docs: Consolidate documentation and fix protocol numbering (partial)
Phase 2 of restructuring plan: - Rename SYS_16_STUDY_INSIGHTS -> SYS_17_STUDY_INSIGHTS - Rename SYS_17_CONTEXT_ENGINEERING -> SYS_18_CONTEXT_ENGINEERING - Promote Bootstrap V3.0 (Context Engineering) as default - Archive old Bootstrap V2.0 - Create knowledge_base/playbook.json for ACE framework - Add OP_08 (Generate Report) to routing tables - Add SYS_16-18 to protocol tables - Update docs/protocols/README.md to version 1.1 - Update CLAUDE.md with new protocols - Create docs/plans/RESTRUCTURING_PLAN.md for continuation Remaining: Phase 2.8 (Cheatsheet), Phases 3-6 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
This commit is contained in:
@@ -39,7 +39,7 @@ This folder contains detailed physics and domain-specific documentation for Atom
|
||||
| `.claude/skills/modules/extractors-catalog.md` | Quick extractor lookup |
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||||
| `.claude/skills/modules/insights-catalog.md` | Quick insight lookup |
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| `docs/protocols/system/SYS_12_EXTRACTOR_LIBRARY.md` | Extractor specifications |
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| `docs/protocols/system/SYS_16_STUDY_INSIGHTS.md` | Insight specifications |
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| `docs/protocols/system/SYS_17_STUDY_INSIGHTS.md` | Insight specifications |
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||||
---
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@@ -315,7 +315,7 @@ studies/
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### Protocol Documentation
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- `docs/protocols/system/SYS_12_EXTRACTOR_LIBRARY.md` - Extractor specifications (E8-E10: Standard Zernike, E20-E21: OPD method)
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- `docs/protocols/system/SYS_16_STUDY_INSIGHTS.md` - Insight specifications (`zernike_wfe`, `zernike_opd_comparison`)
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- `docs/protocols/system/SYS_17_STUDY_INSIGHTS.md` - Insight specifications (`zernike_wfe`, `zernike_opd_comparison`)
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### Skill Modules (Quick Lookup)
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@@ -558,7 +558,7 @@ The `concave` parameter in the code handles this sign flip.
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| `.claude/skills/modules/extractors-catalog.md` | Quick extractor lookup |
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| `.claude/skills/modules/insights-catalog.md` | Quick insight lookup |
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| `docs/protocols/system/SYS_12_EXTRACTOR_LIBRARY.md` | Extractor specifications (E8-E10, E20-E21) |
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| `docs/protocols/system/SYS_16_STUDY_INSIGHTS.md` | Insight specifications |
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| `docs/protocols/system/SYS_17_STUDY_INSIGHTS.md` | Insight specifications |
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---
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@@ -944,5 +944,5 @@ Error response format:
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## See Also
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- [Context Engineering Report](../CONTEXT_ENGINEERING_REPORT.md) - Full implementation report
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- [SYS_17 Protocol](../protocols/system/SYS_17_CONTEXT_ENGINEERING.md) - System protocol
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- [SYS_18 Protocol](../protocols/system/SYS_18_CONTEXT_ENGINEERING.md) - System protocol
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- [Cheatsheet](../../.claude/skills/01_CHEATSHEET.md) - Quick reference
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549
docs/plans/RESTRUCTURING_PLAN.md
Normal file
549
docs/plans/RESTRUCTURING_PLAN.md
Normal file
@@ -0,0 +1,549 @@
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# Atomizer Massive Restructuring Plan
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**Created:** 2026-01-06
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**Purpose:** Comprehensive TODO list for Ralph mode execution with skip permissions
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**Status:** IN PROGRESS (Phase 2 partially complete)
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||||
---
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## Progress Summary
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**Completed:**
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- [x] Phase 1: Safe Cleanup (FULLY DONE)
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- [x] Phase 2.1-2.7: Protocol renaming, Bootstrap V3.0 promotion, routing updates
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**In Progress:**
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- Phase 2.8-2.10: Cheatsheet updates and commit
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**Remaining:**
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- Phases 3-6 and final push
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---
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## RALPH MODE TODO LIST
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### PHASE 2 (Remaining - Documentation)
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#### 2.8 Add OP_08 to 01_CHEATSHEET.md
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```
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File: .claude/skills/01_CHEATSHEET.md
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Action: Add row to "I want to..." table after OP_07 entry (around line 33)
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Add this line:
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| **Generate report** | **OP_08** | `python -m optimization_engine.reporting.report_generator <study>` |
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Also add a section around line 280:
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## Report Generation (OP_08)
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### Quick Commands
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| Task | Command |
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|------|---------|
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| Generate markdown report | `python -m optimization_engine.reporting.markdown_report <study>` |
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| Generate HTML visualization | `python tools/zernike_html_generator.py <study>` |
