Commit Graph

9 Commits

Author SHA1 Message Date
Antoine
d1261d62fd refactor: Major project cleanup and reorganization
## Removed Duplicate Directories
- Deleted old `dashboard/` (replaced by atomizer-dashboard)
- Deleted old `mcp_server/` Python tools (moved model_discovery to optimization_engine)
- Deleted `tests/mcp_server/` (obsolete tests)
- Deleted `launch_dashboard.bat` (old launcher)

## Consolidated Code
- Moved `mcp_server/tools/model_discovery.py` to `optimization_engine/model_discovery/`
- Updated import in `optimization_config_builder.py`
- Deleted stub `extract_mass.py` (use extract_mass_from_bdf instead)
- Deleted unused `intelligent_setup.py` and `hybrid_study_creator.py`
- Archived `result_extractors/` to `archive/deprecated/`

## Documentation Cleanup
- Deleted deprecated `docs/06_PROTOCOLS_DETAILED/` (14 files)
- Archived dated dev docs to `docs/08_ARCHIVE/sessions/`
- Archived old plans to `docs/08_ARCHIVE/plans/`
- Updated `docs/protocols/README.md` with SYS_15

## Skills Consolidation
- Archived redundant study creation skills to `.claude/skills/archive/`
- Kept `core/study-creation-core.md` as canonical

## Housekeeping
- Updated `.gitignore` to prevent `nul` and `_dat_run*.dat`

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-12 11:24:02 -05:00
Antoine
c1f2634636 docs: Add user guide for proper Atomizer usage and evolution
Comprehensive guide teaching users how to interact with Atomizer so that
the learning system evolves correctly. Covers:

- The right mindset (colleague, not tool)
- Starting sessions with proper context
- Communicating goals, constraints, preferences
- Creating and running optimization studies
- Analyzing and validating results
- Reporting errors effectively
- Contributing to LAC (recording insights, outcomes, workarounds)
- Ending sessions properly to capture learnings

Includes:
- Mermaid diagrams for learning loop and flows
- Good vs bad examples for every interaction type
- Complete example session transcript
- Quick reference card for common patterns
- Golden rules summary

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-11 22:12:28 -05:00
Antoine
f83dc6839f docs: Add comprehensive architecture overview with Mermaid diagrams
Complete visual guide to understanding Atomizer's architecture including:
- Session lifecycle (startup, active, closing)
- Protocol Operating System (4-layer architecture)
- Learning Atomizer Core (LAC) data flow
- Task classification and routing
- AVERVS execution framework
- Optimization flow with extractors
- Knowledge accumulation over time
- File structure reference

Includes 15+ Mermaid diagrams for visual learning.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-11 22:05:09 -05:00
Antoine
fc123326e5 feat: Integrate Learning Atomizer Core (LAC) and master instructions
Add persistent knowledge system that enables Atomizer to learn from every
session and improve over time.

## New Files
- knowledge_base/lac.py: LAC class with optimization memory, session insights,
  and skill evolution tracking
- knowledge_base/__init__.py: Package initialization
- .claude/skills/modules/learning-atomizer-core.md: Full LAC skill documentation
- docs/07_DEVELOPMENT/ATOMIZER_CLAUDE_CODE_INSTRUCTIONS.md: Master instructions

## Updated Files
- CLAUDE.md: Added LAC section, communication style, AVERVS execution framework,
  error classification, and "Atomizer Claude" identity
- 00_BOOTSTRAP.md: Added session startup/closing checklists with LAC integration
- 01_CHEATSHEET.md: Added LAC CLI and Python API quick reference
- 02_CONTEXT_LOADER.md: Added LAC query section and anti-pattern

## LAC Features
- Query similar past optimizations before starting new ones
- Record insights (failures, success patterns, workarounds)
- Record optimization outcomes for future reference
- Suggest protocol improvements based on discoveries
- Simple JSONL storage (no database required)

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-11 21:55:01 -05:00
Antoine
9eed4d81eb feat: Add Claude Code terminal integration to dashboard
- Add embedded Claude Code terminal with xterm.js for full CLI experience
- Create WebSocket PTY backend for real-time terminal communication
- Add terminal status endpoint to check CLI availability
- Update dashboard to use Claude Code terminal instead of API chat
- Add optimization control panel with start/stop/validate actions
- Add study context provider for global state management
- Update frontend with new dependencies (xterm.js addons)
- Comprehensive README documentation for all new features

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>
2025-12-04 15:02:13 -05:00
a0c008a593 feat: Add neural loop automation - templates, auto-trainer, CLI
Closes the neural training loop with automated workflow:
- atomizer.py: One-command neural workflow CLI
- auto_trainer.py: Auto-training trigger system (50pt threshold)
- template_loader.py: Study creation from templates
- study_reset.py: Study reset/cleanup utility
- 3 templates: beam stiffness, bracket stress, frequency tuning
- State assessment document (Nov 25)

