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Submission Prep

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submission-prep

Submission Prep is an Agent Skill for documents published in the brycewang-stanford/Auto-Empirical-Research-Skills repository on GitHub: a SKILL.md instruction file an AI agent can load to do this task.

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

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How to use this skill

Bring this guide into your coding agent with a prompt tailored to the tool you use.

  1. Open your project in Codex.
  2. Copy and paste the prompt below.
  3. Review files and risks before approving any action.
Prompt to paste
Inspect the Agent Skill at https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/blob/HEAD/skills/29-quarcs-lab-project20XXy/dot-claude/skills/submission-prep/SKILL.md and all supporting files. Report provenance, permissions, scripts, dependencies, and security risks. Propose an exact installation into .agents/skills/submission-prep, but wait for my approval before writing files or running scripts.

Copying this prompt does not install or run the skill. Review third-party files before use.

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.