@synsci/cli-darwin-x64 1.1.70 → 1.1.72

package/bin/skills/peer-review/references/scoring_rubric.md

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+# Peer Review Scoring Rubric
+
+Detailed scoring criteria with severity calibration for consistent, fair evaluation.
+
+## Overall Score (1-10 Scale)
+
+### Score Anchors
+
+| Score | Label | Criteria |
+|-------|-------|----------|
+| **10** | Outstanding | Exceptional contribution, flawless execution, field-changing potential |
+| **9** | Strong Accept | Significant contribution, excellent methodology, high impact, minor polish needed |
+| **8** | Accept | Solid contribution, rigorous execution, clear value to field |
+| **7** | Accept | Good work with minor methodological or scope limitations, contribution clear |
+| **6** | Weak Accept | Sound methodology, acknowledged limitations, narrow scope but valid |
+| **5** | Borderline | Significant concerns but potentially salvageable with major revisions |
+| **4** | Lean Reject | Multiple major issues affecting validity or interpretation |
+| **3** | Reject | Fundamental methodological flaws or unsupported claims |
+| **2** | Strong Reject | Serious scientific concerns, major rewrite needed |
+| **1** | Clear Reject | Fatally flawed, ethical concerns, or not suitable for venue |
+
+### Score Distribution Expectations
+
+In a well-calibrated review process:
+- **8-10**: ~10-15% of submissions (truly excellent work)
+- **6-7**: ~40-50% of submissions (solid, publishable work)
+- **5**: ~20-25% of submissions (borderline, needs work)
+- **1-4**: ~15-20% of submissions (significant issues)
+
+## Sub-Score Dimensions (1-4 Scale)
+
+### Soundness
+
+Technical correctness of methodology, analysis, and conclusions.
+
+| Score | Description | Indicators |
+|-------|-------------|------------|
+| **4** | Excellent | Methods impeccable, statistics appropriate, conclusions fully supported |
+| **3** | Good | Minor issues but core methodology sound, conclusions mostly supported |
+| **2** | Fair | Notable methodological concerns affecting some conclusions |
+| **1** | Poor | Fundamental flaws invalidating major claims |
+
+**Soundness Red Flags:**
+- Inappropriate statistical tests for data type
+- Missing critical controls
+- Circular analysis (same data for selection and testing)
+- Pseudoreplication
+- Overclaiming from correlational data
+
+### Originality
+
+Novelty of contribution relative to prior work.
+
+| Score | Description | Indicators |
+|-------|-------------|------------|
+| **4** | Highly Novel | New problem, method, or insight advancing the field |
+| **3** | Novel | Clear contribution beyond incremental improvement |
+| **2** | Incremental | Extension of existing work with limited new insight |
+| **1** | Derivative | Minimal novelty, replication without extension |
+
+**Originality Considerations:**
+- Novel problem formulation counts as originality
+- Rigorous negative results can be original contributions
+- Cross-domain application of known methods can be novel
+- Scale or efficiency improvements require substantial gains for high novelty
+
+### Clarity
+
+Quality of writing, organization, and presentation.
+
+| Score | Description | Indicators |
+|-------|-------------|------------|
+| **4** | Excellent | Clear, well-organized, accessible to broad audience |
+| **3** | Good | Generally clear, minor organizational or writing issues |
+| **2** | Fair | Significant clarity issues affecting comprehension |
+| **1** | Poor | Difficult to follow, major organizational problems |
+
+**Clarity Checklist:**
+- Abstract accurately summarizes findings
+- Introduction motivates and contextualizes work
+- Methods reproducible from description
+- Results presented logically
+- Discussion distinguishes data from speculation
+- Figures/tables clear and well-labeled
+
+### Significance
+
+Potential impact on the field.
