exposes APA and BibTeX citations. A preferred-citation can identify a paper or technical report instead of the software. Locator: About CITATION files, lines 24–70, retrieved 2026-08-30.
  • Zenodo archives a public repository and issues a DOI for each GitHub release. Locator: GitHub, Referencing and citing content, lines 21–35, retrieved 2026-08-30: https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content.
  • Quarto can generate citation metadata and citeable HTML from article frontmatter. Locator: Quarto, Creating Citeable Articles, retrieved 2026-08-30: https://quarto.org/docs/authoring/create-citeable-articles.html.
  • arXiv submissions must be topical and refereeable; new authors or categories may require endorsement. Locator: arXiv, Submission Guidelines, lines 177–186, retrieved 2026-08-30: https://info.arxiv.org/help/submit/index.html.
  • JOSS requires more than six months of active public history, demonstrated research impact, open-source practice, iterative development and feature-complete software. It also requires disclosure of generative-model assistance. Locator: JOSS, Submitting a paper, “Scope and significance” and “Pre-review screening criteria”, retrieved 2026-08-30: https://joss.readthedocs.io/en/latest/submitting.html.

Mechanism

The repository retains one Quarto manuscript and one bibliography. GitHub Actions renders HTML and PDF without committing either output. CITATION.cff identifies the software until a reviewed paper supplies the preferred citation. Zenodo stores immutable release snapshots. arXiv and peer-review venues receive the manuscript only after their respective evidence gates are met.

NUIF relevance

Borrow CFF and Zenodo for immediate citation and archival identity.

Adapt the paper claim to the bounded profile-zero experiment. The first manuscript reports the model, executable evidence and limitations; it does not claim universal format coverage or standards status.

Reject treating a Pages site, DOI, preprint or software-paper acceptance as equivalent to standards publication.

Open questions

  • Authors, order, affiliations and ORCID identifiers require human confirmation before archival deposit or manuscript submission.
  • The peer-review venue depends on whether the eventual contribution is an HCI study, a software artifact or an interoperability specification.