Prepare for Submission

Run pre-submission checks and generate a submission checklist for a journal submission.

Steps

1. Render the manuscript if _manuscript/ does not exist or is stale:

   bash scripts/render.sh
   

2. Word count — Count words in the prose body of index.qmd:

   • Exclude YAML front matter, code blocks, embed shortcodes, and the References section
   • Report: total word count, and breakdown by section
   • Flag if over common limits (8,000 or 10,000 words)

3. Anonymization check — Scan index.qmd for content that may violate double-blind review:

   • Author names (from the YAML author field) appearing in the body text
   • First-person self-citations (e.g., "our previous work", "we showed in Author (Year)")
   • Acknowledgments section content that identifies the authors
   • Repository URLs that reveal author identity
   • Report each finding with line numbers

4. Citation audit — Cross-check citations and references:

   • Extract all @key and [@key] citations from index.qmd
   • Extract all keys from references.bib
   • Report:
     • Citations used in text but missing from .bib (errors)
     • Entries in .bib not cited in the manuscript (unused — informational only)

5. Figures and tables inventory — List all embedded outputs:

   • Extract all {{< embed >}} shortcodes from index.qmd
   • For each, check that the referenced notebook and cell label exist
   • Report a table: label, notebook, caption (from cell directive), type (figure/table)

6. Placeholder check — Scan for orphan [FILL:] placeholders in index.qmd:

   grep -n "\[FILL:" index.qmd
   

   Report each with line number and context.

7. Cross-reference check — Scan for @sec-, @fig-, @tbl- references in index.qmd and verify each target exists (section IDs in the document, figure/table labels in notebooks).

8. Generate submission checklist:

   ## Submission Checklist
   
   - [ ] Word count within journal limit: <count> words
   - [ ] No anonymization issues (or list issues to fix)
   - [ ] All citations resolve to references.bib entries
   - [ ] No orphan [FILL:] placeholders in manuscript
   - [ ] All embedded figures/tables have valid notebook sources
   - [ ] All cross-references resolve
   - [ ] Abstract present and complete
   - [ ] Keywords listed
   - [ ] Acknowledgments section reviewed
   - [ ] Data availability statement included
   - [ ] PDF renders without errors
   - [ ] Figures are high resolution
   - [ ] Supplementary materials prepared (if applicable)
   

9. Report the full checklist with pass/fail status for each automated check, and leave manual items unchecked for the user.