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**Full details**: `docs/protocols/operations/OP_08_GENERATE_REPORT.md`
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```
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#### 2.9 SKIP (Already verified V3.0 Bootstrap has no circular refs)
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||||
#### 2.10 Commit Phase 2 Changes
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||||
```bash
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cd c:\Users\antoi\Atomizer
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git add -A
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git commit -m "$(cat <<'EOF'
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docs: Consolidate documentation and fix protocol numbering
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||||
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||||
- Rename SYS_16_STUDY_INSIGHTS -> SYS_17_STUDY_INSIGHTS
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||||
- Rename SYS_17_CONTEXT_ENGINEERING -> SYS_18_CONTEXT_ENGINEERING
|
||||
- Promote Bootstrap V3.0 (Context Engineering) as default
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||||
- Create knowledge_base/playbook.json for ACE framework
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||||
- Add OP_08 (Generate Report) to all routing tables
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||||
- Add SYS_16-18 to all protocol tables
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||||
- Update docs/protocols/README.md version 1.1
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||||
- Update CLAUDE.md with new protocols
|
||||
|
||||
🤖 Generated with [Claude Code](https://claude.com/claude-code)
|
||||
|
||||
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
|
||||
EOF
|
||||
)"
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
### PHASE 3: Code Organization
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||||
|
||||
#### 3.1 Move ensemble_surrogate.py
|
||||
```bash
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||||
cd c:\Users\antoi\Atomizer
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||||
git mv optimization_engine/surrogates/ensemble_surrogate.py optimization_engine/processors/surrogates/ensemble_surrogate.py
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||||
```
|
||||
|
||||
#### 3.2 Update processors/surrogates/__init__.py
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||||
```
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||||
File: optimization_engine/processors/surrogates/__init__.py
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||||
Action: Add to __getattr__ function and __all__ list:
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||||
|
||||
In __getattr__, add these elif blocks:
|
||||
elif name == 'EnsembleSurrogate':
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||||
from .ensemble_surrogate import EnsembleSurrogate
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||||
return EnsembleSurrogate
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||||
elif name == 'OODDetector':
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||||
from .ensemble_surrogate import OODDetector
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||||
return OODDetector
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||||
elif name == 'create_and_train_ensemble':
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from .ensemble_surrogate import create_and_train_ensemble
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return create_and_train_ensemble
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|
||||
In __all__, add:
|
||||
'EnsembleSurrogate',
|
||||
'OODDetector',
|
||||
'create_and_train_ensemble',
|
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```
|
||||
|
||||
#### 3.3 Add deprecation shim to surrogates/__init__.py
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||||
```
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||||
File: optimization_engine/surrogates/__init__.py
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||||
Replace contents with:
|
||||
|
||||
"""
|
||||
DEPRECATED: This module has been moved to optimization_engine.processors.surrogates
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||||
|
||||
Please update your imports:
|
||||
from optimization_engine.processors.surrogates import EnsembleSurrogate
|
||||
|
||||
This module will be removed in a future version.
|
||||
"""
|
||||
|
||||
import warnings
|
||||
|
||||
warnings.warn(
|
||||
"optimization_engine.surrogates is deprecated. "
|
||||
"Use optimization_engine.processors.surrogates instead.",
|
||||
DeprecationWarning,
|
||||
stacklevel=2
|
||||
)
|
||||
|
||||
# Redirect imports
|
||||
from optimization_engine.processors.surrogates import (
|
||||
EnsembleSurrogate,
|
||||
OODDetector,
|
||||
create_and_train_ensemble
|
||||
)
|
||||
|
||||
__all__ = ['EnsembleSurrogate', 'OODDetector', 'create_and_train_ensemble']
|
||||
```
|
||||
|
||||
#### 3.4 Check future/ imports
|
||||
```bash
|
||||
cd c:\Users\antoi\Atomizer
|
||||
grep -r "from optimization_engine.future" --include="*.py" | grep -v "future/" | head -20
|
||||
```
|
||||
Analyze output and decide which modules need to move out of future/
|
||||
|
||||
#### 3.5 Move workflow_decomposer.py (if imported by production code)
|
||||
If grep shows imports from config/ or core/:
|
||||
```bash
|
||||
git mv optimization_engine/future/workflow_decomposer.py optimization_engine/config/workflow_decomposer.py
|
||||
# Update imports in capability_matcher.py and any other files
|
||||
```
|
||||
|
||||
#### 3.6 Create tests/ directory structure
|
||||
```bash
|
||||
cd c:\Users\antoi\Atomizer
|
||||
mkdir -p tests/unit/gnn tests/unit/extractors tests/integration tests/fixtures/sample_data
|
||||
```
|
||||
|
||||
#### 3.7 Move test files from archive/test_scripts/
|
||||
```bash
|
||||
cd c:\Users\antoi\Atomizer
|
||||
git mv archive/test_scripts/test_neural_surrogate.py tests/unit/
|
||||
git mv archive/test_scripts/test_nn_surrogate.py tests/unit/
|
||||
git mv archive/test_scripts/test_parametric_surrogate.py tests/unit/
|
||||
git mv archive/test_scripts/test_adaptive_characterization.py tests/unit/
|
||||
git mv archive/test_scripts/test_training_data_export.py tests/unit/
|
||||
git mv optimization_engine/gnn/test_*.py tests/unit/gnn/ 2>/dev/null || true
|
||||
git mv optimization_engine/extractors/test_phase3_extractors.py tests/unit/extractors/ 2>/dev/null || true
|
||||
```
|
||||
|
||||
#### 3.8 Create tests/conftest.py
|
||||
```
|
||||
File: tests/conftest.py
|
||||
Content:
|
||||
"""
|
||||
Pytest configuration and shared fixtures for Atomizer tests.
