paper-writing

name	paper-writing
description	Workflow 3: Full paper writing pipeline. Orchestrates paper-plan → paper-figure → paper-write → paper-compile → auto-paper-improvement-loop to go from a narrative report to a polished, submission-ready PDF. Use when user says "写论文全流程", "write paper pipeline", "从报告到PDF", "paper writing", or wants the complete paper generation workflow.
argument-hint	["narrative-report-path-or-topic"]
allowed-tools	Bash(*), Read, Write, Edit, Grep, Glob, Agent, Skill, mcp__codex__codex, mcp__codex__codex-reply

Workflow 3: Paper Writing Pipeline

Orchestrate a complete paper writing workflow for: $ARGUMENTS

Overview

This skill chains five sub-skills into a single automated pipeline:

/paper-plan → /paper-figure → /paper-write → /paper-compile → /auto-paper-improvement-loop
  (outline)     (plots)        (LaTeX)        (build PDF)       (review & polish ×2)

Each phase builds on the previous one's output. The final deliverable is a polished, reviewed paper/ directory with LaTeX source and compiled PDF.

In this hybrid pack, the pipeline itself is unchanged, but paper-plan and paper-write use Orchestra-adapted shared references for stronger story framing and prose guidance.

Constants

• VENUE = ICLR — Target venue. Options: ICLR, NeurIPS, ICML. Affects style file, page limit, citation format.
• MAX_IMPROVEMENT_ROUNDS = 2 — Number of review→fix→recompile rounds in the improvement loop.
• REVIEWER_MODEL = gpt-5.4 — Model used via Codex MCP for plan review, figure review, writing review, and improvement loop.
• AUTO_PROCEED = true — Auto-continue between phases. Set false to pause and wait for user approval after each phase.
• HUMAN_CHECKPOINT = false — When true, the improvement loop (Phase 5) pauses after each round's review to let you see the score and provide custom modification instructions. When false (default), the loop runs fully autonomously. Passed through to /auto-paper-improvement-loop.
• ILLUSTRATION = gemini — AI illustration mode: gemini (default, needs GEMINI_API_KEY), mermaid (free, no API key), or false (skip, manual only).

Override inline: /paper-writing "NARRATIVE_REPORT.md" — venue: NeurIPS, illustration: mermaid, human checkpoint: true

Inputs

This pipeline accepts one of:

1. NARRATIVE_REPORT.md (best) — structured research narrative with claims, experiments, results, figures
2. Research direction + experiment results — the skill will help draft the narrative first
3. Existing PAPER_PLAN.md — skip Phase 1, start from Phase 2

The more detailed the input (especially figure descriptions and quantitative results), the better the output.

Pipeline

Phase 1: Paper Plan

Invoke /paper-plan to create the structural outline:

/paper-plan "$ARGUMENTS"

What this does:

• Parse NARRATIVE_REPORT.md for claims, evidence, and figure descriptions
• Build a Claims-Evidence Matrix — every claim maps to evidence, every experiment supports a claim
• Design section structure (5-8 sections depending on paper type)
• Plan figure/table placement with data sources
• Scaffold citation structure
• The external reviewer reviews the plan for completeness

Output: PAPER_PLAN.md with section plan, figure plan, citation scaffolding.

Checkpoint: Present the plan summary to the user.

📐 Paper plan complete:
- Title: [proposed title]
- Sections: [N] ([list])
- Figures: [N] auto-generated + [M] manual
- Target: [VENUE], [PAGE_LIMIT] pages

Shall I proceed with figure generation?

• User approves (or AUTO_PROCEED=true) → proceed to Phase 2.
• User requests changes → adjust plan and re-present.

Phase 2: Figure Generation

Invoke /paper-figure to generate data-driven plots and tables:

/paper-figure "PAPER_PLAN.md"

What this does:

• Read figure plan from PAPER_PLAN.md
• Generate matplotlib/seaborn plots from JSON/CSV data
• Generate LaTeX comparison tables
• Create figures/latex_includes.tex for easy insertion
• The external reviewer reviews figure quality and captions

Output: figures/ directory with PDFs, generation scripts, and LaTeX snippets.

Phase 2b: AI Illustration Generation

Skip this step entirely if illustration is false.

If the paper plan includes architecture diagrams, pipeline figures, or method illustrations:

When illustration: gemini (default) — invoke /paper-illustration:

/paper-illustration "[method description from PAPER_PLAN.md or NARRATIVE_REPORT.md]"

• Claude plans → Gemini optimizes → Nano Banana Pro renders → Claude reviews (score ≥ 9)
• Output: figures/ai_generated/*.png
• Requires GEMINI_API_KEY environment variable

When illustration: mermaid — invoke /mermaid-diagram:

/mermaid-diagram "[method description from PAPER_PLAN.md]"

• Generates Mermaid syntax diagrams (flowchart, sequence, class, etc.)
• Output: figures/*.mmd + figures/*.png
• Free, no API key needed

When illustration: false — skip entirely. Architecture diagrams must be created manually (draw.io, Figma, TikZ).

Checkpoint: List generated vs manual figures.

📊 Figures complete:
- Data plots (auto): [list]
- AI illustrations (auto): [list, if illustration ≠ false]
- Manual (need your input): [list]
- LaTeX snippets: figures/latex_includes.tex

[If manual figures needed]: Please add them to figures/ before I proceed.
[If all auto]: Shall I proceed with LaTeX writing?