Usage: python atomizer.py neural-optimize --study my_study --trials 500

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-11-26 07:53:00 -05:00
e3bdb08a22 feat: Major update with validators, skills, dashboard, and docs reorganization
- Add validation framework (config, model, results, study validators)
- Add Claude Code skills (create-study, run-optimization, generate-report,
  troubleshoot, analyze-model)
- Add Atomizer Dashboard (React frontend + FastAPI backend)
- Reorganize docs into structured directories (00-09)
- Add neural surrogate modules and training infrastructure
- Add multi-objective optimization support

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>
2025-11-25 19:23:58 -05:00
3bff7cf6b3 feat: Add structured logging system for production-ready error handling (Phase 1.3)
Implements comprehensive, production-ready logging infrastructure to replace
ad-hoc print() statements across the codebase. This establishes a consistent
logging standard for MVP stability.

## What Changed

**New Files:**
- optimization_engine/logger.py (330 lines)
  - AtomizerLogger class with trial-specific methods
  - Color-coded console output (Windows 10+ and Unix)
  - Automatic file logging with rotation (50MB, 3 backups)
  - Zero external dependencies (stdlib only)

- docs/07_DEVELOPMENT/Phase_1_3_Implementation_Plan.md
  - Complete Phase 1.3 implementation plan
  - API documentation and usage examples
  - Migration strategy for existing studies

## Features

1. **Structured Trial Logging:**
   - logger.trial_start() - Log trial with design variables
   - logger.trial_complete() - Log results with objectives/constraints
   - logger.trial_failed() - Log failures with error details
   - logger.study_start() - Log study initialization
   - logger.study_complete() - Log final summary

2. **Production Features:**
   - ANSI color-coded console output (DEBUG=cyan, INFO=green, etc.)
   - Automatic file logging to {study_dir}/optimization.log
   - Log rotation: 50MB max, 3 backup files
   - Timestamps and structured format for dashboard parsing

3. **Simple API:**
   ```python
   from optimization_engine.logger import get_logger
   logger = get_logger(__name__, study_dir=Path("studies/foo/2_results"))
   logger.study_start("foo", n_trials=30, sampler="NSGAIISampler")
   logger.trial_start(1, design_vars)
   logger.trial_complete(1, objectives, constraints, feasible=True)
   ```

## Testing

- Verified color output on Windows 10
- Tested file logging and rotation
- Confirmed trial-specific methods format correctly
- UTF-8 encoding handles special characters

## Next Steps (Phase 1.3.1)

- Integrate logging into drone_gimbal_arm_optimization (reference implementation)
- Create migration guide for existing studies
- Update create-study skill to include logger setup

## Technical Details

Current state analyzed:
- 1416 occurrences of logging/print across 79 files
- 411 occurrences of try:/except/raise across 59 files
- Mix of print(), traceback, and inconsistent formatting

This logging system provides the foundation for:
- Dashboard integration (structured trial logs)
- Error recovery (checkpoint system in Phase 1.3.2)
- Production debugging (file logs with rotation)

Related: Phase 1.2 (Configuration Validation)

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Co-Authored-By: Claude <noreply@anthropic.com>
2025-11-24 09:27:27 -05:00
155f5a8522 feat: Add configuration validation system for MVP stability (Phase 1.2)
Implements JSON Schema validation for optimization configurations to ensure
consistency across all studies and prevent configuration errors.

Added:
- optimization_engine/schemas/optimization_config_schema.json
  - Comprehensive schema for Protocol 10 & 11 configurations
  - Validates objectives, constraints, design variables, simulation settings
  - Enforces standard field names (goal, bounds, parameter, threshold)

- optimization_engine/config_manager.py
  - ConfigManager class with schema validation
  - CLI tool: python config_manager.py <config.json>
  - Type-safe accessor methods for config elements
  - Custom validations: bounds check, multi-objective consistency, location check

- optimization_engine/schemas/README.md
  - Complete documentation of standard configuration format
  - Validation examples and common error fixes
  - Migration guidance for legacy configs

- docs/07_DEVELOPMENT/Phase_1_2_Implementation_Plan.md
  - Detailed implementation plan for remaining Phase 1.2 tasks
  - Migration tool design, integration guide, testing plan

Testing:
- Validated drone_gimbal_arm_optimization config successfully
- ConfigManager works with drone_gimbal format (new standard)
- Identifies legacy format issues in bracket studies

Standards Established:
- Configuration location: studies/{name}/1_setup/
- Objective direction: "goal" not "type"
- Design var bounds: "bounds": [min, max] not "min"/"max"
- Design var name: "parameter" not "name"
- Constraint threshold: "threshold" not "value"

Next Steps (Phase 1.2.1+):
- Config migration tool for legacy studies
- Integration with run_optimization.py
- Update create-study Claude skill with schema reference
- Migrate bracket studies to new format

Relates to: Phase 1.2 MVP Development Plan

🤖 Generated with Claude Code

Co-Authored-By: Claude <noreply@anthropic.com>
2025-11-24 09:21:55 -05:00