|
||||
"""
|
||||
|
||||
import pytest
|
||||
import sys
|
||||
from pathlib import Path
|
||||
|
||||
# Add project root to path
|
||||
sys.path.insert(0, str(Path(__file__).parent.parent))
|
||||
|
||||
@pytest.fixture
|
||||
def sample_study_dir(tmp_path):
|
||||
"""Create a temporary study directory structure."""
|
||||
study = tmp_path / "test_study"
|
||||
(study / "1_setup").mkdir(parents=True)
|
||||
(study / "2_iterations").mkdir()
|
||||
(study / "3_results").mkdir()
|
||||
return study
|
||||
|
||||
@pytest.fixture
|
||||
def sample_config():
|
||||
"""Sample optimization config for testing."""
|
||||
return {
|
||||
"study_name": "test_study",
|
||||
"design_variables": [
|
||||
{"name": "param1", "lower": 0, "upper": 10, "type": "continuous"}
|
||||
],
|
||||
"objectives": [
|
||||
{"name": "minimize_mass", "direction": "minimize"}
|
||||
]
|
||||
}
|
||||
```
|
||||
|
||||
#### 3.9 Rename bracket_displacement_maximizing/results to 3_results
|
||||
```bash
|
||||
cd c:\Users\antoi\Atomizer
|
||||
# Check if results/ exists first
|
||||
if [ -d "studies/bracket_displacement_maximizing/results" ]; then
|
||||
git mv studies/bracket_displacement_maximizing/results studies/bracket_displacement_maximizing/3_results
|
||||
fi
|
||||
```
|
||||
|
||||
#### 3.10 Rename Drone_Gimbal/2_results to 3_results
|
||||
```bash
|
||||
cd c:\Users\antoi\Atomizer
|
||||
# Check if 2_results/ exists first
|
||||
if [ -d "studies/Drone_Gimbal/2_results" ]; then
|
||||
git mv studies/Drone_Gimbal/2_results studies/Drone_Gimbal/3_results
|
||||
fi
|
||||
```
|
||||
|
||||
#### 3.11 Commit Phase 3 Changes
|
||||
```bash
|
||||
cd c:\Users\antoi\Atomizer
|
||||
git add -A
|
||||
git commit -m "$(cat <<'EOF'
|
||||
refactor: Reorganize code structure and create tests directory
|
||||
|
||||
- Consolidate surrogates module to processors/surrogates/
|
||||
- Add deprecation shim for old import path
|
||||
- Create tests/ directory with pytest structure
|
||||
- Move test files from archive/test_scripts/
|
||||
- Standardize study folder naming (3_results/)
|
||||
|
||||
🤖 Generated with [Claude Code](https://claude.com/claude-code)
|
||||
|
||||
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
|
||||
EOF
|
||||
)"
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
### PHASE 4: Dependency Management
|
||||
|
||||
#### 4.1-4.2 Add neural and gnn optional deps to pyproject.toml
|
||||
```
|
||||
File: pyproject.toml
|
||||
After the [project.optional-dependencies] section, add:
|
||||
|
||||
neural = [
|
||||
"torch>=2.0.0",
|
||||
"torch-geometric>=2.3.0",
|
||||
"tensorboard>=2.13.0",
|
||||
]
|
||||
|
||||
gnn = [
|
||||
"torch>=2.0.0",
|
||||
"torch-geometric>=2.3.0",
|
||||
]
|
||||
|
||||
all = ["atomizer[neural,gnn,dev,dashboard]"]
|
||||
```
|
||||
|
||||
#### 4.3 Remove mcp optional deps
|
||||
```
|
||||
File: pyproject.toml
|
||||
Delete this section:
|
||||
|
||||
mcp = [
|
||||
"mcp>=0.1.0",
|
||||
]
|
||||
```
|
||||
|
||||
#### 4.4 Remove mcp_server from packages.find
|
||||
```
|
||||
File: pyproject.toml
|
||||
Change:
|
||||
include = ["mcp_server*", "optimization_engine*", "nx_journals*"]
|
||||
To:
|
||||
include = ["optimization_engine*", "nx_journals*"]
|
||||
```
|
||||
|
||||
#### 4.5 Commit Phase 4 Changes
|
||||
```bash
|
||||
cd c:\Users\antoi\Atomizer
|
||||
git add pyproject.toml
|
||||
git commit -m "$(cat <<'EOF'
|
||||
build: Add optional dependency groups and clean up pyproject.toml
|
||||
|
||||
- Add neural optional group (torch, torch-geometric, tensorboard)
|
||||
- Add gnn optional group (torch, torch-geometric)
|
||||
- Add all optional group for convenience
|
||||
- Remove mcp optional group (not implemented)
|
||||
- Remove mcp_server from packages.find (not implemented)
|
||||
|
||||
🤖 Generated with [Claude Code](https://claude.com/claude-code)
|
||||
|
||||
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
