quartobot 0.2.0

Citation resolution and manuscript-as-software CI for Quarto.

quartobot

Citation resolution and manuscript-as-software CI for Quarto.

uv tool install quartobot

Or from git for the unreleased main:

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

Documentation: quartobot.github.io/quartobot.

What it does

Authors write persistent-identifier cite keys directly in prose:

We follow @doi:10.1371/journal.pcbi.1007128, with the dataset described
in @pmid:31479462 and methods inspired by @arxiv:2104.10729.

A Quarto project.pre-render: hook resolves each key to canonical metadata before pandoc-citeproc runs, writes the result to a references.json you can commit, and the manuscript renders the same way on every machine — no quartobot install needed at render time, no live Crossref / PubMed / arXiv hit per render. CI gets the same behavior the author saw locally, and a network blip mid-render is no longer a build failure.

Around that resolution step, the project ships:

1. The Python CLI — scan, validate, resolve, init, and mcp. resolve is the pre-render hook itself; scan and validate are CI-lint surfaces (cite-key inventory, static _quarto.yml checks); init scaffolds the pattern into an existing project; mcp starts a stdio MCP server so an agent in Claude Desktop, Codex, or Gemini Code Assist can call the same resolver as part of a drafting workflow.

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

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

The book variant (quartobot-book) covers longer works on Quarto's book project type.

Supported cite-key prefixes

@doi:, @pmid:, @arxiv:, @isbn:, @url:, @wikidata:, @pmc:, plus hand-curated keys from a project .bib. Resolution goes through manubot's citekey_to_csl_item — eight years of accumulated source-API quirks behind a single function call. quartobot itself doesn't reimplement resolution; it provides the Quarto integration, CI scaffolding, and the agent-facing MCP surface.

Why this exists

manubot/manubot#332 ("Quarto integration") was opened by Anthony Gitter in April 2022 after a conversation with Sean Davis. Four years on, no PR, no assignee — but Quarto Manuscripts shipped as a first-party project type, and the integration turned out to be small once the resolver question was settled. This repo is the work to close 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

• Documentation site — install, CLI reference, MCP setup, templates, migration guides
• Design
• Citation pipeline — why a pre-render hook, not a pandoc filter
• Prior art
• Contributing
• Code of conduct
• Changelog

License

MIT.

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quartobot is an independent community project. It builds on Quarto but is not affiliated with or endorsed by Posit, PBC, the makers of Quarto.