@bohuyeshan/openagent-labforge-core 3.11.5 → 3.13.0

package/generated/skills-bundles/full/skills/research/document-authoring/auto-claude__paper-compile/SKILL.md

@@ -6,247 +6,248 @@ allowed-tools: "Bash(*), Read, Write, Edit, Grep, Glob"
 metadata:
   category: "research/document-authoring"
 ---
-# Paper Compile: LaTeX to Submission-Ready PDF
-
-Compile the LaTeX paper and fix any issues: **$ARGUMENTS**
-
-## Constants
-
-- **COMPILER = `latexmk`** — LaTeX build tool. Handles multi-pass compilation automatically.
-- **ENGINE = `pdflatex`** — LaTeX engine. Options: `pdflatex` (default), `xelatex` (for CJK/custom fonts), `lualatex`.
-- **MAX_COMPILE_ATTEMPTS = 3** — Maximum attempts to fix errors and recompile.
-- **PAPER_DIR = `paper/`** — Directory containing LaTeX source files.
-- **MAX_PAGES** — Main body page limit (to end of Conclusion, excluding references & appendix). ICLR=9, NeurIPS=9, ICML=8.
-
-## Workflow
-
-### Step 1: Verify Prerequisites
-
-Check that the compilation environment is ready:
-
-```bash
-# Check LaTeX installation
-which pdflatex && which latexmk && which bibtex
-
-# If not installed, provide instructions:
-# macOS: brew install --cask mactex-no-gui
-# Ubuntu: sudo apt-get install texlive-full
-# Server: conda install -c conda-forge texlive-core
-```
-
-Verify all required files exist:
-
-```bash
-# Must exist
-ls $PAPER_DIR/main.tex
-
-# Should exist
-ls $PAPER_DIR/references.bib
-ls $PAPER_DIR/sections/*.tex
-ls $PAPER_DIR/figures/*.pdf 2>/dev/null || ls $PAPER_DIR/figures/*.png 2>/dev/null
-```
-
-### Step 2: First Compilation Attempt
-
-```bash
-cd $PAPER_DIR
-
-# Clean previous build artifacts
-latexmk -C
-
-# Full compilation (pdflatex + bibtex + pdflatex × 2)
-latexmk -pdf -interaction=nonstopmode -halt-on-error main.tex 2>&1 | tee compile.log
-```
-
-### Step 3: Error Diagnosis and Auto-Fix
-
-If compilation fails, read `compile.log` and fix common errors:
-
-**Missing packages:**
-```
-! LaTeX Error: File `somepackage.sty' not found.
-```
-→ Install via `tlmgr install somepackage` or remove the `\usepackage` if unused.
-
-**Undefined references:**
-```
-LaTeX Warning: Reference `fig:xyz' on page 3 undefined
-```
-→ Check `\label{fig:xyz}` exists in the correct figure environment.
-
-**Missing figures:**
-```
-! LaTeX Error: File `figures/fig1.pdf' not found.
-```
-→ Check if the file exists with a different extension (.png vs .pdf). Update the `\includegraphics` path.
-
-**Citation undefined:**
-```
-LaTeX Warning: Citation `smith2024' undefined
-```
-→ Add the missing entry to `references.bib` or fix the citation key.
-
-**`[VERIFY]` markers in text:**
-→ Search for `[VERIFY]` markers left by `/paper-write`. These indicate unverified citations or facts. Search for the correct information or flag to the user.
-
-**Overfull hbox:**
-```
-Overfull \hbox (12.5pt too wide) in paragraph at lines 42--45
-```
-→ Minor: usually ignorable. If severe (>20pt), rephrase the text or adjust figure width.
-
-**BibTeX errors:**
-```
-I was expecting a `,' or a `}'---line 15 of references.bib
-```
-→ Fix BibTeX syntax (missing comma, unmatched braces, special characters in title).
-
-**`\crefname` undefined for custom theorem types:**
-→ Ensure `\crefname{assumption}{Assumption}{Assumptions}` and similar are in the preamble after `\newtheorem{assumption}`.
-
-### Step 4: Iterative Fix Loop
-
-```
-for attempt in 1..MAX_COMPILE_ATTEMPTS:
-    compile()
-    if success:
-        break
-    parse_errors()
-    auto_fix()
-```
-
-For each error:
-1. Read the error message from `compile.log`
-2. Locate the source file and line number
-3. Apply the fix
-4. Recompile
-
-### Step 5: Post-Compilation Checks
-
-After successful compilation, verify the output:
-
-```bash
-# Check PDF exists and has content
-ls -la main.pdf
-# Check page count
-pdfinfo main.pdf | grep Pages
-
-# macOS: open for visual inspection
-# open main.pdf
-```
-
-**Automated checks:**
-
-- [ ] PDF file exists and is > 100KB (not empty/corrupt)
-- [ ] Total page count is reasonable (MAX_PAGES + appendix + references)
-- [ ] No "??" in the PDF (undefined references — grep the log)
-- [ ] No "[?]" in the PDF (undefined citations — grep the log)
-- [ ] Figures are rendered (not missing image placeholders)
-
-```bash
-# Check for undefined references
-grep -c "LaTeX Warning.*undefined" compile.log
-
-# Check for missing citations
-grep -c "Citation.*undefined" compile.log
-```
-
-### Step 6: Page Count Verification
-
-**CRITICAL**: Verify main body fits within MAX_PAGES.