|
||||
EOF
|
||||
)"
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
### PHASE 5: Study Organization
|
||||
|
||||
#### 5.1 Create archive directory
|
||||
```bash
|
||||
cd c:\Users\antoi\Atomizer
|
||||
mkdir -p studies/M1_Mirror/_archive
|
||||
```
|
||||
|
||||
#### 5.2 Move V1-V8 cost_reduction studies
|
||||
```bash
|
||||
cd c:\Users\antoi\Atomizer/studies/M1_Mirror
|
||||
# Move cost_reduction V2-V8 (V1 doesn't exist as base is just "cost_reduction")
|
||||
for v in V2 V3 V4 V5 V6 V7 V8; do
|
||||
if [ -d "m1_mirror_cost_reduction_$v" ]; then
|
||||
mv "m1_mirror_cost_reduction_$v" _archive/
|
||||
fi
|
||||
done
|
||||
```
|
||||
|
||||
#### 5.3 Move V1-V8 flat_back studies
|
||||
```bash
|
||||
cd c:\Users\antoi\Atomizer/studies/M1_Mirror
|
||||
# Move flat_back V1-V8 (note: V2 may not exist)
|
||||
for v in V1 V3 V4 V5 V6 V7 V8; do
|
||||
if [ -d "m1_mirror_cost_reduction_flat_back_$v" ]; then
|
||||
mv "m1_mirror_cost_reduction_flat_back_$v" _archive/
|
||||
fi
|
||||
done
|
||||
```
|
||||
|
||||
#### 5.4 Create MANIFEST.md
|
||||
```
|
||||
File: studies/M1_Mirror/_archive/MANIFEST.md
|
||||
Content:
|
||||
|
||||
# M1 Mirror Archived Studies
|
||||
|
||||
**Archived:** 2026-01-06
|
||||
**Reason:** Repository cleanup - keeping only V9+ studies active
|
||||
|
||||
## Archived Studies
|
||||
|
||||
### Cost Reduction Series
|
||||
| Study | Trials | Best WS | Notes |
|
||||
|-------|--------|---------|-------|
|
||||
| V2 | TBD | TBD | Early exploration |
|
||||
| V3 | TBD | TBD | - |
|
||||
| V4 | TBD | TBD | - |
|
||||
| V5 | TBD | TBD | - |
|
||||
| V6 | TBD | TBD | - |
|
||||
| V7 | TBD | TBD | - |
|
||||
| V8 | TBD | TBD | - |
|
||||
|
||||
### Cost Reduction Flat Back Series
|
||||
| Study | Trials | Best WS | Notes |
|
||||
|-------|--------|---------|-------|
|
||||
| V1 | TBD | TBD | Initial flat back design |
|
||||
| V3 | TBD | TBD | V2 was skipped |
|
||||
| V4 | TBD | TBD | - |
|
||||
| V5 | TBD | TBD | - |
|
||||
| V6 | TBD | TBD | - |
|
||||
| V7 | TBD | TBD | - |
|
||||
| V8 | TBD | TBD | - |
|
||||
|
||||
## Restoration Instructions
|
||||
|
||||
To restore a study:
|
||||
1. Move from _archive/ to parent directory
|
||||
2. Verify database integrity: `sqlite3 3_results/study.db ".tables"`
|
||||
3. Check optimization_config.json exists
|
||||
```
|
||||
|
||||
#### 5.5 Commit Phase 5 Changes
|
||||
```bash
|
||||
cd c:\Users\antoi\Atomizer
|
||||
git add -A
|
||||
git commit -m "$(cat <<'EOF'
|
||||
chore: Archive old M1_Mirror studies (V1-V8)
|
||||
|
||||
- Create studies/M1_Mirror/_archive/ directory
|
||||
- Move cost_reduction V2-V8 to archive
|
||||
- Move flat_back V1-V8 to archive
|
||||
- Create MANIFEST.md documenting archived studies
|
||||
- Keep V9+ studies active for reference
|
||||
|
||||
🤖 Generated with [Claude Code](https://claude.com/claude-code)
|
||||
|
||||
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
|
||||
EOF
|
||||
)"
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
### PHASE 6: Documentation Polish
|
||||
|
||||
#### 6.1 Update README.md with LLM section
|
||||
```
|
||||
File: README.md
|
||||
Add this section after the main description:
|
||||
|
||||
## For AI Assistants
|
||||
|
||||
Atomizer is designed for LLM-first interaction. Key resources:
|
||||
|
||||
- **[CLAUDE.md](CLAUDE.md)** - System instructions for Claude Code
|
||||
- **[.claude/skills/](/.claude/skills/)** - LLM skill modules
|
||||
- **[docs/protocols/](docs/protocols/)** - Protocol Operating System
|
||||
|
||||
### Knowledge Base (LAC)
|
||||
|
||||
The Learning Atomizer Core (`knowledge_base/lac/`) accumulates optimization knowledge:
|
||||
- `session_insights/` - Learnings from past sessions
|
||||
- `optimization_memory/` - Optimization outcomes by geometry type
|
||||
- `playbook.json` - ACE framework knowledge store
|
||||
|
||||
For detailed AI interaction guidance, see CLAUDE.md.
