Paper Compile

---
description: LaTeX compile → PDF — latexmk compile + auto-fix + page count/anonymity/font/[UNCONFIRMED] checks + submission checklist
argument-hint: "[paper-dir] [--fix] [--checklist]"
---

# /paper-compile

> Compile a LaTeX paper to PDF, auto-fix common errors, and verify submission requirements.
> Input: the paper/ directory generated by /paper-draft. Run latexmk compilation,
> parse errors and attempt auto-fix (missing packages, undefined references, figure paths).
> Verify page limit, anonymous compliance, font embedding, and clearance of [UNCONFIRMED] markers.
> Generate a submission checklist.

## Inputs

- `paper_dir` (optional, default `paper/`): LaTeX project directory containing `main.tex`
- `--fix` (optional): enable auto-fix mode (automatically install missing packages, correct paths)
- `--checklist` (optional): generate a detailed submission checklist (check only, no compilation)

## Outputs

- `paper/main.pdf` — compiled PDF
- **COMPILE_REPORT** (printed to terminal) — compilation status, check results, submission checklist
- If `--fix`: modified .tex files (auto-fixed)

## Wiki Interaction

### Reads
- `wiki/outputs/paper-plan-*.md` — retrieve venue information (page limit, anonymity requirements)
- `.claude/skills/shared-references/citation-verification.md` — [UNCONFIRMED] marker check rules

### Writes
- `paper/main.pdf` — compilation output
- `wiki/log.md` — appended compilation log

### Graph edges created
- None

## Workflow

**Precondition**: confirm `paper/main.tex` exists. Confirm `latexmk` is installed (`which latexmk`).

### Step 1: Compile

1. **First compilation**:
   ```bash
   cd paper/ && latexmk -pdf -interaction=nonstopmode main.tex 2>&1
   ```

2. **Parse compilation output**:
   - Collect all errors (`! ...`)
   - Collect all warnings (`Warning:` / `Overfull` / `Underfull`)
   - Classify:
     - **Missing package**: `! LaTeX Error: File 'xxx.sty' not found`
     - **Undefined reference**: `LaTeX Warning: Reference 'xxx' on page N undefined`
     - **Undefined citation**: `LaTeX Warning: Citation 'xxx' on page N undefined`
     - **Missing figure**: `! LaTeX Error: File 'figures/xxx' not found`
     - **Syntax error**: other errors beginning with `!`
     - **Overfull/Underfull**: typesetting warnings (non-blocking)

3. **If compilation succeeds** (main.pdf generated): proceed to Step 3
4. **If compilation fails**: proceed to Step 2

### Step 2: Auto-Fix

If `--fix` is enabled, attempt to auto-fix each error type:

**2a. Missing package**:
```bash
# check if the package is installable via TeX Live
tlmgr info {package-name} 2>/dev/null
# if installable and user confirms:
tlmgr install {package-name}
```
If not installable: comment out the `\usepackage{xxx}` line and annotate `% TODO: install package {xxx}`

**2b. Undefined reference/citation**:
- Undefined reference: check if the corresponding `\label{}` exists; if not, add a placeholder label
- Undefined citation: check if `references.bib` contains the key
  - If not: attempt to match from wiki papers and add an [UNCONFIRMED] entry
  - If present but bibtex has not run: re-run `latexmk` (latexmk usually handles this automatically)

**2c. Missing figure**:
- Check if `paper/figures/` contains a file with a different extension (.pdf vs .png vs .eps)
- If found: correct the `\includegraphics` path
- If not found: replace with placeholder `\missingfigure{xxx}` (requires `todonotes` package)

**2d. Syntax error**:
- Common fixes: unclosed `{}`, mismatched `\begin{}`/`\end{}`, illegal characters
- Attempt to locate the error line number; provide specific fix suggestions
- If auto-fix is not possible: report error location and suggestions

**Re-compile after fixes** (up to 3 fix-compile cycles):
```bash
cd paper/ && latexmk -pdf -interaction=nonstopmode main.tex 2>&1
```

### Step 3: Verification Checks

After successful compilation, run the following checks:

**3a. Page count check**:
```bash
# get PDF page count
python3 -c "
import subprocess
result = subprocess.run(['pdfinfo', 'paper/main.pdf'], capture_output=True, text=True)
for line in result.stdout.splitlines():
    if line.startswith('Pages:'):
        print(line.split(':')[1].strip())
"
```
Compare against the venue page limit (retrieved from the PAPER_PLAN venue or the venue table in academic-writing.md).
- Exceeds limit: report number of pages over limit; suggest compressing or moving content to appendix
- Under limit: report remaining space; suggest adding content

**3b. Anonymity check**:
Scan all .tex files:
- Search for author names (if `\author{}` is non-empty → warn)
- Search for institution names (university, lab, institute → warn)
- Search for GitHub/GitLab links (may reveal identity → warn)
- Search for "our previous work" / "we previously" → should use third-person citation
- Search for `\thanks{}` / `\acknowledgments` → remove for anonymous submission

