paper-bundle

Convert manuscripts and grants into validated .paperbundle.zip files for the RM Paper Builder.

Updated Mar 20, 2026
One-click install
npx skills add https://github.com/McGheeLab/McGheeLabWebsite --skill paper-bundle-mcgheelab
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: paper-bundle
Source: https://github.com/McGheeLab/McGheeLabWebsite/tree/main/.claude/skills/paper-bundle
Command: npx skills add https://github.com/McGheeLab/McGheeLabWebsite --skill paper-bundle-mcgheelab

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve? Researchers with manuscripts or grant proposals in Markdown, LaTeX, Word, or PDF formats cannot directly edit them in the McGhee Lab RM Paper Builder; this Skill converts those sources into a portable .paperbundle.zip that imports as a fully editable paper draft. ## Core Features & Use Cases - Multi-format conversion: Reads .md, .tex, .docx, and .pdf sources (via pandoc, pdfimages, or direct reads) and maps content into the paper.json manifest with sections, blocks, figures, tables, and equations. - Citation and asset handling: Builds a references[] array from .bib or inline citations, rewrites numeric [N] markers to citation keys on import, and packages real image/PDF bytes in an assets/ directory indexed by the manifest. - Validation and packaging: Runs scripts/build_bundle.py to catch silent-coercion traps (bad table cells, unknown kinds, missing assets, out-of-range citations) before zipping the bundle. - Use Case: Turn an NSF proposal PDF into a grant paper with biosketch and budget attached as grant_docs, then upload the resulting .paperbundle.zip via the Import paper button on the RM Paper Builder page. ## Quick Start Ask the assistant to turn your manuscript file, such as draft.tex or proposal.pdf, into a .paperbundle.zip for import into the RM Paper Builder.

Frequently Asked Questions about paper-bundle

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I import a manuscript into the RM Paper Builder?

Convert your manuscript into a .paperbundle.zip containing a paper.json manifest and an assets/ directory, then upload it via the Import paper button on the paper-builder page. The importer builds the section tree, uploads images, and imports references automatically.

What source formats can be converted to a paper bundle?

The skill reads Markdown and LaTeX directly, converts .docx via pandoc with media extraction, and reads PDFs with page ranges using pdfimages for figure extraction. You can also describe a paper from scratch and have the tree drafted manually.

How are citations handled in a paper bundle?

Place references in citation order in the references[] array using unified metadata (title, authors, year, DOI), then cite with numeric [N] markers in body text. On import, the engine creates library entries and rewrites [N] markers to [@citekey] automatically.

Why does my figure import blank into the paper builder?

A figure imports blank when its attrs.storage_path has no matching assets[] entry or the image file is missing from the assets/ directory. The build_bundle.py script flags this mismatch before you upload.

Can I import a grant proposal PDF as attached documents?

Yes, for paper_type grant you route pre-made PDFs like biosketches and budgets through grant_docs[] with matching assets[] entries instead of parsing them into sections. The narrative sections such as specific_aims remain normal prose sections.

What are the limitations of the paper bundle format?

Only tree.sections is strictly required, but unknown section or block kinds are silently coerced to custom or paragraph, and malformed table cells are dropped. Images are limited to 15 MB each, and the bundle never writes to Firestore or Storage directly.