+
+| Score | Description | Indicators |
+|-------|-------------|------------|
+| **4** | High Impact | Likely to influence research direction or practice |
+| **3** | Significant | Clear value to researchers in the area |
+| **2** | Moderate | Useful but limited impact expected |
+| **1** | Low | Minimal expected influence |
+
+**Significance Factors:**
+- Size and activity of affected research community
+- Practical applications enabled
+- Theoretical insights provided
+- Reproducibility and extensibility of work
+
+## Severity Calibration
+
+### Issue Classification
+
+| Severity | Definition | Score Impact | Frequency |
+|----------|------------|--------------|-----------|
+| **Critical** | Invalidates conclusions, requires fundamental revision | -3 to -4 | <5% of reviews |
+| **Major** | Significantly affects interpretation, addressable with effort | -1 to -2 | 20-30% |
+| **Moderate** | Notable limitation, acknowledged is acceptable | -0.5 to -1 | 40-50% |
+| **Minor** | Polish issue, easy to fix | -0 to -0.5 | Common |
+
+### Critical Issues (Reserve for True Invalidity)
+
+Only use "Critical" severity for:
+- Statistical tests fundamentally inappropriate (e.g., t-test on non-independent data)
+- Missing controls that prevent any valid interpretation
+- Fabrication or falsification concerns
+- Undisclosed conflicts of interest affecting conclusions
+- Ethical violations (missing IRB for human subjects)
+
+### What Is NOT Critical
+
+These are Major or Moderate, not Critical:
+- Missing some baselines (if primary comparison valid)
+- Synthetic data only (standard in many fields)
+- Limited generalization (scope issue)
+- Acknowledged limitations
+- Reproducibility details missing (fixable)
+
+## Score Adjustment Rules
+
+### Limitation Acknowledgment Bonus
+
+If authors explicitly acknowledge a limitation:
+- Reduce penalty by 50% (e.g., -2 → -1)
+- Never penalize >1 point for acknowledged issues
+- Credit honest self-assessment in summary
+
+### Reproducibility Credit
+
+If the paper provides:
+- Detailed methods section
+- Random seeds and hyperparameters
+- Code/data availability statement
+- Confidence intervals and effect sizes
+
+→ Apply score floor of 6 (cannot go below Weak Accept)
+
+### Scope Adjustment
+
+A narrow-but-sound study on an interesting problem:
+- Should score 6-7 (Weak Accept to Accept)
+- Should NOT score 5 or below unless methodology flawed
+- Evaluate on what it does, not what it doesn't attempt
+
+## Calibration Examples
+
+### Example A: Narrow-but-Sound ML Paper
+
+**Paper Profile:**
+- Novel method for specific NLP task
+- Synthetic benchmark data only
+- Thorough ablations and error analysis
+- Authors acknowledge limited real-world validation
+- Code and data available
+
+**Calibrated Score: 6-7 (Weak Accept)**
+- Soundness: 3/4 (methodology rigorous within scope)
+- Originality: 3/4 (clear contribution)
+- Clarity: 3/4 (well-written)
+- Significance: 2/4 (limited by scope)
+
+**Reasoning:** Sound methodology + acknowledged limitations + reproducibility = floor of 6
+
+### Example B: Overstated Claims
+
+**Paper Profile:**
+- Interesting research question
+- Appropriate methods
+- But: Conclusions significantly overstate findings
+- Claims causation from correlational data
+- Generalizes beyond data support
+
+**Calibrated Score: 5 (Borderline)**
+- Soundness: 2/4 (overclaiming)
+- Originality: 3/4 (good question)
+- Clarity: 3/4 (well-written)
+- Significance: 2/4 (limited by overclaiming)
+
+**Reasoning:** Overclaiming is a Major issue (-2), methodology otherwise sound
+
+### Example C: Strong Work with Minor Issues
+
+**Paper Profile:**
+- Significant contribution
+- Rigorous methodology
+- Comprehensive experiments
+- Minor: Some figure labels small
+- Minor: A few citations missing
+
+**Calibrated Score: 8 (Accept)**
+- Soundness: 4/4
+- Originality: 3/4
+- Clarity: 3/4 (minor presentation issues)
+- Significance: 4/4
+
+**Reasoning:** Minor issues don't affect validity or interpretation
+
+## Common Calibration Errors
+
+### Over-Penalization Patterns
+
+| Error | Correct Approach |
+|-------|------------------|
+| -2 for synthetic data alone | Synthetic data is standard; only penalize if claimed to be real-world |
+| -2 for narrow scope | Scope affects Significance sub-score, not Soundness |
+| -2 for acknowledged limitations | -0.5 to -1 max for acknowledged issues |
+| Critical for missing baselines | Major at most; Critical only if no valid comparisons exist |
+
+### Under-Penalization Patterns
+
+| Error | Correct Approach |
+|-------|------------------|
+| Ignoring statistical issues | Inappropriate tests can invalidate conclusions |
+| Overlooking pseudoreplication | This is often a Critical issue |
+| Accepting overclaiming | Major issue even if methods are sound |
+| Missing ethics concerns | Should be flagged regardless of other quality |
+
+## Final Scoring Algorithm
+
+1. Start at 7 (default for competent submission)
+2. Add +1 to +3 for exceptional elements (novelty, rigor, impact)
+3. Subtract for issues based on severity
+4. Apply limitation acknowledgment bonus
+5. Apply reproducibility credit floor
+6. Verify score matches calibration examples
+7. Ensure sub-scores are consistent with overall

package/bin/skills/pptx-posters/SKILL.md

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+---
+name: pptx-posters
+description: "Create research posters using HTML/CSS that can be exported to PDF or PPTX. Use this skill ONLY when the user explicitly requests PowerPoint/PPTX poster format. For standard research posters, use latex-posters instead. This skill provides modern web-based poster design with responsive layouts and easy visual integration."
