@synsci/cli-darwin-x64 1.1.97 → 1.1.99

package/bin/skills/scientific-schematics/SKILL.md

@@ -1,615 +0,0 @@
----
-name: scientific-schematics
-description: "Create publication-quality scientific diagrams using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations."
-allowed-tools: [Read, Write, Edit, Bash]
----
-
-# Scientific Schematics and Diagrams
-
-## Overview
-
-Scientific schematics and diagrams transform complex concepts into clear visual representations for publication. **This skill uses Nano Banana Pro AI for diagram generation with Gemini 3 Pro quality review.**
-
-**How it works:**
-- Describe your diagram in natural language
-- Nano Banana Pro generates publication-quality images automatically
-- **Gemini 3 Pro reviews quality** against document-type thresholds
-- **Smart iteration**: Only regenerates if quality is below threshold
-- Publication-ready output in minutes
-- No coding, templates, or manual drawing required
-
-**Quality Thresholds by Document Type:**
-| Document Type | Threshold | Description |
-|---------------|-----------|-------------|
-| journal | 8.5/10 | Nature, Science, peer-reviewed journals |
-| conference | 8.0/10 | Conference papers |
-| thesis | 8.0/10 | Dissertations, theses |
-| grant | 8.0/10 | Grant proposals |
-| preprint | 7.5/10 | arXiv, bioRxiv, etc. |
-| report | 7.5/10 | Technical reports |
-| poster | 7.0/10 | Academic posters |
-| presentation | 6.5/10 | Slides, talks |
-| default | 7.5/10 | General purpose |
-
-**Simply describe what you want, and Nano Banana Pro creates it.** All diagrams are stored in the figures/ subfolder and referenced in papers/posters.
-
-## Quick Start: Generate Any Diagram
-
-Create any scientific diagram by simply describing it. Nano Banana Pro handles everything automatically with **smart iteration**:
-
-```bash
-# Generate for journal paper (highest quality threshold: 8.5/10)
-python scripts/generate_schematic.py "CONSORT participant flow diagram with 500 screened, 150 excluded, 350 randomized" -o figures/consort.png --doc-type journal
-
-# Generate for presentation (lower threshold: 6.5/10 - faster)
-python scripts/generate_schematic.py "Transformer encoder-decoder architecture showing multi-head attention" -o figures/transformer.png --doc-type presentation
-
-# Generate for poster (moderate threshold: 7.0/10)
-python scripts/generate_schematic.py "MAPK signaling pathway from EGFR to gene transcription" -o figures/mapk_pathway.png --doc-type poster
-
-# Custom max iterations (max 2)
-python scripts/generate_schematic.py "Complex circuit diagram with op-amp, resistors, and capacitors" -o figures/circuit.png --iterations 2 --doc-type journal
-```
-
-**What happens behind the scenes:**
-1. **Generation 1**: Nano Banana Pro creates initial image following scientific diagram best practices
-2. **Review 1**: **Gemini 3 Pro** evaluates quality against document-type threshold
-3. **Decision**: If quality >= threshold → **DONE** (no more iterations needed!)
-4. **If below threshold**: Improved prompt based on critique, regenerate
-5. **Repeat**: Until quality meets threshold OR max iterations reached
-
-**Smart Iteration Benefits:**
-- ✅ Saves API calls if first generation is good enough
-- ✅ Higher quality standards for journal papers
-- ✅ Faster turnaround for presentations/posters
-- ✅ Appropriate quality for each use case
-
-**Output**: Versioned images plus a detailed review log with quality scores, critiques, and early-stop information.
