feat: Add Studio UI, intake system, and extractor improvements
Dashboard: - Add Studio page with drag-drop model upload and Claude chat - Add intake system for study creation workflow - Improve session manager and context builder - Add intake API routes and frontend components Optimization Engine: - Add CLI module for command-line operations - Add intake module for study preprocessing - Add validation module with gate checks - Improve Zernike extractor documentation - Update spec models with better validation - Enhance solve_simulation robustness Documentation: - Add ATOMIZER_STUDIO.md planning doc - Add ATOMIZER_UX_SYSTEM.md for UX patterns - Update extractor library docs - Add study-readme-generator skill Tools: - Add test scripts for extraction validation - Add Zernike recentering test Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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.claude/skills/modules/study-readme-generator.md
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# Study README Generator Skill
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**Skill ID**: STUDY_README_GENERATOR
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**Version**: 1.0
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**Purpose**: Generate intelligent, context-aware README.md files for optimization studies
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## When to Use
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This skill is invoked automatically during the study intake workflow when:
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1. A study moves from `introspected` to `configured` status
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2. User explicitly requests README generation
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3. Finalizing a study from the inbox
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## Input Context
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The README generator receives:
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```json
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{
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"study_name": "bracket_mass_opt_v1",
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"topic": "Brackets",
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"description": "User's description from intake form",
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"spec": { /* Full AtomizerSpec v2.0 */ },
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"introspection": {
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"expressions": [...],
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"mass_kg": 1.234,
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"solver_type": "NX_Nastran"
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},
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"context_files": {
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"goals.md": "User's goals markdown content",
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"notes.txt": "Any additional notes"
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}
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}
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```
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## Output Format
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Generate a README.md with these sections:
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### 1. Title & Overview
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```markdown
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# {Study Name}
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**Topic**: {Topic}
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**Created**: {Date}
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**Status**: {Status}
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{One paragraph executive summary of the optimization goal}
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```
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### 2. Engineering Problem
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```markdown
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## Engineering Problem
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{Describe the physical problem being solved}
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### Model Description
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- **Geometry**: {Describe the part/assembly}
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- **Material**: {If known from introspection}
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- **Baseline Mass**: {mass_kg} kg
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### Loading Conditions
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{Describe loads and boundary conditions if available}
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```
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### 3. Optimization Formulation
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```markdown
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## Optimization Formulation
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### Design Variables ({count})
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| Variable | Expression | Range | Units |
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|----------|------------|-------|-------|
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| {name} | {expr_name} | [{min}, {max}] | {units} |
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### Objectives ({count})
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| Objective | Direction | Weight | Source |
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|-----------|-----------|--------|--------|
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| {name} | {direction} | {weight} | {extractor} |
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### Constraints ({count})
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| Constraint | Condition | Threshold | Type |
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|------------|-----------|-----------|------|
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| {name} | {operator} | {threshold} | {type} |
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```
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### 4. Methodology
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```markdown
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## Methodology
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### Algorithm
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- **Primary**: {algorithm_type}
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- **Max Trials**: {max_trials}
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- **Surrogate**: {if enabled}
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### Physics Extraction
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{Describe extractors used}
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### Convergence Criteria
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{Describe stopping conditions}
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```
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### 5. Expected Outcomes
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```markdown
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## Expected Outcomes
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Based on the optimization setup:
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- Expected improvement: {estimate if baseline available}
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- Key trade-offs: {identify from objectives/constraints}
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- Risk factors: {any warnings from validation}
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```
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## Generation Guidelines
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1. **Be Specific**: Use actual values from the spec, not placeholders
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2. **Be Concise**: Engineers don't want to read novels
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3. **Be Accurate**: Only state facts that can be verified from input
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4. **Be Helpful**: Include insights that aid understanding
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5. **No Fluff**: Avoid marketing language or excessive praise
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## Claude Prompt Template
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```
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You are generating a README.md for an FEA optimization study.
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CONTEXT:
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{json_context}
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RULES:
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1. Use the actual data provided - never use placeholder values
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2. Write in technical engineering language appropriate for structural engineers
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3. Keep each section concise but complete
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4. If information is missing, note it as "TBD" or skip the section
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5. Include physical units wherever applicable
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6. Format tables properly with alignment
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Generate the README.md content:
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```
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## Example Output
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```markdown
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# Bracket Mass Optimization V1
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**Topic**: Simple_Bracket
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**Created**: 2026-01-22
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**Status**: Configured
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Optimize the mass of a structural L-bracket while maintaining stress below yield and displacement within tolerance.
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## Engineering Problem
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### Model Description
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- **Geometry**: L-shaped mounting bracket with web and flange
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- **Material**: Steel (assumed based on typical applications)
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- **Baseline Mass**: 0.847 kg
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### Loading Conditions
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Static loading with force applied at mounting holes. Fixed constraints at base.
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## Optimization Formulation
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### Design Variables (3)
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| Variable | Expression | Range | Units |
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|----------|------------|-------|-------|
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| Web Thickness | web_thickness | [2.0, 10.0] | mm |
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| Flange Width | flange_width | [15.0, 40.0] | mm |
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| Fillet Radius | fillet_radius | [2.0, 8.0] | mm |
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### Objectives (1)
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| Objective | Direction | Weight | Source |
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|-----------|-----------|--------|--------|
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| Total Mass | minimize | 1.0 | mass_extractor |
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### Constraints (1)
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| Constraint | Condition | Threshold | Type |
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|------------|-----------|-----------|------|
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| Max Stress | <= | 250 MPa | hard |
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## Methodology
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### Algorithm
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- **Primary**: TPE (Tree-structured Parzen Estimator)
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- **Max Trials**: 100
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- **Surrogate**: Disabled
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### Physics Extraction
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- Mass: Extracted from NX expression `total_mass`
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- Stress: Von Mises stress from SOL101 static analysis
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### Convergence Criteria
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- Max trials: 100
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- Early stopping: 20 trials without improvement
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## Expected Outcomes
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Based on the optimization setup:
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- Expected improvement: 15-30% mass reduction (typical for thickness optimization)
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- Key trade-offs: Mass vs. stress margin
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- Risk factors: None identified
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```
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## Integration Points
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- **Backend**: `api/services/claude_readme.py` calls Claude API with this prompt
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- **Endpoint**: `POST /api/intake/{study_name}/readme`
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- **Trigger**: Automatic on status transition to `configured`
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