build-upload

name	build-upload
description	Use this skill when ready to compile a manuscript for journal submission, rebuilding after edits, or preparing a revision package. Triggers on "build upload package", "compile manuscript", "generate submission files", "rebuild manuscript", "prepare revision".

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
                            (quartopress.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()

    # 0. Sync templates → rendered sections (parameterized numbers)
    sync_sections()       # Replaces <<VAR>> placeholders with Stats values

    # 1. Validate prose (arithmetic + semantic consistency)
    validate_prose()      # Catches stale numbers, plural mismatches, etc.

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

    # 3. Build tables (quartopress.table_builder)
    build_all_tables()    # Each table from CSV/data -> .docx with three-line borders

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

    # 5. Response to editor/reviewers
    build_response()      # Markdown -> .docx

Steps 0-1 are critical. Never render the manuscript without syncing templates first — this ensures all numbers in prose match the current data. See the parameterized-manuscript skill for the full pattern.

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.

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 /fix-ai-tells)

Quick Commands

# Full rebuild
uv run python scripts/build_upload.py

# Tables only
uv run python scripts/build_tables.py