Build Upload Package

Build Upload Package

Generate a complete journal upload package from Quarto manuscript sources and data files.

When to Use

Use this skill when:

• Ready to compile the manuscript for submission
• Rebuilding after edits to any section, table data, or figure
• Preparing a revision package with response to reviewers

Build Pipeline

Source Files                    Build Steps                     Output Files
─────────────                   ───────────                     ────────────
_sections/*.qmd    ──┐
references.bib     ──┼──► Quarto render ──────────────────►   Manuscript.docx
citation-style.csl ──┘    (cross-refs + citations resolved)

data/tables/*.csv  ──────► build_tables.py ───────────────►   Table 1-N.docx
                           (prs_table_builder)

data/figures/*     ──────► figure scripts ─────────────────►  Figure 1-N.tiff

legends text       ──────► appended to Manuscript.docx ───►  (in manuscript)

response letter    ──────► python-docx ────────────────────►  Response.docx

Build Script Structure

The master build_upload.py follows this pattern:

def main():
    setup_output_dir()

    # 1. Render manuscript (Quarto)
    build_manuscript()    # Assembles sections, replaces cross-refs, renders .docx

    # 2. Build tables (prs_table_builder)
    build_all_tables()    # Each table from CSV/data → .docx with three-line borders

    # 3. Copy figures
    copy_figures()        # TIFF files to output with submission naming

    # 4. Response to editor/reviewers
    build_response()      # Markdown → .docx

Cross-Reference Handling

Since tables and figures are separate files (not embedded), Quarto cross-references (@tbl-, @fig-) won't resolve. The build script handles this:

_CROSS_REF_MAP = {
    "@tbl-characteristics": "Table 1",
    "@tbl-specs": "Table 2",
    "@fig-workflow": "Figure 1",
    "@fig-metrics": "Figure 2",
}

Numbering rule: Tables and figures are numbered in order of first reference in manuscript text.

Figure Legends and SDC Legends

Appended to the manuscript after References as plain text:

# FIGURE LEGENDS

**Figure 1.** Description of figure 1.

**Figure 2.** Description of figure 2.

# SUPPLEMENTAL DIGITAL CONTENT LEGENDS

**Supplementary Table S1.** Description of SDC item.

Validation Checklist

After building, verify:

• Word count on title page matches actual body text count
• Abstract word count accurate and under limit
• All tables present and numbered correctly
• All figures present as TIFF files
• Figure/table references in text match file numbering
• Legends present after references
• No stale cross-references (?@tbl-, ?@fig-)
• No AI writing tells (run ai-tell-fixer agent)

Quick Commands

# Full rebuild
uv run python scripts/build_upload.py

# Tables only
uv run python scripts/build_tables.py

# Word count check
cat manuscript/_sections/_introduction.qmd _methods.qmd _results.qmd _discussion.qmd | \
  sed '/^<!--/d' | sed 's/\[@[^]]*\]//g' | wc -w