-
-### Configuration
-
-Set your OpenRouter API key:
-```bash
-export OPENROUTER_API_KEY='your_api_key_here'
-```
-
-Get an API key at: https://openrouter.ai/keys
-
-### AI Generation Best Practices
-
-**Effective Prompts for Scientific Diagrams:**
-
-✓ **Good prompts** (specific, detailed):
-- "CONSORT flowchart showing participant flow from screening (n=500) through randomization to final analysis"
-- "Transformer neural network architecture with encoder stack on left, decoder stack on right, showing multi-head attention and cross-attention connections"
-- "Biological signaling cascade: EGFR receptor → RAS → RAF → MEK → ERK → nucleus, with phosphorylation steps labeled"
-- "Block diagram of IoT system: sensors → microcontroller → WiFi module → cloud server → mobile app"
-
-✗ **Avoid vague prompts**:
-- "Make a flowchart" (too generic)
-- "Neural network" (which type? what components?)
-- "Pathway diagram" (which pathway? what molecules?)
-
-**Key elements to include:**
-- **Type**: Flowchart, architecture diagram, pathway, circuit, etc.
-- **Components**: Specific elements to include
-- **Flow/Direction**: How elements connect (left-to-right, top-to-bottom)
-- **Labels**: Key annotations or text to include
-- **Style**: Any specific visual requirements
-
-**Scientific Quality Guidelines** (automatically applied):
-- Clean white/light background
-- High contrast for readability
-- Clear, readable labels (minimum 10pt)
-- Professional typography (sans-serif fonts)
-- Colorblind-friendly colors (Okabe-Ito palette)
-- Proper spacing to prevent crowding
-- Scale bars, legends, axes where appropriate
-
-## When to Use This Skill
-
-This skill should be used when:
-- Creating neural network architecture diagrams (Transformers, CNNs, RNNs, etc.)
-- Illustrating system architectures and data flow diagrams
-- Drawing methodology flowcharts for study design (CONSORT, PRISMA)
-- Visualizing algorithm workflows and processing pipelines
-- Creating circuit diagrams and electrical schematics
-- Depicting biological pathways and molecular interactions
-- Generating network topologies and hierarchical structures
-- Illustrating conceptual frameworks and theoretical models
-- Designing block diagrams for technical papers
-
-## How to Use This Skill
-
-**Simply describe your diagram in natural language.** Nano Banana Pro generates it automatically:
-
-```bash
-python scripts/generate_schematic.py "your diagram description" -o output.png
-```
-
-**That's it!** The AI handles:
-- ✓ Layout and composition
-- ✓ Labels and annotations
-- ✓ Colors and styling
-- ✓ Quality review and refinement
-- ✓ Publication-ready output
-
-**Works for all diagram types:**
-- Flowcharts (CONSORT, PRISMA, etc.)
-- Neural network architectures
-- Biological pathways
-- Circuit diagrams
-- System architectures
-- Block diagrams
-- Any scientific visualization
-
-**No coding, no templates, no manual drawing required.**
-
----
-
-# AI Generation Mode (Nano Banana Pro + Gemini 3 Pro Review)
-
-## Smart Iterative Refinement Workflow
-
-The AI generation system uses **smart iteration** - it only regenerates if quality is below the threshold for your document type:
-
-### How Smart Iteration Works
-
-```
-┌─────────────────────────────────────────────────────┐
-│  1. Generate image with Nano Banana Pro             │
-│                    ↓                                │
-│  2. Review quality with Gemini 3 Pro                │
-│                    ↓                                │
-│  3. Score >= threshold?                             │
-│       YES → DONE! (early stop)                      │
-│       NO  → Improve prompt, go to step 1            │
-│                    ↓                                │
-│  4. Repeat until quality met OR max iterations      │
-└─────────────────────────────────────────────────────┘
-```
-
-### Iteration 1: Initial Generation
-**Prompt Construction:**
-```
-Scientific diagram guidelines + User request
-```
-
-**Output:** `diagram_v1.png`
-
-### Quality Review by Gemini 3 Pro
-
-Gemini 3 Pro evaluates the diagram on:
-1. **Scientific Accuracy** (0-2 points) - Correct concepts, notation, relationships
-2. **Clarity and Readability** (0-2 points) - Easy to understand, clear hierarchy
-3. **Label Quality** (0-2 points) - Complete, readable, consistent labels
-4. **Layout and Composition** (0-2 points) - Logical flow, balanced, no overlaps
-5. **Professional Appearance** (0-2 points) - Publication-ready quality
-
-**Example Review Output:**
-```
-SCORE: 8.0
-
-STRENGTHS:
-- Clear flow from top to bottom
-- All phases properly labeled
-- Professional typography
-
-ISSUES:
-- Participant counts slightly small
-- Minor overlap on exclusion box
-
-VERDICT: ACCEPTABLE (for poster, threshold 7.0)
-```
-
-### Decision Point: Continue or Stop?
