Autosci Paper Compile

/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:

   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:

# 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):

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:

# 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:

# 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:

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

# 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:

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