submission-prep

Documents

Runs pre-submission checks (word count, anonymization, citations, placeholders, cross-refs) and generates a checklist. Use before journal submission.

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Prompt to paste

I want to install this Agent Skill for this project in Codex.

Source SKILL.md: https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/blob/HEAD/skills/29-quarcs-lab-project20XXy/dot-claude/skills/submission-prep/SKILL.md

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Prepare for Submission

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

Steps

Render the manuscript if _manuscript/ does not exist or is stale:
```
bash scripts/render.sh
```
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)
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
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)
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)
Placeholder check — Scan for orphan [FILL:] placeholders in index.qmd:
```
grep -n "\[FILL:" index.qmd
```
Report each with line number and context.
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).

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)

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