@bohuyeshan/openagent-labforge-core 3.11.2 → 3.11.3

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

@@ -0,0 +1,252 @@
+---
+name: "auto-claude/paper-compile"
+description: "Compile LaTeX paper to PDF, fix errors, and verify output. Use when user says \"编译论文\", \"compile paper\", \"build PDF\", \"生成PDF\", or wants to compile LaTeX into a submission-ready PDF."
+argument-hint: ["paper-directory"]
+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 |

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

@@ -0,0 +1,254 @@
+---
+name: "auto-claude/paper-plan"
+description: "Generate a structured paper outline from review conclusions and experiment results. Use when user says \"写大纲\", \"paper outline\", \"plan the paper\", \"论文规划\", or wants to create a paper plan before writing."
+argument-hint: ["topic-or-narrative-doc"]
+allowed-tools: "Bash(*), Read, Write, Edit, Grep, Glob, Agent, WebSearch, WebFetch, mcp__codex__codex, mcp__codex__codex-reply"
+metadata:
+  category: "research/document-authoring"
+---
+# Paper Plan: From Review Conclusions to Paper Outline
+
+Generate a structured, section-by-section paper outline from: **$ARGUMENTS**
+
+## Constants
+
+- **REVIEWER_MODEL = `gpt-5.4`** — Model used via Codex MCP for outline review. Must be an OpenAI model.
+- **TARGET_VENUE = `ICLR`** — Default venue. User can override (e.g., `/paper-plan "topic" — venue: NeurIPS`). Supported: `ICLR`, `NeurIPS`, `ICML`.
+- **MAX_PAGES** — Main body page limit, measured from first page to end of Conclusion section (excluding references, appendix, and acknowledgements). ICLR=9, NeurIPS=9, ICML=8.
+
+## Inputs
+
+The skill expects one or more of these in the project directory:
+
+1. **NARRATIVE_REPORT.md** or **STORY.md** — research narrative with claims and evidence
+2. **Experiment results** — JSON files in `figures/`, screen logs, tables
+3. **IDEA_REPORT.md** — from idea-discovery pipeline (if applicable)
+
+If none exist, ask the user to describe the paper's contribution in 3-5 sentences.
+
+## Workflow
+
+### Step 1: Extract Claims and Evidence
+
+Read all available narrative documents and extract:
+
+1. **Core claims** (3-5 main contributions)
+2. **Evidence** for each claim (which experiments, which metrics, which figures)
+3. **Known weaknesses** (from reviewer feedback)
+4. **Suggested framing** (from review conclusions)
+
+Build a **Claims-Evidence Matrix**:
+
+```markdown
+| Claim | Evidence | Status | Section |
+|-------|----------|--------|---------|
+| [claim 1] | [exp A, metric B] | Supported | §3.2 |
+| [claim 2] | [exp C] | Partially supported | §4.1 |
+```
+
+### Step 2: Determine Paper Type and Structure
+
+Based on TARGET_VENUE and paper content, classify and select structure.
+
+**IMPORTANT**: The section count is FLEXIBLE (5-8 sections). Choose what fits the content best. The templates below are starting points, not rigid constraints.
+
+**Empirical/Diagnostic paper:**
+```
+1. Introduction (1.5 pages)
+2. Related Work (1 page)
+3. Method / Setup (1.5 pages)
+4. Experiments (3 pages)
+5. Analysis / Discussion (1 page)
+6. Conclusion (0.5 pages)
+```
+
+**Theory + Experiments paper:**
+```
+1. Introduction (1.5 pages)
+2. Related Work (1 page)
+3. Preliminaries & Modeling (1.5 pages)
+4. Experiments (1.5 pages)
+5. Theory Part A (1.5 pages)
+6. Theory Part B (1.5 pages)
+7. Conclusion (0.5 pages)
+— Total: 9 pages
+```
+Theory papers often need 7 sections (splitting theory into estimation + optimization, or setup + analysis). The total page budget MUST sum to MAX_PAGES.
+
+Theory papers should:
+- Include **proof sketch** locations (not just theorem statements)
+- Plan a **comparison table** of prior theoretical bounds vs. this paper's bounds
+- Identify which proofs go in appendix vs. main body
+
+**Method paper:**
+```
+1. Introduction (1.5 pages)
+2. Related Work (1 page)
+3. Method (2 pages)
+4. Experiments (2.5 pages)
+5. Ablation / Analysis (1 page)
+6. Conclusion (0.5 pages)
+```
+
+### Step 3: Section-by-Section Planning
+
+For each section, specify:
+
+```markdown
+### §0 Abstract
+- **One-sentence problem**: [what gap this paper addresses]
+- **Approach**: [what we do, in one sentence]
+- **Key result**: [most compelling quantitative finding]
+- **Implication**: [why it matters]
+- **Estimated length**: 150-250 words
+- **Self-contained check**: can a reader understand this without the paper?
+
+### §1 Introduction
+- **Opening hook**: [1-2 sentences that motivate the problem]
+- **Gap**: [what's missing in prior work]
+- **Key questions**: [the research questions this paper answers]
+- **Contributions**: [numbered list, matching Claims-Evidence Matrix]
+- **Hero figure**: [describe what Figure 1 should show — MUST include clear comparison if applicable]
+- **Estimated length**: 1.5 pages
+- **Key citations**: [3-5 papers to cite here]
+
+### §2 Related Work
+- **Subtopics**: [2-4 categories of related work]
+- **Positioning**: [how this paper differs from each category]
+- **Minimum length**: 1 full page (at least 3-4 paragraphs with substantive synthesis)
+- **Must NOT be just a list** — synthesize, compare, and position
+
+### §3 Method / Setup / Preliminaries
+- **Notation**: [key symbols and their meanings]