-
-| If Score... | Action |
-|-------------|--------|
-| >= threshold | **STOP** - Quality is good enough for this document type |
-| < threshold | Continue to next iteration with improved prompt |
-
-**Example:**
-- For a **poster** (threshold 7.0): Score of 7.5 → **DONE after 1 iteration!**
-- For a **journal** (threshold 8.5): Score of 7.5 → Continue improving
-
-### Subsequent Iterations (Only If Needed)
-
-If quality is below threshold, the system:
-1. Extracts specific issues from Gemini 3 Pro's review
-2. Enhances the prompt with improvement instructions
-3. Regenerates with Nano Banana Pro
-4. Reviews again with Gemini 3 Pro
-5. Repeats until threshold met or max iterations reached
-
-### Review Log
-All iterations are saved with a JSON review log that includes early-stop information:
-```json
-{
-  "user_prompt": "CONSORT participant flow diagram...",
-  "doc_type": "poster",
-  "quality_threshold": 7.0,
-  "iterations": [
-    {
-      "iteration": 1,
-      "image_path": "figures/consort_v1.png",
-      "score": 7.5,
-      "needs_improvement": false,
-      "critique": "SCORE: 7.5\nSTRENGTHS:..."
-    }
-  ],
-  "final_score": 7.5,
-  "early_stop": true,
-  "early_stop_reason": "Quality score 7.5 meets threshold 7.0 for poster"
-}
-```
-
-**Note:** With smart iteration, you may see only 1 iteration instead of the full 2 if quality is achieved early!
-
-## Advanced AI Generation Usage
-
-### Python API
-
-```python
-from scripts.generate_schematic_ai import ScientificSchematicGenerator
-
-# Initialize generator
-generator = ScientificSchematicGenerator(
-    api_key="your_openrouter_key",
-    verbose=True
-)
-
-# Generate with iterative refinement (max 2 iterations)
-results = generator.generate_iterative(
-    user_prompt="Transformer architecture diagram",
-    output_path="figures/transformer.png",
-    iterations=2
-)
-
-# Access results
-print(f"Final score: {results['final_score']}/10")
-print(f"Final image: {results['final_image']}")
-
-# Review individual iterations
-for iteration in results['iterations']:
-    print(f"Iteration {iteration['iteration']}: {iteration['score']}/10")
-    print(f"Critique: {iteration['critique']}")
-```
-
-### Command-Line Options
-
-```bash
-# Basic usage (default threshold 7.5/10)
-python scripts/generate_schematic.py "diagram description" -o output.png
-
-# Specify document type for appropriate quality threshold
-python scripts/generate_schematic.py "diagram" -o out.png --doc-type journal      # 8.5/10
-python scripts/generate_schematic.py "diagram" -o out.png --doc-type conference   # 8.0/10
-python scripts/generate_schematic.py "diagram" -o out.png --doc-type poster       # 7.0/10
-python scripts/generate_schematic.py "diagram" -o out.png --doc-type presentation # 6.5/10
-
-# Custom max iterations (1-2)
-python scripts/generate_schematic.py "complex diagram" -o diagram.png --iterations 2
-
-# Verbose output (see all API calls and reviews)
-python scripts/generate_schematic.py "flowchart" -o flow.png -v
-
-# Provide API key via flag
-python scripts/generate_schematic.py "diagram" -o out.png --api-key "sk-or-v1-..."