|
||||
```
|
||||
|
||||
#### 6.2-6.4 Create optimization_memory JSONL files
|
||||
```bash
|
||||
cd c:\Users\antoi\Atomizer
|
||||
mkdir -p knowledge_base/lac/optimization_memory
|
||||
```
|
||||
|
||||
```
|
||||
File: knowledge_base/lac/optimization_memory/bracket.jsonl
|
||||
Content (one JSON per line):
|
||||
{"geometry_type": "bracket", "study_name": "example", "method": "TPE", "objectives": ["mass"], "trials": 0, "converged": false, "notes": "Schema file - replace with real data"}
|
||||
```
|
||||
|
||||
```
|
||||
File: knowledge_base/lac/optimization_memory/beam.jsonl
|
||||
Content:
|
||||
{"geometry_type": "beam", "study_name": "example", "method": "TPE", "objectives": ["mass"], "trials": 0, "converged": false, "notes": "Schema file - replace with real data"}
|
||||
```
|
||||
|
||||
```
|
||||
File: knowledge_base/lac/optimization_memory/mirror.jsonl
|
||||
Content:
|
||||
{"geometry_type": "mirror", "study_name": "m1_mirror_adaptive_V14", "method": "IMSO", "objectives": ["wfe_40_20", "mass_kg"], "trials": 100, "converged": true, "notes": "SAT v3 achieved WS=205.58"}
|
||||
```
|
||||
|
||||
#### 6.5 Move implementation plans to docs/plans
|
||||
```bash
|
||||
cd c:\Users\antoi\Atomizer
|
||||
git mv .claude/skills/modules/DYNAMIC_RESPONSE_IMPLEMENTATION_PLAN.md docs/plans/
|
||||
git mv .claude/skills/modules/OPTIMIZATION_ENGINE_MIGRATION_PLAN.md docs/plans/
|
||||
git mv .claude/skills/modules/atomizer_fast_solver_technologies.md docs/plans/
|
||||
```
|
||||
|
||||
#### 6.6 Final consistency verification
|
||||
```bash
|
||||
cd c:\Users\antoi\Atomizer
|
||||
# Verify protocol files exist
|
||||
ls docs/protocols/operations/OP_0*.md
|
||||
ls docs/protocols/system/SYS_1*.md
|
||||
|
||||
# Verify imports work
|
||||
python -c "import optimization_engine; print('OK')"
|
||||
|
||||
# Verify no broken references
|
||||
grep -r "SYS_16_STUDY" . --include="*.md" | head -5 # Should be empty
|
||||
grep -r "SYS_17_CONTEXT" . --include="*.md" | head -5 # Should be empty
|
||||
|
||||
# Count todos completed
|
||||
echo "Verification complete"
|
||||
```
|
||||
|
||||
#### 6.7 Commit Phase 6 Changes
|
||||
```bash
|
||||
cd c:\Users\antoi\Atomizer
|
||||
git add -A
|
||||
git commit -m "$(cat <<'EOF'
|
||||
docs: Final documentation polish and consistency fixes
|
||||
|
||||
- Update README.md with LLM assistant section
|
||||
- Create optimization_memory JSONL structure
|
||||
- Move implementation plans from skills/modules to docs/plans
|
||||
- Verify all protocol references are consistent
|
||||
|
||||
🤖 Generated with [Claude Code](https://claude.com/claude-code)
|
||||
|
||||
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
|
||||
EOF
|
||||
)"
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
### FINAL: Push to Both Remotes
|
||||
|
||||
```bash
|
||||
cd c:\Users\antoi\Atomizer
|
||||
git push origin main
|
||||
git push github main
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## Quick Reference
|
||||
|
||||
### Files Modified in This Restructuring
|
||||
|
||||
**Documentation (Phase 2):**
|
||||
- `docs/protocols/README.md` - Updated protocol listings
|
||||
- `docs/protocols/system/SYS_17_STUDY_INSIGHTS.md` - Renamed from SYS_16
|
||||
- `docs/protocols/system/SYS_18_CONTEXT_ENGINEERING.md` - Renamed from SYS_17
|
||||
- `CLAUDE.md` - Updated routing tables
|
||||
- `.claude/skills/00_BOOTSTRAP.md` - Replaced with V3.0
|
||||
- `.claude/skills/01_CHEATSHEET.md` - Added OP_08
|
||||
- `knowledge_base/playbook.json` - Created
|
||||
|
||||
**Code (Phase 3):**
|
||||
- `optimization_engine/processors/surrogates/__init__.py` - Added exports
|
||||
- `optimization_engine/surrogates/__init__.py` - Deprecation shim
|
||||
- `tests/conftest.py` - Created
|
||||
|
||||
**Dependencies (Phase 4):**
|
||||
- `pyproject.toml` - Updated optional groups
|
||||
|
||||
**Studies (Phase 5):**
|
||||
- `studies/M1_Mirror/_archive/` - Created with V1-V8 studies