+allowed-tools: [Read, Write, Edit, Bash]
+---
+
+# PPTX Research Posters (HTML-Based)
+
+## Overview
+
+**⚠️ USE THIS SKILL ONLY WHEN USER EXPLICITLY REQUESTS PPTX/POWERPOINT POSTER FORMAT.**
+
+For standard research posters, use the **latex-posters** skill instead, which provides better typographic control and is the default for academic conferences.
+
+This skill creates research posters using HTML/CSS, which can then be exported to PDF or converted to PowerPoint format. The web-based approach offers:
+- Modern, responsive layouts
+- Easy integration of AI-generated visuals
+- Quick iteration and preview in browser
+- Export to PDF via browser print function
+- Conversion to PPTX if specifically needed
+
+## When to Use This Skill
+
+**ONLY use this skill when:**
+- User explicitly requests "PPTX poster", "PowerPoint poster", or "PPT poster"
+- User specifically asks for HTML-based poster
+- User needs to edit poster in PowerPoint after creation
+- LaTeX is not available or user requests non-LaTeX solution
+
+**DO NOT use this skill when:**
+- User asks for a "poster" without specifying format → Use latex-posters
+- User asks for "research poster" or "conference poster" → Use latex-posters
+- User mentions LaTeX, tikzposter, beamerposter, or baposter → Use latex-posters
+
+## AI-Powered Visual Element Generation
+
+**STANDARD WORKFLOW: Generate ALL major visual elements using AI before creating the HTML poster.**
+
+This is the recommended approach for creating visually compelling posters:
+1. Plan all visual elements needed (hero image, intro, methods, results, conclusions)
+2. Generate each element using scientific-schematics or Nano Banana Pro
+3. Assemble generated images in the HTML template
+4. Add text content around the visuals
+
+**Target: 60-70% of poster area should be AI-generated visuals, 30-40% text.**
+
+---
+
+### CRITICAL: Poster-Size Font Requirements
+
+**⚠️ ALL text within AI-generated visualizations MUST be poster-readable.**
+
+When generating graphics for posters, you MUST include font size specifications in EVERY prompt. Poster graphics are viewed from 4-6 feet away, so text must be LARGE.
