manuscript-setup

name	manuscript-setup
description	Use this skill when starting a new manuscript project, adding quartopress build pipeline to an existing project, converting a draft into a structured Quarto project, or setting up table/figure generation. Triggers on "scaffold manuscript", "set up manuscript", "new manuscript project", "quartopress init", "create manuscript structure".

Manuscript Setup

Scaffold a new or augment an existing Quarto-based manuscript project for journal submission using the quartopress pipeline.

When to Use

Use this skill when:

• Starting a new manuscript project from scratch
• Adding quartopress build pipeline to an existing project
• Converting an existing draft into a structured Quarto project
• Setting up table/figure generation in a project that already has .qmd files

Prerequisites

Install quartopress: uv pip install quartopress

New vs. Existing Projects

New project: quartopress-init ./my-manuscript --title "My Study" Creates the full directory structure, all section templates, build scripts, and bibliography files.

Existing project: quartopress-init . Detects what's already present (.qmd sections, .bib files, build scripts, table builder) and adds only what's missing. Never overwrites existing files unless --force is used.

Project Structure

The scaffold creates:

manuscript-project/
├── manuscript/
│   ├── manuscript.qmd              # Master Quarto file (includes all sections)
│   ├── _sections/
│   │   ├── _title_page.qmd         # Title, authors, affiliations
│   │   ├── _abstract.qmd           # Structured abstract
│   │   ├── _introduction.qmd       # Background, gap, objectives
│   │   ├── _methods.qmd            # Study design, measures, analysis
│   │   ├── _results.qmd            # Primary and secondary outcomes
│   │   └── _discussion.qmd         # Interpretation, limitations, conclusions
│   ├── _templates/
│   │   └── journal-reference.docx  # Journal Word template (controls formatting)
│   ├── references.bib              # BibTeX bibliography
│   └── citation-style.csl          # Citation style (AMA, Vancouver, etc.)
├── data/
│   ├── tables/                     # CSV source files for tables
│   └── figures/                    # Data files for figure generation
├── scripts/
│   ├── build_tables.py             # Declarative table definitions
│   └── build_upload.py             # Master build script
├── output/                         # Generated submission files
└── review/                         # Reviewer feedback and responses

Setup Steps

1. Run quartopress-init with appropriate flags
2. Configure the master Quarto file (reference-doc, bibliography, csl)
3. Create section files from templates
4. Set up the build pipeline (table definitions, figure copy paths, cross-reference map)
5. Configure for target journal using /set-journal

Journal Configurations

Journal	Word Limit	Abstract	Figures	Tables	Reference Style
PRS	3,000 (+500 ext)	250, structured	300 DPI TIFF	Separate .docx	AMA
JPRAS	4,000	250, unstructured	300 DPI TIFF/EPS	Embedded	Vancouver
Ann Plast Surg	3,000	200, unstructured	300 DPI TIFF	Embedded	AMA

Key Principles

1. Sections as separate files — enables parallel editing and targeted AI review
2. Tables from data — CSV is the source of truth; .docx is generated output
3. Figures from code — data-driven, reproducible, never hardcoded
4. One build command — uv run python scripts/build_upload.py generates everything
5. Cross-references resolved at build time — Quarto handles citations; build script handles table/figure numbering