|
||||
|
||||
**Final Polish (Phase 6):**
|
||||
- `README.md` - Added LLM section
|
||||
- `knowledge_base/lac/optimization_memory/` - Created structure
|
||||
- `docs/plans/` - Moved implementation plans
|
||||
|
||||
---
|
||||
|
||||
## Success Criteria Checklist
|
||||
|
||||
- [ ] All imports work: `python -c "import optimization_engine"`
|
||||
- [ ] Dashboard starts: `python launch_dashboard.py`
|
||||
- [ ] No SYS_16 duplication (only SELF_AWARE_TURBO)
|
||||
- [ ] Bootstrap V3.0 is active version
|
||||
- [ ] OP_08 discoverable in all routing tables
|
||||
- [ ] Studies use consistent 3_results/ naming
|
||||
- [ ] Tests directory exists with conftest.py
|
||||
- [ ] All changes pushed to both remotes
|
||||
@@ -1,7 +1,7 @@
|
||||
# Atomizer Protocol Operating System (POS)
|
||||
|
||||
**Version**: 1.0
|
||||
**Last Updated**: 2025-12-05
|
||||
**Version**: 1.1
|
||||
**Last Updated**: 2026-01-06
|
||||
|
||||
---
|
||||
|
||||
@@ -22,13 +22,19 @@ protocols/
|
||||
│ ├── OP_03_MONITOR_PROGRESS.md
|
||||
│ ├── OP_04_ANALYZE_RESULTS.md
|
||||
│ ├── OP_05_EXPORT_TRAINING_DATA.md
|
||||
│ └── OP_06_TROUBLESHOOT.md
|
||||
│ ├── OP_06_TROUBLESHOOT.md
|
||||
│ ├── OP_07_DISK_OPTIMIZATION.md
|
||||
│ └── OP_08_GENERATE_REPORT.md
|
||||
├── system/ # Layer 3: Core specifications
|
||||
│ ├── SYS_10_IMSO.md
|
||||
│ ├── SYS_11_MULTI_OBJECTIVE.md
|
||||
│ ├── SYS_12_EXTRACTOR_LIBRARY.md
|
||||
│ ├── SYS_13_DASHBOARD_TRACKING.md
|
||||
│ └── SYS_14_NEURAL_ACCELERATION.md
|
||||
│ ├── SYS_14_NEURAL_ACCELERATION.md
|
||||
│ ├── SYS_15_METHOD_SELECTOR.md
|
||||
│ ├── SYS_16_SELF_AWARE_TURBO.md
|
||||
│ ├── SYS_17_STUDY_INSIGHTS.md
|
||||
│ └── SYS_18_CONTEXT_ENGINEERING.md
|
||||
└── extensions/ # Layer 4: Extensibility guides
|
||||
├── EXT_01_CREATE_EXTRACTOR.md
|
||||
├── EXT_02_CREATE_HOOK.md
|
||||
@@ -56,6 +62,8 @@ Day-to-day how-to guides:
|
||||
- **OP_04**: Analyze results
|
||||
- **OP_05**: Export training data
|
||||
- **OP_06**: Troubleshoot issues
|
||||
- **OP_07**: Disk optimization (free space)
|
||||
- **OP_08**: Generate study report
|
||||
|
||||
### Layer 3: System (`system/`)
|
||||
Core technical specifications:
|
||||
@@ -65,6 +73,9 @@ Core technical specifications:
|
||||
- **SYS_13**: Real-Time Dashboard Tracking
|
||||
- **SYS_14**: Neural Network Acceleration
|
||||
- **SYS_15**: Method Selector
|
||||
- **SYS_16**: Self-Aware Turbo (SAT) Method
|
||||
- **SYS_17**: Study Insights (Physics Visualization)
|
||||
- **SYS_18**: Context Engineering (ACE Framework)
|
||||
|
||||
### Layer 4: Extensions (`extensions/`)
|
||||
Guides for extending Atomizer:
|
||||
@@ -130,6 +141,8 @@ LOAD_WITH: [{dependencies}]
|
||||
| Analyze results | [OP_04](operations/OP_04_ANALYZE_RESULTS.md) |
|
||||
| Export neural data | [OP_05](operations/OP_05_EXPORT_TRAINING_DATA.md) |
|
||||
| Fix errors | [OP_06](operations/OP_06_TROUBLESHOOT.md) |
|
||||
| Free disk space | [OP_07](operations/OP_07_DISK_OPTIMIZATION.md) |
|
||||
| Generate report | [OP_08](operations/OP_08_GENERATE_REPORT.md) |
|
||||
| Add extractor | [EXT_01](extensions/EXT_01_CREATE_EXTRACTOR.md) |
|
||||
|
||||
### By Protocol Number
|
||||
@@ -142,6 +155,9 @@ LOAD_WITH: [{dependencies}]
|
||||
| 13 | Dashboard | [System](system/SYS_13_DASHBOARD_TRACKING.md) |
|
||||
| 14 | Neural | [System](system/SYS_14_NEURAL_ACCELERATION.md) |
|
||||
| 15 | Method Selector | [System](system/SYS_15_METHOD_SELECTOR.md) |
|
||||
| 16 | Self-Aware Turbo | [System](system/SYS_16_SELF_AWARE_TURBO.md) |
|
||||
| 17 | Study Insights | [System](system/SYS_17_STUDY_INSIGHTS.md) |
|
||||
| 18 | Context Engineering | [System](system/SYS_18_CONTEXT_ENGINEERING.md) |
|
||||
|
||||
---
|
||||
|
||||
@@ -160,3 +176,4 @@ LOAD_WITH: [{dependencies}]
|
||||
| Version | Date | Changes |
|
||||
|---------|------|---------|
|
||||
| 1.0 | 2025-12-05 | Initial Protocol Operating System |
|
||||
| 1.1 | 2026-01-06 | Added OP_07, OP_08; SYS_16, SYS_17, SYS_18; Fixed SYS_16 duplication |