+
+**MANDATORY prompt requirements for EVERY poster graphic:**
+
+```
+POSTER FORMAT REQUIREMENTS (STRICTLY ENFORCE):
+- ABSOLUTE MAXIMUM 3-4 elements per graphic (3 is ideal)
+- ABSOLUTE MAXIMUM 10 words total in the entire graphic
+- NO complex workflows with 5+ steps (split into 2-3 simple graphics instead)
+- NO multi-level nested diagrams (flatten to single level)
+- NO case studies with multiple sub-sections (one key point per case)
+- ALL text GIANT BOLD (80pt+ for labels, 120pt+ for key numbers)
+- High contrast ONLY (dark on white OR white on dark, NO gradients with text)
+- MANDATORY 50% white space minimum (half the graphic should be empty)
+- Thick lines only (5px+ minimum), large icons (200px+ minimum)
+- ONE SINGLE MESSAGE per graphic (not 3 related messages)
+```
+
+**⚠️ BEFORE GENERATING: Review your prompt and count elements**
+- If your description has 5+ items → STOP. Split into multiple graphics
+- If your workflow has 5+ stages → STOP. Show only 3-4 high-level steps
+- If your comparison has 4+ methods → STOP. Show only top 3 or Our vs Best Baseline
+
+**Example - WRONG (7-stage workflow):**
+```bash
+# ❌ Creates tiny unreadable text
+python scripts/generate_schematic.py "Drug discovery workflow: Stage 1 Target ID, Stage 2 Synthesis, Stage 3 Screening, Stage 4 Lead Opt, Stage 5 Validation, Stage 6 Clinical Trial, Stage 7 FDA Approval with metrics." -o figures/workflow.png
+```
+
+**Example - CORRECT (3 mega-stages):**
+```bash
+# ✅ Same content, simplified to readable poster format
+python scripts/generate_schematic.py "POSTER FORMAT for A0. ULTRA-SIMPLE 3-box workflow: 'DISCOVER' → 'VALIDATE' → 'APPROVE'. Each word in GIANT bold (120pt+). Thick arrows (10px). 60% white space. ONLY these 3 words. NO substeps. Readable from 12 feet." -o figures/workflow_simple.png
+```
+
+---
+
+### CRITICAL: Preventing Content Overflow
+
+**⚠️ POSTERS MUST NOT HAVE TEXT OR CONTENT CUT OFF AT EDGES.**
+
+**Prevention Rules:**
+
+**1. Limit Content Sections (MAXIMUM 5-6 sections):**
+```
+✅ GOOD - 5 sections with room to breathe:
+   - Title/Header
+   - Introduction/Problem
+   - Methods
+   - Results (1-2 key findings)
+   - Conclusions
+
+❌ BAD - 8+ sections crammed together
+```
+
+**2. Word Count Limits:**
+- **Per section**: 50-100 words maximum
+- **Total poster**: 300-800 words MAXIMUM
+- **If you have more content**: Cut it or make a handout
+
+---
+
+## Core Capabilities
+
+### 1. HTML/CSS Poster Design
+
+The HTML template (`assets/poster_html_template.html`) provides:
+- Fixed poster dimensions (36×48 inches = 2592×3456 pt)
+- Professional header with gradient styling
+- Three-column content layout
+- Block-based sections with modern styling
+- Footer with references and contact info
+
+### 2. Poster Structure
+
+**Standard Layout:**
+```
+┌─────────────────────────────────────────┐
+│  HEADER: Title, Authors, Hero Image     │
+├─────────────┬─────────────┬─────────────┤
+│ Introduction│   Results   │  Discussion │
+│             │             │             │
+│   Methods   │   (charts)  │ Conclusions │
+│             │             │             │
+│  (diagram)  │   (data)    │   (summary) │
+├─────────────┴─────────────┴─────────────┤
+│  FOOTER: References & Contact Info      │
+└─────────────────────────────────────────┘
+```
+
+### 3. Visual Integration
+
+Each section should prominently feature AI-generated visuals:
+
+**Hero Image (Header):**
+```html
+<img src="figures/hero.png" class="hero-image">
+```
+
+**Section Graphics:**
+```html
+<div class="block">
+  <h2 class="block-title">Methods</h2>
+  <div class="block-content">
+    <img src="figures/workflow.png" class="block-image">
+    <ul>
+      <li>Brief methodology point</li>
+    </ul>
+  </div>
+</div>
+```
+
+### 4. Generating Visual Elements
+
+**Before creating the HTML, generate all visual elements:**
+
+```bash
+# Create figures directory
+mkdir -p figures
+
+# Hero image - SIMPLE, impactful
+python scripts/generate_schematic.py "POSTER FORMAT for A0. Hero banner: '[TOPIC]' in HUGE text (120pt+). Dark blue gradient background. ONE iconic visual. Minimal text. Readable from 15 feet." -o figures/hero.png
+
+# Introduction visual - ONLY 3 elements