-
-Main body = first page through end of Conclusion section (not necessarily §5 — could be §6, §7, or §8 depending on structure).
-References and appendix are NOT counted.
-
-**Precise check using `pdftotext`:**
-```bash
-# Extract text and find where Conclusion ends vs References begin
-pdftotext main.pdf - | python3 -c "
-import sys
-text = sys.stdin.read()
-pages = text.split('\f')
-for i, page in enumerate(pages):
-    if 'Ethics Statement' in page or 'Reproducibility' in page:
-        print(f'Conclusion ends on page {i+1}')
-    if any(w in page for w in ['References', 'Bibliography']):
-        lines = [l for l in page.split('\n') if l.strip()]
-        for l in lines[:3]:
-            if 'References' in l or 'Bibliography' in l:
-                print(f'References start on page {i+1}')
-                break
-"
-```
-
-If Conclusion ends mid-page and References start on the same page, the main body is that page number (e.g., if both are on page 9, main body = ~8.5 pages, which is fine for a 9-page limit since it leaves room for the References header).
-
-If over limit:
-- Identify which sections are longest
-- Suggest specific cuts (move proofs to appendix, compress tables, tighten writing)
-- Report: "Main body is X pages (limit: MAX_PAGES). Suggestion: move [specific content] to appendix."
-
-### Step 6.5: Stale File Detection
-
-Check for orphaned section files not referenced by `main.tex`:
-
-```bash
-# Find all .tex files in sections/ and check which are \input'ed by main.tex
-for f in paper/sections/*.tex; do
-    base=$(basename "$f")
-    if ! grep -q "$base" paper/main.tex; then
-        echo "WARNING: $f is not referenced by main.tex — consider removing"
-    fi
-done
-```
-
-This prevents confusion from leftover files when section structure changes (e.g., old `5_conclusion.tex` left behind after restructuring to 7 sections).
-
-### Step 7: Submission Readiness
-
-For conference submission, additional checks:
-
-- [ ] **Anonymous**: no author names, affiliations, or self-citations that reveal identity
-- [ ] **Page limit**: main body within MAX_PAGES (to end of Conclusion)
-- [ ] **Font embedding**: all fonts embedded in PDF
-  ```bash
-  pdffonts main.pdf | grep -v "yes"  # should return nothing (or only header)
-  ```
-- [ ] **No supplementary mixed in**: appendix clearly after `\newpage\appendix`
-- [ ] **File size**: reasonable (< 50MB for most venues, < 10MB preferred)
-- [ ] **No `[VERIFY]` markers**: search the PDF text for leftover markers
-
-### Step 8: Output Summary
-
-```markdown
-## Compilation Report
-
-- **Status**: SUCCESS / FAILED
-- **PDF**: paper/main.pdf
-- **Pages**: X (main body to Conclusion) + Y (references) + Z (appendix)
-- **Within page limit**: YES/NO (MAX_PAGES = N)
-- **Errors fixed**: [list of auto-fixed issues]
-- **Warnings remaining**: [list of non-critical warnings]
-- **Undefined references**: 0
-- **Undefined citations**: 0
-
-### Next Steps
-- [ ] Visual inspection of PDF
-- [ ] Run `/paper-write` to fix any content issues
-- [ ] Submit to [venue] via OpenReview / CMT / HotCRP
-```
-
-## Key Rules
-
-- **Never delete the user's source files** — only modify to fix errors
-- **Keep compile.log** — useful for debugging
-- **Don't suppress warnings** — report them, let the user decide
-- **If LaTeX is not installed**, provide clear installation instructions rather than failing silently
-- **Font embedding is critical** — some venues reject PDFs with non-embedded fonts
-- **Page count = main body to Conclusion** — this is the metric that matters for submission
-
-## Common Venue Requirements
-
-| Venue | Style File | Citation | Page Limit (main body) | Submission |
-|-------|-----------|----------|------------------------|------------|
-| ICLR 2026 | `iclr2026_conference.sty` | `natbib` (`\citep`/`\citet`) | 9 pages (to Conclusion end) | OpenReview |
-| NeurIPS 2025 | `neurips_2025.sty` | `natbib` (`\citep`/`\citet`) | 9 pages (to Conclusion end) | OpenReview |
-| ICML 2025 | `icml2025.sty` | `natbib` (`\citep`/`\citet`) | 8 pages (to Conclusion end) | OpenReview |
+
+# Paper Compile: LaTeX to Submission-Ready PDF
+
+Compile the LaTeX paper and fix any issues: **$ARGUMENTS**
+
+## Constants
+
+- **COMPILER = `latexmk`** — LaTeX build tool. Handles multi-pass compilation automatically.