-
-# Combine options
-python scripts/generate_schematic.py "neural network" -o nn.png --doc-type journal --iterations 2 -v
-```
-
-### Prompt Engineering Tips
-
-**1. Be Specific About Layout:**
-```
-✓ "Flowchart with vertical flow, top to bottom"
-✓ "Architecture diagram with encoder on left, decoder on right"
-✓ "Circular pathway diagram with clockwise flow"
-```
-
-**2. Include Quantitative Details:**
-```
-✓ "Neural network with input layer (784 nodes), hidden layer (128 nodes), output (10 nodes)"
-✓ "Flowchart showing n=500 screened, n=150 excluded, n=350 randomized"
-✓ "Circuit with 1kΩ resistor, 10µF capacitor, 5V source"
-```
-
-**3. Specify Visual Style:**
-```
-✓ "Minimalist block diagram with clean lines"
-✓ "Detailed biological pathway with protein structures"
-✓ "Technical schematic with engineering notation"
-```
-
-**4. Request Specific Labels:**
-```
-✓ "Label all arrows with activation/inhibition"
-✓ "Include layer dimensions in each box"
-✓ "Show time progression with timestamps"
-```
-
-**5. Mention Color Requirements:**
-```
-✓ "Use colorblind-friendly colors"
-✓ "Grayscale-compatible design"
-✓ "Color-code by function: blue for input, green for processing, red for output"
-```
-
-## AI Generation Examples
-
-### Example 1: CONSORT Flowchart
-```bash
-python scripts/generate_schematic.py \
-  "CONSORT participant flow diagram for randomized controlled trial. \
-   Start with 'Assessed for eligibility (n=500)' at top. \
-   Show 'Excluded (n=150)' with reasons: age<18 (n=80), declined (n=50), other (n=20). \
-   Then 'Randomized (n=350)' splits into two arms: \
-   'Treatment group (n=175)' and 'Control group (n=175)'. \
-   Each arm shows 'Lost to follow-up' (n=15 and n=10). \
-   End with 'Analyzed' (n=160 and n=165). \
-   Use blue boxes for process steps, orange for exclusion, green for final analysis." \
-  -o figures/consort.png
-```
-
-### Example 2: Neural Network Architecture
-```bash
-python scripts/generate_schematic.py \
-  "Transformer encoder-decoder architecture diagram. \
-   Left side: Encoder stack with input embedding, positional encoding, \
-   multi-head self-attention, add & norm, feed-forward, add & norm. \
-   Right side: Decoder stack with output embedding, positional encoding, \
-   masked self-attention, add & norm, cross-attention (receiving from encoder), \
-   add & norm, feed-forward, add & norm, linear & softmax. \
-   Show cross-attention connection from encoder to decoder with dashed line. \
-   Use light blue for encoder, light red for decoder. \
-   Label all components clearly." \
-  -o figures/transformer.png --iterations 2
-```
-
-### Example 3: Biological Pathway
-```bash
-python scripts/generate_schematic.py \
-  "MAPK signaling pathway diagram. \
-   Start with EGFR receptor at cell membrane (top). \
-   Arrow down to RAS (with GTP label). \
-   Arrow to RAF kinase. \
-   Arrow to MEK kinase. \
-   Arrow to ERK kinase. \
-   Final arrow to nucleus showing gene transcription. \
-   Label each arrow with 'phosphorylation' or 'activation'. \
-   Use rounded rectangles for proteins, different colors for each. \
-   Include membrane boundary line at top." \
-  -o figures/mapk_pathway.png
-```
-
-### Example 4: System Architecture
-```bash
-python scripts/generate_schematic.py \
-  "IoT system architecture block diagram. \
-   Bottom layer: Sensors (temperature, humidity, motion) in green boxes. \
-   Middle layer: Microcontroller (ESP32) in blue box. \
-   Connections to WiFi module (orange box) and Display (purple box). \
-   Top layer: Cloud server (gray box) connected to mobile app (light blue box). \
-   Show data flow arrows between all components. \
-   Label connections with protocols: I2C, UART, WiFi, HTTPS." \
-  -o figures/iot_architecture.png
-```
-
----
-
-## Command-Line Usage
-
-The main entry point for generating scientific schematics:
-
-```bash
-# Basic usage
-python scripts/generate_schematic.py "diagram description" -o output.png
-
-# Custom iterations (max 2)
-python scripts/generate_schematic.py "complex diagram" -o diagram.png --iterations 2
-
-# Verbose mode
-python scripts/generate_schematic.py "diagram" -o out.png -v
-```
-
-**Note:** The Nano Banana Pro AI generation system includes automatic quality review in its iterative refinement process. Each iteration is evaluated for scientific accuracy, clarity, and accessibility.