+- **Problem formulation**: [formal setup]
+- **Method description**: [algorithm, model, or experimental design]
+- **Formal statements**: [theorems, propositions if applicable]
+- **Proof sketch locations**: [which key steps appear here vs. appendix]
+- **Estimated length**: 1.5-2 pages
+
+### §4 Experiments / Main Results
+- **Figures planned**:
+  - Fig 1: [description, type: bar/line/table/architecture, WHAT COMPARISON it shows]
+  - Fig 2: [description]
+  - Table 1: [what it shows, which methods/baselines compared]
+- **Data source**: [which JSON files / experiment results]
+
+### §5 Conclusion
+- **Restatement**: [contributions rephrased, not copy-pasted from intro]
+- **Limitations**: [honest assessment — reviewers value this]
+- **Future work**: [1-2 concrete directions]
+- **Estimated length**: 0.5 pages
+```
+
+### Step 4: Figure Plan
+
+List every figure and table:
+
+```markdown
+## Figure Plan
+
+| ID | Type | Description | Data Source | Priority |
+|----|------|-------------|-------------|----------|
+| Fig 1 | Hero/Architecture | System overview + comparison | manual | HIGH |
+| Fig 2 | Line plot | Training curves comparison | figures/exp_A.json | HIGH |
+| Fig 3 | Bar chart | Ablation results | figures/ablation.json | MEDIUM |
+| Table 1 | Comparison table | Main results vs. baselines | figures/main_results.json | HIGH |
+| Table 2 | Theory comparison | Prior bounds vs. ours | manual | HIGH (theory papers) |
+```
+
+**CRITICAL for Figure 1 / Hero Figure**: Describe in detail what the figure should contain, including:
+- Which methods are being compared
+- What the visual difference should demonstrate
+- Caption draft that clearly states the comparison
+
+### Step 5: Citation Scaffolding
+
+For each section, list required citations:
+
+```markdown
+## Citation Plan
+- §1 Intro: [paper1], [paper2], [paper3] (problem motivation)
+- §2 Related: [paper4]-[paper10] (categorized by subtopic)
+- §3 Method: [paper11] (baseline), [paper12] (technique we build on)
+```
+
+**Citation rules** (from claude-scholar + Imbad0202/academic-research-skills):
+1. NEVER generate BibTeX from memory — always verify via search or existing .bib files
+2. Every citation must be verified: correct authors, year, venue
+3. Flag any citation you're unsure about with `[VERIFY]`
+4. Prefer published versions over arXiv preprints when available
+
+### Step 6: Cross-Review with REVIEWER_MODEL
+
+Send the complete outline to GPT-5.4 xhigh for feedback:
+
+```
+mcp__codex__codex:
+  model: gpt-5.4
+  config: {"model_reasoning_effort": "xhigh"}
+  prompt: |
+    Review this paper outline for a [VENUE] submission.
+    [full outline including Claims-Evidence Matrix]
+
+    Score 1-10 on:
+    1. Logical flow — does the story build naturally?
+    2. Claim-evidence alignment — every claim backed?
+    3. Missing experiments or analysis
+    4. Positioning relative to prior work
+    5. Page budget feasibility (MAX_PAGES = main body to Conclusion end, excluding refs/appendix)
+
+    For each weakness, suggest the MINIMUM fix.
+    Be specific and actionable — "add X" not "consider more experiments".
+```
+
+Apply feedback before finalizing.
+
+### Step 7: Output
+
+Save the final outline to `PAPER_PLAN.md` in the project root:
+
+```markdown
+# Paper Plan
+
+**Title**: [working title]
+**Venue**: [target venue]
+**Type**: [empirical/theory/method]
+**Date**: [today]
+**Page budget**: [MAX_PAGES] pages (main body to Conclusion end, excluding references & appendix)
+**Section count**: [N] (must match the number of section files that will be created)
+
+## Claims-Evidence Matrix
+[from Step 1]
+
+## Structure
+[from Step 2-3, section by section]
+
+## Figure Plan
+[from Step 4, with detailed hero figure description]
+
+## Citation Plan
+[from Step 5]
+
+## Reviewer Feedback
+[from Step 6, summarized]
+
+## Next Steps
+- [ ] /paper-figure to generate all figures
+- [ ] /paper-write to draft LaTeX
+- [ ] /paper-compile to build PDF
+```
+
+## Key Rules
+
+- **Do NOT generate author information** — leave author block as placeholder or anonymous
+- **Be honest about evidence gaps** — mark claims as "needs experiment" rather than overclaiming
+- **Page budget is hard** — if content exceeds MAX_PAGES, suggest what to move to appendix
+- **MAX_PAGES counts main body only** — from first page to end of Conclusion. References and appendix are NOT counted.
+- **Venue-specific norms** — all three venues (ICLR/NeurIPS/ICML) use `natbib` (`\citep`/`\citet`)
+- **Claims-Evidence Matrix is the backbone** — every claim must map to evidence, every experiment must support a claim
+- **Figures need detailed descriptions** — especially the hero figure, which must clearly specify comparisons and visual expectations
+- **Section count is flexible** — 5-8 sections depending on paper type. Don't force content into a rigid 5-section template.
+
+## Acknowledgements
+
+Outline methodology inspired by [Research-Paper-Writing-Skills](https://github.com/Master-cai/Research-Paper-Writing-Skills) (claim-evidence mapping), [claude-scholar](https://github.com/Galaxy-Dawn/claude-scholar) (citation verification), and [Imbad0202/academic-research-skills](https://github.com/Imbad0202/academic-research-skills) (claim verification protocol).