quartobot 0.1.0

The manubot manuscript-as-software pattern, on Quarto.

quartobot

The manubot manuscript-as-software pattern, on Quarto.

Status: v0.1 in flight. CLI commands ship; the Quarto extension and the manuscript template ship. An architecture pivot is under discussion in docs/citation-pipeline.md that would collapse the extension into a single pre-render hook calling the CLI directly — read the design doc before non-trivial work, and watch the v0.1 milestone for tagging.

What this is

Manubot has, for eight years, run scholarly manuscripts as a git repository that builds itself on every commit, resolves citations from DOIs and PubMed IDs automatically, hands out an immutable permalink per commit, and collaborates through pull requests. The pattern is published (Himmelstein et al. 2019) and has been used for hundreds of preprints.

Quarto now covers more of scholarly publishing than manubot ever did — manuscripts, books, websites, slides, dashboards, courseware — but the manubot pattern does not yet exist there natively. That's the gap this repo closes.

The shipping surface is a Python CLI and (optionally) a GitHub template:

1. quartobot — a Python CLI. quartobot resolve pre-fetches citations through manubot's resolver library, so CI never sees a Crossref hiccup mid-render. quartobot scan summarizes cite keys grouped by prefix with duplicate detection. quartobot validate is the CI-lint surface (static checks against _quarto.yml). quartobot init scaffolds the pattern into an existing Quarto project. Authors write @doi:10.1371/journal.pcbi.1007128, @pmid:31479462, @arxiv:2104.10729, @isbn:…, or bare DOIs in their prose, and citations resolve.

   uv tool install git+https://github.com/seandavi/quartobot
   

2. quartobot-manuscript — a GitHub template that combines Quarto Manuscripts, the CLI's pre-render hook, and a CI workflow that gives every commit an immutable permalink at /v/<sha>/, embeds that permalink in the rendered HTML, posts PR previews via sticky comment, and deploys HTML + PDF + DOCX to GitHub Pages.

   gh repo create my-paper --template seandavi/quartobot-manuscript
   

Under the current (filter-based) architecture, a Quarto extension quarto-manubot-cite also ships at quarto add seandavi/quartobot. The pivot proposal in docs/citation-pipeline.md collapses that extension into a one-line pre-render hook calling the CLI — the extension shrinks to optional wiring, the CLI becomes the load-bearing surface. PyPI publishing and the standalone template repo are part of the v0.1 tag.

Why this exists

manubot/manubot#332 ("Quarto integration") was opened by Anthony Gitter in April 2022 after a conversation with Sean Davis. Four years later, no PR, no assignee — but pandoc-manubot-cite shipped inside the manubot package and Quarto Manuscripts shipped as a first-party project type. The integration is small once you stop trying to rebuild the resolver. This repo is the work to resolve that issue.

Working example

seandavi/2026-venice-spatial-hackathon-manuscript runs the CI / permalink / banner half of the pattern on a live 25-author preprint from the Bioconductor Spatial Hackathon. That's the working reference the template is being lifted from.

See also

• Design — DESIGN.md
• Prior art — docs/prior-art.md
• Publication plan — docs/publication-plan.md
• Conversation notes — docs/conversation-notes.md
• Contributing — CONTRIBUTING.md
• Code of conduct — CODE_OF_CONDUCT.md

License

MIT.