-
-## Best Practices Summary
-
-### Design Principles
-
-1. **Clarity over complexity** - Simplify, remove unnecessary elements
-2. **Consistent styling** - Use templates and style files
-3. **Colorblind accessibility** - Use Okabe-Ito palette, redundant encoding
-4. **Appropriate typography** - Sans-serif fonts, minimum 7-8 pt
-5. **Vector format** - Always use PDF/SVG for publication
-
-### Technical Requirements
-
-1. **Resolution** - Vector preferred, or 300+ DPI for raster
-2. **File format** - PDF for LaTeX, SVG for web, PNG as fallback
-3. **Color space** - RGB for digital, CMYK for print (convert if needed)
-4. **Line weights** - Minimum 0.5 pt, typical 1-2 pt
-5. **Text size** - 7-8 pt minimum at final size
-
-### Integration Guidelines
-
-1. **Include in LaTeX** - Use `\includegraphics{}` for generated images
-2. **Caption thoroughly** - Describe all elements and abbreviations
-3. **Reference in text** - Explain diagram in narrative flow
-4. **Maintain consistency** - Same style across all figures in paper
-5. **Version control** - Keep prompts and generated images in repository
-
-## Troubleshooting Common Issues
-
-### AI Generation Issues
-
-**Problem**: Overlapping text or elements
-- **Solution**: AI generation automatically handles spacing
-- **Solution**: Increase iterations: `--iterations 2` for better refinement
-
-**Problem**: Elements not connecting properly
-- **Solution**: Make your prompt more specific about connections and layout
-- **Solution**: Increase iterations for better refinement
-
-### Image Quality Issues
-
-**Problem**: Export quality poor
-- **Solution**: AI generation produces high-quality images automatically
-- **Solution**: Increase iterations for better results: `--iterations 2`
-
-**Problem**: Elements overlap after generation
-- **Solution**: AI generation automatically handles spacing
-- **Solution**: Increase iterations: `--iterations 2` for better refinement
-- **Solution**: Make your prompt more specific about layout and spacing requirements
-
-### Quality Check Issues
-
-**Problem**: False positive overlap detection
-- **Solution**: Adjust threshold: `detect_overlaps(image_path, threshold=0.98)`
-- **Solution**: Manually review flagged regions in visual report
-
-**Problem**: Generated image quality is low
-- **Solution**: AI generation produces high-quality images by default
-- **Solution**: Increase iterations for better results: `--iterations 2`
-
-**Problem**: Colorblind simulation shows poor contrast
-- **Solution**: Switch to Okabe-Ito palette explicitly in code
-- **Solution**: Add redundant encoding (shapes, patterns, line styles)
-- **Solution**: Increase color saturation and lightness differences
-
-**Problem**: High-severity overlaps detected
-- **Solution**: Review overlap_report.json for exact positions
-- **Solution**: Increase spacing in those specific regions
-- **Solution**: Re-run with adjusted parameters and verify again
-
-**Problem**: Visual report generation fails
-- **Solution**: Check Pillow and matplotlib installations
-- **Solution**: Ensure image file is readable: `Image.open(path).verify()`
-- **Solution**: Check sufficient disk space for report generation
-
-### Accessibility Problems
-
-**Problem**: Colors indistinguishable in grayscale
-- **Solution**: Run accessibility checker: `verify_accessibility(image_path)`
-- **Solution**: Add patterns, shapes, or line styles for redundancy
-- **Solution**: Increase contrast between adjacent elements
-
-**Problem**: Text too small when printed
-- **Solution**: Run resolution validator: `validate_resolution(image_path)`
-- **Solution**: Design at final size, use minimum 7-8 pt fonts
-- **Solution**: Check physical dimensions in resolution report
-
-**Problem**: Accessibility checks consistently fail
-- **Solution**: Review accessibility_report.json for specific failures
-- **Solution**: Increase color contrast by at least 20%
-- **Solution**: Test with actual grayscale conversion before finalizing
-
-## Resources and References
-