+python scripts/generate_schematic.py "POSTER FORMAT for A0. SIMPLE visual with ONLY 3 icons: [icon1] → [icon2] → [icon3]. ONE word labels (80pt+). 50% white space. Readable from 8 feet." -o figures/intro.png
+
+# Methods flowchart - ONLY 4 steps
+python scripts/generate_schematic.py "POSTER FORMAT for A0. SIMPLE flowchart with ONLY 4 boxes: STEP1 → STEP2 → STEP3 → STEP4. GIANT labels (100pt+). Thick arrows. 50% white space. NO sub-steps." -o figures/workflow.png
+
+# Results visualization - ONLY 3 bars
+python scripts/generate_schematic.py "POSTER FORMAT for A0. SIMPLE bar chart with ONLY 3 bars: BASELINE (70%), EXISTING (85%), OURS (95%). GIANT percentages ON bars (120pt+). NO axis, NO legend. 50% white space." -o figures/results.png
+
+# Conclusions - EXACTLY 3 key findings
+python scripts/generate_schematic.py "POSTER FORMAT for A0. EXACTLY 3 cards: '95%' (150pt) 'ACCURACY' (60pt), '2X' (150pt) 'FASTER' (60pt), checkmark 'READY' (60pt). 50% white space. NO other text." -o figures/conclusions.png
+```
+
+---
+
+## Workflow for PPTX Poster Creation
+
+### Stage 1: Planning
+
+1. **Confirm PPTX is explicitly requested**
+2. **Determine poster requirements:**
+   - Size: 36×48 inches (most common) or A0
+   - Orientation: Portrait (most common)
+3. **Develop content outline:**
+   - Identify 1-3 core messages
+   - Plan 3-5 visual elements
+   - Draft minimal text (300-800 words total)
+
+### Stage 2: Generate Visual Elements (AI-Powered)
+
+**CRITICAL: Generate SIMPLE figures with MINIMAL content.**
+
+```bash
+mkdir -p figures
+
+# Generate each element with POSTER FORMAT specifications
+# (See examples in Section 4 above)
+```
+
+### Stage 3: Create HTML Poster
+
+1. **Copy the template:**
+   ```bash
+   cp skills/pptx-posters/assets/poster_html_template.html poster.html
+   ```
+
+2. **Update content:**
+   - Replace placeholder title and authors
+   - Insert AI-generated images
+   - Add minimal supporting text
+   - Update references and contact info
+
+3. **Preview in browser:**
+   ```bash
+   open poster.html  # macOS
+   # or
+   xdg-open poster.html  # Linux
+   ```
+
+### Stage 4: Export to PDF
+
+**Browser Print Method:**
+1. Open poster.html in Chrome or Firefox
+2. Print (Cmd/Ctrl + P)
+3. Select "Save as PDF"
+4. Set paper size to match poster dimensions
+5. Remove margins
+6. Enable "Background graphics"
+
+**Command Line (if Chrome available):**
+```bash
+# Chrome headless PDF export
+google-chrome --headless --print-to-pdf=poster.pdf \
+  --print-to-pdf-no-header \
+  --no-margins \
+  poster.html
+```
+
+### Stage 5: Convert to PPTX (If Required)
+
+**Option 1: PDF to PPTX conversion**
+```bash
+# Using LibreOffice
+libreoffice --headless --convert-to pptx poster.pdf
+
+# Or use online converters for simple cases
+```
+
+**Option 2: Direct PPTX creation with python-pptx**
+```python
+from pptx import Presentation
+from pptx.util import Inches, Pt
+
+prs = Presentation()
+prs.slide_width = Inches(48)
+prs.slide_height = Inches(36)
+
+slide = prs.slides.add_slide(prs.slide_layouts[6])  # Blank
+
+# Add images from figures/
+slide.shapes.add_picture("figures/hero.png", Inches(0), Inches(0), width=Inches(48))
+# ... add other elements
+
+prs.save("poster.pptx")
+```
+
+---
+
+## HTML Template Structure
+
+The provided template (`assets/poster_html_template.html`) includes:
+
+### CSS Variables for Customization
+
+```css
+/* Poster dimensions */
+body {
+  width: 2592pt;   /* 36 inches */
+  height: 3456pt;  /* 48 inches */
+}
+
+/* Color scheme - customize these */
+.header {
+  background: linear-gradient(135deg, #1a365d 0%, #2b6cb0 50%, #3182ce 100%);
+}
+
+/* Typography */
+.poster-title { font-size: 108pt; }
+.authors { font-size: 48pt; }
+.block-title { font-size: 52pt; }
+.block-content { font-size: 34pt; }
+```
+
+### Key Classes
+
+| Class | Purpose | Font Size |
+|-------|---------|-----------|
+| `.poster-title` | Main title | 108pt |
+| `.authors` | Author names | 48pt |
+| `.affiliations` | Institutions | 38pt |
+| `.block-title` | Section headers | 52pt |
+| `.block-content` | Body text | 34pt |
+| `.key-finding` | Highlight box | 36pt |
+
+---
+
+## Quality Checklist
+
+### Step 0: Pre-Generation Review (MANDATORY)
+
+**For EACH planned graphic, verify:**
+- [ ] Can describe in 3-4 items or less? (NOT 5+)
+- [ ] Is it a simple workflow (3-4 steps, NOT 7+)?