Phase 3: LaTeX Writing

Invoke /paper-write to generate section-by-section LaTeX:

/paper-write "PAPER_PLAN.md"

What this does:

• Write each section following the plan, with proper LaTeX formatting
• Insert figure/table references from figures/latex_includes.tex
• Build references.bib from citation scaffolding
• Clean stale files from previous section structures
• Automated bib cleaning (remove uncited entries)
• De-AI polish (remove "delve", "pivotal", "landscape"...)
• The external reviewer reviews each section for quality

Output: paper/ directory with main.tex, sections/*.tex, references.bib, math_commands.tex.

Checkpoint: Report section completion.

✍️ LaTeX writing complete:
- Sections: [N] written ([list])
- Citations: [N] unique keys in references.bib
- Stale files cleaned: [list, if any]

Shall I proceed with compilation?

Phase 4: Compilation

Invoke /paper-compile to build the PDF:

/paper-compile "paper/"

What this does:

• Run _utils/compile_utils.sh for pre-compile cleanup (special chars, path fix, hidelinks)
• Manual step-by-step compilation (pdflatex/xelatex → bibtex → pdflatex/xelatex × 2)
• Auto-fix common errors (missing packages, undefined refs, BibTeX syntax)
• Up to 3 compilation attempts
• Post-compilation checks: undefined refs, page count, font embedding

Output: paper/main.pdf

Checkpoint: Report compilation results.

🔨 Compilation complete:
- Status: SUCCESS
- Pages: [X] (main body) + [Y] (references) + [Z] (appendix)
- Within page limit: YES/NO
- Undefined references: 0
- Undefined citations: 0

Shall I proceed with the improvement loop?

Phase 5: Auto Improvement Loop

Invoke /auto-paper-improvement-loop to polish the paper:

/auto-paper-improvement-loop "paper/"

What this does (2 rounds):

Round 1: The external reviewer reviews the full paper → identifies CRITICAL/MAJOR/MINOR issues → Claude Code implements fixes → recompile → save main_round1.pdf

Round 2: The external reviewer re-reviews with conversation context → identifies remaining issues → Claude Code implements fixes → recompile → save main_round2.pdf

Typical improvements:

• Fix assumption-model mismatches
• Soften overclaims to match evidence
• Add missing interpretations and notation
• Strengthen limitations section
• Add theory-aligned experiments if needed

Output: Three PDFs for comparison + PAPER_IMPROVEMENT_LOG.md.

Format check (included in improvement loop Step 8): After final recompilation, auto-detect and fix overfull hboxes (content exceeding margins), verify page count vs venue limit, and ensure compact formatting. Any overfull > 10pt is fixed before generating the final PDF.

Phase 6: Final Report

# Paper Writing Pipeline Report

**Input**: [NARRATIVE_REPORT.md or topic]
**Venue**: [ICLR/NeurIPS/ICML]
**Date**: [today]

## Pipeline Summary

| Phase | Status | Output |
|-------|--------|--------|
| 1. Paper Plan | ✅ | PAPER_PLAN.md |
| 2. Figures | ✅ | figures/ ([N] auto + [M] manual) |
| 3. LaTeX Writing | ✅ | paper/sections/*.tex ([N] sections, [M] citations) |
| 4. Compilation | ✅ | paper/main.pdf ([X] pages) |
| 5. Improvement | ✅ | [score0]/10 → [score2]/10 |

## Improvement Scores
| Round | Score | Key Changes |
|-------|-------|-------------|
| Round 0 | X/10 | Baseline |
| Round 1 | Y/10 | [summary] |
| Round 2 | Z/10 | [summary] |

## Deliverables
- paper/main.pdf — Final polished paper
- paper/main_round0_original.pdf — Before improvement
- paper/main_round1.pdf — After round 1
- paper/main_round2.pdf — After round 2
- paper/PAPER_IMPROVEMENT_LOG.md — Full review log

## Remaining Issues (if any)
- [items from final review that weren't addressed]

## Next Steps
- [ ] Visual inspection of PDF
- [ ] Add any missing manual figures
- [ ] Submit to [venue] via OpenReview / CMT / HotCRP

Key Rules

• Large file handling: For long output files (reports, reviews, etc.), ALWAYS use Bash heredoc (cat << 'EOF' > file and cat << 'EOF' >> file) to write in chunks instead of the Write tool. The Write tool may silently fail on large content due to output token limits, causing empty parameters. Do NOT use the Write tool for files longer than ~150 lines.

• Don't skip phases. Each phase builds on the previous one — skipping leads to errors.

• Checkpoint between phases when AUTO_PROCEED=false. Present results and wait for approval.

• Manual figures first. If the paper needs architecture diagrams or qualitative results, the user must provide them before Phase 3.

• Compilation must succeed before entering the improvement loop. Fix all errors first.

• Preserve all PDFs. The user needs round0/round1/round2 for comparison.

• Document everything. The pipeline report should be self-contained.

• Respect page limits. If the paper exceeds the venue limit, suggest specific cuts before the improvement loop.

Composing with Other Workflows

/idea-discovery "direction"         ← Workflow 1: find ideas
implement                           ← write code
/run-experiment                     ← deploy experiments
/auto-review-loop "paper topic"     ← Workflow 2: iterate research
/paper-writing "NARRATIVE_REPORT.md"  ← Workflow 3: you are here
                                         submit! 🎉

Or use /research-pipeline for the Workflow 1+2 end-to-end flow,
then /paper-writing for the final writing step.

Typical Timeline

Phase	Duration	Can sleep?
1. Paper Plan	5-10 min	No
2. Figures	5-15 min	No
3. LaTeX Writing	15-30 min	Yes ✅
4. Compilation	2-5 min	No
5. Improvement	15-30 min	Yes ✅

Total: ~45-90 min for a full paper from narrative report to polished PDF.