-### Detailed References
-
-Load these files for comprehensive information on specific topics:
-
-- **`references/diagram_types.md`** - Catalog of scientific diagram types with examples
-- **`references/best_practices.md`** - Publication standards and accessibility guidelines
-
-### External Resources
-
-**Python Libraries**
-- Schemdraw Documentation: https://schemdraw.readthedocs.io/
-- NetworkX Documentation: https://networkx.org/documentation/
-- Matplotlib Documentation: https://matplotlib.org/
-
-**Publication Standards**
-- Nature Figure Guidelines: https://www.nature.com/nature/for-authors/final-submission
-- Science Figure Guidelines: https://www.science.org/content/page/instructions-preparing-initial-manuscript
-- CONSORT Diagram: http://www.consort-statement.org/consort-statement/flow-diagram
-
-## Integration with Other Skills
-
-This skill works synergistically with:
-
-- **Scientific Writing** - Diagrams follow figure best practices
-- **Scientific Visualization** - Shares color palettes and styling
-- **LaTeX Posters** - Generate diagrams for poster presentations
-- **Research Grants** - Methodology diagrams for proposals
-- **Peer Review** - Evaluate diagram clarity and accessibility
-
-## Quick Reference Checklist
-
-Before submitting diagrams, verify:
-
-### Visual Quality
-- [ ] High-quality image format (PNG from AI generation)
-- [ ] No overlapping elements (AI handles automatically)
-- [ ] Adequate spacing between all components (AI optimizes)
-- [ ] Clean, professional alignment
-- [ ] All arrows connect properly to intended targets
-
-### Accessibility
-- [ ] Colorblind-safe palette (Okabe-Ito) used
-- [ ] Works in grayscale (tested with accessibility checker)
-- [ ] Sufficient contrast between elements (verified)
-- [ ] Redundant encoding where appropriate (shapes + colors)
-- [ ] Colorblind simulation passes all checks
-
-### Typography and Readability
-- [ ] Text minimum 7-8 pt at final size
-- [ ] All elements labeled clearly and completely
-- [ ] Consistent font family and sizing
-- [ ] No text overlaps or cutoffs
-- [ ] Units included where applicable
-
-### Publication Standards
-- [ ] Consistent styling with other figures in manuscript
-- [ ] Comprehensive caption written with all abbreviations defined
-- [ ] Referenced appropriately in manuscript text
-- [ ] Meets journal-specific dimension requirements
-- [ ] Exported in required format for journal (PDF/EPS/TIFF)
-
-### Quality Verification (Required)
-- [ ] Ran `run_quality_checks()` and achieved PASS status
-- [ ] Reviewed overlap detection report (zero high-severity overlaps)
-- [ ] Passed accessibility verification (grayscale and colorblind)
-- [ ] Resolution validated at target DPI (300+ for print)
-- [ ] Visual quality report generated and reviewed
-- [ ] All quality reports saved with figure files
-
-### Documentation and Version Control
-- [ ] Source files (.tex, .py) saved for future revision
-- [ ] Quality reports archived in `quality_reports/` directory
-- [ ] Configuration parameters documented (colors, spacing, sizes)
-- [ ] Git commit includes source, output, and quality reports
-- [ ] README or comments explain how to regenerate figure
-
-### Final Integration Check
-- [ ] Figure displays correctly in compiled manuscript
-- [ ] Cross-references work (`\ref{}` points to correct figure)
-- [ ] Figure number matches text citations
-- [ ] Caption appears on correct page relative to figure
-- [ ] No compilation warnings or errors related to figure
-
-## Environment Setup
-
-```bash
-# Required
-export OPENROUTER_API_KEY='your_api_key_here'
-
-# Get key at: https://openrouter.ai/keys
-```
-
-## Getting Started
-
-**Simplest possible usage:**
-```bash
-python scripts/generate_schematic.py "your diagram description" -o output.png
-```
-
----
-
-Use this skill to create clear, accessible, publication-quality diagrams that effectively communicate complex scientific concepts. The AI-powered workflow with iterative refinement ensures diagrams meet professional standards.