+- [ ] Can describe all text in 10 words or less?
+- [ ] Does it convey ONE message (not multiple)?
+
+**Reject these patterns:**
+- ❌ "7-stage workflow" → Simplify to "3 mega-stages"
+- ❌ "Multiple case studies" → One case per graphic
+- ❌ "Timeline 2015-2024 annual" → "ONLY 3 key years"
+- ❌ "Compare 6 methods" → "ONLY 2: ours vs best"
+
+### Step 2b: Post-Generation Review (MANDATORY)
+
+**For EACH generated figure at 25% zoom:**
+
+**✅ PASS criteria (ALL must be true):**
+- [ ] Can read ALL text clearly
+- [ ] Count: 3-4 elements or fewer
+- [ ] White space: 50%+ empty
+- [ ] Understand in 2 seconds
+- [ ] NOT a complex 5+ stage workflow
+- [ ] NOT multiple nested sections
+
+**❌ FAIL criteria (regenerate if ANY true):**
+- [ ] Text small/hard to read → Regenerate with "150pt+"
+- [ ] More than 4 elements → Regenerate "ONLY 3 elements"
+- [ ] Less than 50% white space → Regenerate "60% white space"
+- [ ] Complex multi-stage → SPLIT into 2-3 graphics
+- [ ] Multiple cases cramped → SPLIT into separate graphics
+
+### After Export
+
+- [ ] NO content cut off at ANY of the 4 edges (check carefully)
+- [ ] All images display correctly
+- [ ] Colors render as expected
+- [ ] Text readable at 25% scale
+- [ ] Graphics look SIMPLE (not like complex 7-stage workflows)
+
+---
+
+## Common Pitfalls to Avoid
+
+**AI-Generated Graphics Mistakes:**
+- ❌ Too many elements (10+ items) → Keep to 3-5 max
+- ❌ Text too small → Specify "GIANT (100pt+)" in prompts
+- ❌ No white space → Add "50% white space" to every prompt
+- ❌ Complex flowcharts (8+ steps) → Limit to 4-5 steps
+
+**HTML/Export Mistakes:**
+- ❌ Content exceeding poster dimensions → Check overflow in browser
+- ❌ Missing background graphics in PDF → Enable in print settings
+- ❌ Wrong paper size in PDF → Match poster dimensions exactly
+- ❌ Low-resolution images → Use 300 DPI minimum
+
+**Content Mistakes:**
+- ❌ Too much text (over 1000 words) → Cut to 300-800 words
+- ❌ Too many sections (7+) → Consolidate to 5-6
+- ❌ No clear visual hierarchy → Make key findings prominent
+
+---
+
+## Integration with Other Skills
+
+This skill works with:
+- **Scientific Schematics**: Generate all poster diagrams and flowcharts
+- **Generate Image / Nano Banana Pro**: Create stylized graphics and hero images
+- **LaTeX Posters**: DEFAULT skill for poster creation (use this instead unless PPTX explicitly requested)
+
+---
+
+## Template Assets
+
+Available in `assets/` directory:
+
+- `poster_html_template.html`: Main HTML poster template (36×48 inches)
+- `poster_quality_checklist.md`: Pre-submission validation checklist
+
+## References
+
+Available in `references/` directory:
+
+- `poster_content_guide.md`: Content organization and writing guidelines
+- `poster_design_principles.md`: Typography, color theory, and visual hierarchy
+- `poster_layout_design.md`: Layout principles and grid systems