+- **ENGINE = `pdflatex`** — LaTeX engine. Options: `pdflatex` (default), `xelatex` (for CJK/custom fonts), `lualatex`.
+- **MAX_COMPILE_ATTEMPTS = 3** — Maximum attempts to fix errors and recompile.
+- **PAPER_DIR = `paper/`** — Directory containing LaTeX source files.
+- **MAX_PAGES** — Main body page limit (to end of Conclusion, excluding references & appendix). ICLR=9, NeurIPS=9, ICML=8.
+
+## Workflow
+
+### Step 1: Verify Prerequisites
+
+Check that the compilation environment is ready:
+
+```bash
+# Check LaTeX installation
+which pdflatex && which latexmk && which bibtex
+
+# If not installed, provide instructions:
+# macOS: brew install --cask mactex-no-gui
+# Ubuntu: sudo apt-get install texlive-full
+# Server: conda install -c conda-forge texlive-core
+```
+
+Verify all required files exist:
+
+```bash
+# Must exist
+ls $PAPER_DIR/main.tex
+
+# Should exist
+ls $PAPER_DIR/references.bib
+ls $PAPER_DIR/sections/*.tex
+ls $PAPER_DIR/figures/*.pdf 2>/dev/null || ls $PAPER_DIR/figures/*.png 2>/dev/null
+```
+
+### Step 2: First Compilation Attempt
+
+```bash
+cd $PAPER_DIR
+
+# Clean previous build artifacts
+latexmk -C
+
+# Full compilation (pdflatex + bibtex + pdflatex × 2)
+latexmk -pdf -interaction=nonstopmode -halt-on-error main.tex 2>&1 | tee compile.log
+```
+
+### Step 3: Error Diagnosis and Auto-Fix
+
+If compilation fails, read `compile.log` and fix common errors:
+
+**Missing packages:**
+```
+! LaTeX Error: File `somepackage.sty' not found.
+```
+→ Install via `tlmgr install somepackage` or remove the `\usepackage` if unused.
+
+**Undefined references:**
+```
+LaTeX Warning: Reference `fig:xyz' on page 3 undefined
+```
+→ Check `\label{fig:xyz}` exists in the correct figure environment.
+
+**Missing figures:**
+```
+! LaTeX Error: File `figures/fig1.pdf' not found.
+```
+→ Check if the file exists with a different extension (.png vs .pdf). Update the `\includegraphics` path.
+
+**Citation undefined:**
+```
+LaTeX Warning: Citation `smith2024' undefined
+```
+→ Add the missing entry to `references.bib` or fix the citation key.
+
+**`[VERIFY]` markers in text:**
+→ Search for `[VERIFY]` markers left by `/paper-write`. These indicate unverified citations or facts. Search for the correct information or flag to the user.
+
+**Overfull hbox:**
+```
+Overfull \hbox (12.5pt too wide) in paragraph at lines 42--45
+```
+→ Minor: usually ignorable. If severe (>20pt), rephrase the text or adjust figure width.
+
+**BibTeX errors:**
+```
+I was expecting a `,' or a `}'---line 15 of references.bib
+```
+→ Fix BibTeX syntax (missing comma, unmatched braces, special characters in title).
+
+**`\crefname` undefined for custom theorem types:**
+→ Ensure `\crefname{assumption}{Assumption}{Assumptions}` and similar are in the preamble after `\newtheorem{assumption}`.
+
+### Step 4: Iterative Fix Loop
+
+```
+for attempt in 1..MAX_COMPILE_ATTEMPTS:
+    compile()
+    if success:
+        break
+    parse_errors()
+    auto_fix()
+```
+
+For each error:
+1. Read the error message from `compile.log`
+2. Locate the source file and line number
+3. Apply the fix
+4. Recompile
+
+### Step 5: Post-Compilation Checks
+
+After successful compilation, verify the output:
+
+```bash
+# Check PDF exists and has content
+ls -la main.pdf
+# Check page count
+pdfinfo main.pdf | grep Pages
+
+# macOS: open for visual inspection
+# open main.pdf
+```
+
+**Automated checks:**
+
+- [ ] PDF file exists and is > 100KB (not empty/corrupt)
+- [ ] Total page count is reasonable (MAX_PAGES + appendix + references)
+- [ ] No "??" in the PDF (undefined references — grep the log)
+- [ ] No "[?]" in the PDF (undefined citations — grep the log)
+- [ ] Figures are rendered (not missing image placeholders)
+
+```bash
+# Check for undefined references
+grep -c "LaTeX Warning.*undefined" compile.log
+
+# Check for missing citations
+grep -c "Citation.*undefined" compile.log
+```
+
+### Step 6: Page Count Verification
+
+**CRITICAL**: Verify main body fits within MAX_PAGES.