**3c. [UNCONFIRMED] marker check**:
```bash
# scan references.bib and all .tex files
grep -rn "VERIFY" paper/
```
- If [UNCONFIRMED] markers exist: list each one; flag as **submission blocker**
- Per citation-verification.md: [UNCONFIRMED] is a hard submission blocker

**3d. Font embedding check**:
```bash
pdffonts paper/main.pdf
```
- Check the "emb" column: all fonts should be "yes"
- Unembedded fonts: report font names; suggest adding font embedding to compile options

**3e. Content completeness check**:
- Search for `TODO`, `FIXME`, `XXX` markers
- Search for `\missingfigure`, empty sections (`\section{X}` followed by no content)
- Search for unreferenced figures/tables (`\includegraphics` present but no `\ref`)
- Check that the abstract exists and is non-empty

### Step 4: Generate Submission Checklist and Report

```markdown
# Compile Report

## Compilation
- Status: {SUCCESS / FAILED}
- Compiler: latexmk + pdflatex
- Rounds: {N} (including auto-fix rounds)
- Errors: {N} (fixed: {M}, remaining: {K})
- Warnings: {N} (overfull: {O}, underfull: {U}, other: {W})

## Verification Results

| Check | Status | Details |
|-------|--------|---------|
| Page count | {PASS/FAIL} | {N} pages (limit: {L}) |
| Anonymous | {PASS/WARN} | {details} |
| [UNCONFIRMED] citations | {PASS/FAIL} | {N} remaining |
| Fonts embedded | {PASS/FAIL} | {details} |
| No TODOs | {PASS/WARN} | {N} remaining |
| Figures referenced | {PASS/WARN} | {details} |
| Abstract present | {PASS/FAIL} | {details} |

## Submission Checklist

- [ ] PDF compiles without errors
- [ ] Page count within venue limit ({L} pages)
- [ ] All [UNCONFIRMED] citations resolved
- [ ] Anonymous submission (no author info)
- [ ] All fonts embedded
- [ ] No TODO/FIXME markers
- [ ] All figures referenced in text
- [ ] Abstract present and complete
- [ ] Supplementary material prepared (if applicable)
- [ ] Paper title matches submission system

## Blocking Issues
{list of FAIL items that must be resolved before submission}

## Warnings (non-blocking)
{list of WARN items for consideration}

## Next Steps
- {specific actions to resolve blocking issues}
- Run `/refine paper/main.tex --focus writing` for final polish
- Manual review of anonymous compliance
```

Append log:
```bash
python3 tools/research_wiki.py log wiki/ \
  "paper-compile | {SUCCESS/FAILED} | {pages} pages, {errors} errors, {verify_count} [UNCONFIRMED], {checks_passed}/{checks_total} checks passed"
```

## Constraints

- **Do not modify wiki content**: only operate on the paper/ directory and wiki/log.md
- **Auto-fix requires --fix**: by default, only report errors; do not fix
- **[UNCONFIRMED] is a hard blocker**: [UNCONFIRMED] present in submission checklist = not submittable
- **Maximum 3 fix-compile rounds**: prevent infinite fix loops
- **Do not delete user content**: auto-fix only adds or corrects; does not delete hand-written content
- **pdfinfo/pdffonts dependency**: if not installed, skip the corresponding check and annotate "tool not available"
- **Anonymity check is heuristic**: may produce false positives; annotate as WARN rather than FAIL

## Error Handling

- **main.tex not found**: error; suggest running /paper-draft first
- **latexmk not installed**: error; provide installation command (`sudo apt install texlive-full` or `brew install --cask mactex`)
- **Compilation failed and auto-fix unsuccessful**: output full error log + locate specific .tex file and line number
- **pdfinfo/pdffonts not installed**: skip page count / font checks; annotate in report
- **PAPER_PLAN not found**: skip venue info extraction; use default limit (10 pages); warn user
- **Permission issue** (tlmgr requires sudo): report list of packages requiring manual installation

## Dependencies

### Tools（via Bash）
- `latexmk` — LaTeX compilation
- `pdfinfo` — PDF page count check (poppler-utils)
- `pdffonts` — font embedding check (poppler-utils)
- `python3 tools/research_wiki.py log wiki/ "<message>"` — append log

### MCP Servers
- None

### Claude Code Native
- `Read` — read .tex files and compilation logs
- `Edit` — auto-fix .tex files (--fix mode)
- `Bash` — execute compilation and check commands
- `Grep` — search for [UNCONFIRMED], TODO, anonymity violations

### Shared References
- `.claude/skills/shared-references/citation-verification.md` — [UNCONFIRMED] marker check rules
- `.claude/skills/shared-references/academic-writing.md` — venue page limit reference

### Called by
- `/research` Stage 5 (paper compilation stage)
- Manual user invocation