|
||||
|
||||
276
docs/protocols/operations/OP_08_GENERATE_REPORT.md
Normal file
276
docs/protocols/operations/OP_08_GENERATE_REPORT.md
Normal file
@@ -0,0 +1,276 @@
|
||||
# OP_08: Generate Study Report
|
||||
|
||||
<!--
|
||||
PROTOCOL: Automated Study Report Generation
|
||||
LAYER: Operations
|
||||
VERSION: 1.0
|
||||
STATUS: Active
|
||||
LAST_UPDATED: 2026-01-06
|
||||
PRIVILEGE: user
|
||||
LOAD_WITH: []
|
||||
-->
|
||||
|
||||
## Overview
|
||||
|
||||
This protocol covers automated generation of comprehensive study reports via the Dashboard API or CLI. Reports include executive summaries, optimization metrics, best solutions, and engineering recommendations.
|
||||
|
||||
---
|
||||
|
||||
## When to Use
|
||||
|
||||
| Trigger | Action |
|
||||
|---------|--------|
|
||||
| "generate report" | Follow this protocol |
|
||||
| Dashboard "Report" button | API endpoint called |
|
||||
| Optimization complete | Auto-generate option |
|
||||
| CLI `atomizer report <study>` | Direct generation |
|
||||
|
||||
---
|
||||
|
||||
## Quick Reference
|
||||
|
||||
**API Endpoint**: `POST /api/optimization/studies/{study_id}/report/generate`
|
||||
|
||||
**Output**: `STUDY_REPORT.md` in study root directory
|
||||
|
||||
**Formats Supported**: Markdown (default), JSON (data export)
|
||||
|
||||
---
|
||||
|
||||
## Generation Methods
|
||||
|
||||
### 1. Via Dashboard
|
||||
|
||||
Click the "Generate Report" button in the study control panel. The report will be generated and displayed in the Reports tab.
|
||||
|
||||
### 2. Via API
|
||||
|
||||
```bash
|
||||
# Generate report
|
||||
curl -X POST http://localhost:8003/api/optimization/studies/my_study/report/generate
|
||||
|
||||
# Response
|
||||
{
|
||||
"success": true,
|
||||
"content": "# Study Report: ...",
|
||||
"path": "/path/to/STUDY_REPORT.md",
|
||||
"generated_at": "2026-01-06T12:00:00"
|
||||
}
|
||||
```
|
||||
|
||||
### 3. Via CLI
|
||||
|
||||
```bash
|
||||
# Using Claude Code
|
||||
"Generate a report for the bracket_optimization study"
|
||||
|
||||
# Direct Python
|
||||
python -m optimization_engine.reporting.markdown_report studies/bracket_optimization
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## Report Sections
|
||||
|
||||
### Executive Summary
|
||||
|
||||
Generated automatically from trial data:
|
||||
- Total trials completed
|
||||
- Best objective value achieved
|
||||
- Improvement percentage from initial design
|
||||
- Key findings
|
||||
|
||||
### Results Table
|
||||
|
||||
| Metric | Initial | Final | Change |
|
||||
|--------|---------|-------|--------|
|
||||
| Objective 1 | X | Y | Z% |
|
||||
| Objective 2 | X | Y | Z% |
|
||||
|
||||
### Best Solution
|
||||
|
||||
- Trial number
|
||||
- All design variable values
|
||||
- All objective values
|
||||
- Constraint satisfaction status
|
||||
- User attributes (source, validation status)
|
||||
|
||||
### Design Variables Summary
|
||||
|
||||
| Variable | Min | Max | Best Value | Sensitivity |
|
||||
|----------|-----|-----|------------|-------------|
|
||||
| var_1 | 0.0 | 10.0 | 5.23 | High |
|
||||
| var_2 | 0.0 | 20.0 | 12.87 | Medium |
|
||||
|
||||
### Convergence Analysis
|
||||
|
||||
- Trials to 50% improvement
|
||||
- Trials to 90% improvement
|
||||
- Convergence rate assessment
|
||||
- Phase breakdown (exploration, exploitation, refinement)
|
||||
|
||||
### Recommendations
|
||||
|
||||
Auto-generated based on results:
|
||||
- Further optimization suggestions
|
||||
- Sensitivity observations
|
||||
- Next steps for validation
|
||||
|
||||
---
|
||||
|
||||
## Backend Implementation
|
||||
|
||||
**File**: `atomizer-dashboard/backend/api/routes/optimization.py`
|
||||
|
||||
```python
|
||||
@router.post("/studies/{study_id}/report/generate")
|
||||
async def generate_report(study_id: str, format: str = "markdown"):
|
||||
"""
|
||||
Generate comprehensive study report.