+
+Main body = first page through end of Conclusion section (not necessarily §5 — could be §6, §7, or §8 depending on structure).
+References and appendix are NOT counted.
+
+**Precise check using `pdftotext`:**
+```bash
+# Extract text and find where Conclusion ends vs References begin
+pdftotext main.pdf - | python3 -c "
+import sys
+text = sys.stdin.read()
+pages = text.split('\f')
+for i, page in enumerate(pages):
+    if 'Ethics Statement' in page or 'Reproducibility' in page:
+        print(f'Conclusion ends on page {i+1}')
+    if any(w in page for w in ['References', 'Bibliography']):
+        lines = [l for l in page.split('\n') if l.strip()]
+        for l in lines[:3]:
+            if 'References' in l or 'Bibliography' in l:
+                print(f'References start on page {i+1}')
+                break
+"
+```
+
+If Conclusion ends mid-page and References start on the same page, the main body is that page number (e.g., if both are on page 9, main body = ~8.5 pages, which is fine for a 9-page limit since it leaves room for the References header).
+
+If over limit:
+- Identify which sections are longest
+- Suggest specific cuts (move proofs to appendix, compress tables, tighten writing)
+- Report: "Main body is X pages (limit: MAX_PAGES). Suggestion: move [specific content] to appendix."
+
+### Step 6.5: Stale File Detection
+
+Check for orphaned section files not referenced by `main.tex`:
+
+```bash
+# Find all .tex files in sections/ and check which are \input'ed by main.tex
+for f in paper/sections/*.tex; do
+    base=$(basename "$f")
+    if ! grep -q "$base" paper/main.tex; then
+        echo "WARNING: $f is not referenced by main.tex — consider removing"
+    fi
+done
+```
+
+This prevents confusion from leftover files when section structure changes (e.g., old `5_conclusion.tex` left behind after restructuring to 7 sections).
+
+### Step 7: Submission Readiness
+
+For conference submission, additional checks:
+
+- [ ] **Anonymous**: no author names, affiliations, or self-citations that reveal identity
+- [ ] **Page limit**: main body within MAX_PAGES (to end of Conclusion)
+- [ ] **Font embedding**: all fonts embedded in PDF
+  ```bash
+  pdffonts main.pdf | grep -v "yes"  # should return nothing (or only header)
+  ```
+- [ ] **No supplementary mixed in**: appendix clearly after `\newpage\appendix`
+- [ ] **File size**: reasonable (< 50MB for most venues, < 10MB preferred)
+- [ ] **No `[VERIFY]` markers**: search the PDF text for leftover markers
+
+### Step 8: Output Summary
+
+```markdown
+## Compilation Report
+
+- **Status**: SUCCESS / FAILED
+- **PDF**: paper/main.pdf
+- **Pages**: X (main body to Conclusion) + Y (references) + Z (appendix)
+- **Within page limit**: YES/NO (MAX_PAGES = N)
+- **Errors fixed**: [list of auto-fixed issues]
+- **Warnings remaining**: [list of non-critical warnings]
+- **Undefined references**: 0
+- **Undefined citations**: 0
+
+### Next Steps
+- [ ] Visual inspection of PDF
+- [ ] Run `/paper-write` to fix any content issues
+- [ ] Submit to [venue] via OpenReview / CMT / HotCRP
+```
+
+## Key Rules
+
+- **Never delete the user's source files** — only modify to fix errors
+- **Keep compile.log** — useful for debugging
+- **Don't suppress warnings** — report them, let the user decide
+- **If LaTeX is not installed**, provide clear installation instructions rather than failing silently
+- **Font embedding is critical** — some venues reject PDFs with non-embedded fonts
+- **Page count = main body to Conclusion** — this is the metric that matters for submission
+
+## Common Venue Requirements
+
+| Venue | Style File | Citation | Page Limit (main body) | Submission |
+|-------|-----------|----------|------------------------|------------|
+| ICLR 2026 | `iclr2026_conference.sty` | `natbib` (`\citep`/`\citet`) | 9 pages (to Conclusion end) | OpenReview |
+| NeurIPS 2025 | `neurips_2025.sty` | `natbib` (`\citep`/`\citet`) | 9 pages (to Conclusion end) | OpenReview |
+| ICML 2025 | `icml2025.sty` | `natbib` (`\citep`/`\citet`) | 8 pages (to Conclusion end) | OpenReview |