-

package/bin/skills/scientific-schematics/example_usage.sh

@@ -1,89 +0,0 @@
-#!/bin/bash
-# Example usage of AI-powered scientific schematic generation
-# 
-# Prerequisites:
-# 1. Set OPENROUTER_API_KEY environment variable
-# 2. Ensure Python 3.10+ is installed
-# 3. Install requests: pip install requests
-
-set -e
-
-echo "=========================================="
-echo "Scientific Schematics - AI Generation"
-echo "Example Usage Demonstrations"
-echo "=========================================="
-echo ""
-
-# Check for API key
-if [ -z "$OPENROUTER_API_KEY" ]; then
-    echo "❌ Error: OPENROUTER_API_KEY environment variable not set"
-    echo ""
-    echo "Get an API key at: https://openrouter.ai/keys"
-    echo "Then set it with: export OPENROUTER_API_KEY='your_key'"
-    exit 1
-fi
-
-echo "✓ OPENROUTER_API_KEY is set"
-echo ""
-
-# Create output directory
-mkdir -p figures
-echo "✓ Created figures/ directory"
-echo ""
-
-# Example 1: Simple flowchart
-echo "Example 1: CONSORT Flowchart"
-echo "----------------------------"
-python scripts/generate_schematic.py \
-  "CONSORT participant flow diagram. Assessed for eligibility (n=500). Excluded (n=150) with reasons: age<18 (n=80), declined (n=50), other (n=20). Randomized (n=350) into Treatment (n=175) and Control (n=175). Lost to follow-up: 15 and 10. Final analysis: 160 and 165." \
-  -o figures/consort_example.png \
-  --iterations 2
-
-echo ""
-echo "✓ Generated: figures/consort_example.png"
-echo "  - Also created: consort_example_v1.png, v2.png, v3.png"
-echo "  - Review log: consort_example_review_log.json"
-echo ""
-
-# Example 2: Neural network (shorter for demo)
-echo "Example 2: Simple Neural Network"
-echo "--------------------------------"
-python scripts/generate_schematic.py \
-  "Simple feedforward neural network diagram. Input layer with 4 nodes, hidden layer with 6 nodes, output layer with 2 nodes. Show all connections. Label layers clearly." \
-  -o figures/neural_net_example.png \
-  --iterations 2
-
-echo ""
-echo "✓ Generated: figures/neural_net_example.png"
-echo ""
-
-# Example 3: Biological pathway (minimal)
-echo "Example 3: Signaling Pathway"
-echo "---------------------------"
-python scripts/generate_schematic.py \
-  "Simple signaling pathway: Receptor → Kinase A → Kinase B → Transcription Factor → Gene. Show arrows with 'activation' labels. Use different colors for each component." \
-  -o figures/pathway_example.png \
-  --iterations 2
-
-echo ""
-echo "✓ Generated: figures/pathway_example.png"
-echo ""
-
-echo "=========================================="
-echo "All examples completed successfully!"
-echo "=========================================="
-echo ""
-echo "Generated files in figures/:"
-ls -lh figures/*example*.png 2>/dev/null || echo "  (Files will appear after running with valid API key)"
-echo ""
-echo "Review the review_log.json files to see:"
-echo "  - Quality scores for each iteration"
-echo "  - Detailed critiques and suggestions"
-echo "  - Improvement progression"
-echo ""
-echo "Next steps:"
-echo "  1. View the generated images"
-echo "  2. Review the quality scores in *_review_log.json"
-echo "  3. Try your own prompts!"
-echo ""
-