|
||||
|
||||
Args:
|
||||
study_id: Study identifier
|
||||
format: Output format (markdown, json)
|
||||
|
||||
Returns:
|
||||
Generated report content and file path
|
||||
"""
|
||||
# Load configuration
|
||||
config = load_config(study_dir)
|
||||
|
||||
# Query database for all trials
|
||||
trials = get_all_completed_trials(db)
|
||||
best_trial = get_best_trial(db)
|
||||
|
||||
# Calculate metrics
|
||||
stats = calculate_statistics(trials)
|
||||
|
||||
# Generate markdown
|
||||
report = generate_markdown_report(study_id, config, trials, best_trial, stats)
|
||||
|
||||
# Save to file
|
||||
report_path = study_dir / "STUDY_REPORT.md"
|
||||
report_path.write_text(report)
|
||||
|
||||
return {
|
||||
"success": True,
|
||||
"content": report,
|
||||
"path": str(report_path),
|
||||
"generated_at": datetime.now().isoformat()
|
||||
}
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## Report Template
|
||||
|
||||
The generated report follows this structure:
|
||||
|
||||
```markdown
|
||||
# {Study Name} - Optimization Report
|
||||
|
||||
**Generated:** {timestamp}
|
||||
**Status:** {Completed/In Progress}
|
||||
|
||||
---
|
||||
|
||||
## Executive Summary
|
||||
|
||||
This optimization study completed **{n_trials} trials** and achieved a
|
||||
**{improvement}%** improvement in the primary objective.
|
||||
|
||||
| Metric | Value |
|
||||
|--------|-------|
|
||||
| Total Trials | {n} |
|
||||
| Best Value | {best} |
|
||||
| Initial Value | {initial} |
|
||||
| Improvement | {pct}% |
|
||||
|
||||
---
|
||||
|
||||
## Objectives
|
||||
|
||||
| Name | Direction | Weight | Best Value |
|
||||
|------|-----------|--------|------------|
|
||||
| {obj_name} | minimize | 1.0 | {value} |
|
||||
|
||||
---
|
||||
|
||||
## Design Variables
|
||||
|
||||
| Name | Min | Max | Best Value |
|
||||
|------|-----|-----|------------|
|
||||
| {var_name} | {min} | {max} | {best} |
|
||||
|
||||
---
|
||||
|
||||
## Best Solution
|
||||
|
||||
**Trial #{n}** achieved the optimal result.
|
||||
|
||||
### Parameters
|
||||
- var_1: {value}
|
||||
- var_2: {value}
|
||||
|
||||
### Objectives
|
||||
- objective_1: {value}
|
||||
|
||||
### Constraints
|
||||
- All constraints satisfied: Yes/No
|
||||
|
||||
---
|
||||
|
||||
## Convergence Analysis
|
||||
|
||||
- Initial best: {value} (trial 1)
|
||||
- Final best: {value} (trial {n})
|
||||
- 90% improvement reached at trial {n}
|
||||
|
||||
---
|
||||
|
||||
## Recommendations
|
||||
|
||||
1. Validate best solution with high-fidelity FEA
|
||||
2. Consider sensitivity analysis around optimal design point
|
||||
3. Check manufacturing feasibility of optimal parameters
|
||||
|
||||
---
|
||||
|
||||
*Generated by Atomizer Dashboard*
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## Prerequisites
|
||||
|
||||
Before generating a report:
|
||||
- [ ] Study must have at least 1 completed trial
|
||||
- [ ] study.db must exist in results directory
|
||||
- [ ] optimization_config.json must be present
|
||||
|
||||
---
|
||||
|
||||
## Error Handling
|
||||
|
||||
| Error | Cause | Solution |
|
||||
|-------|-------|----------|
|
||||
| "No trials found" | Empty database | Run optimization first |
|
||||
| "Config not found" | Missing config file | Verify study setup |
|
||||
| "Database locked" | Optimization running | Wait or pause first |
|
||||
| "Invalid study" | Study path not found | Check study ID |
|
||||
|
||||
---
|
||||
|
||||
## Cross-References
|
||||
|
||||
- **Preceded By**: [OP_04_ANALYZE_RESULTS](./OP_04_ANALYZE_RESULTS.md)
|
||||
- **Related**: [SYS_13_DASHBOARD](../system/SYS_13_DASHBOARD.md)
|
||||
- **Triggered By**: Dashboard Report button
|
||||
|
||||
---
|
||||
|
||||
## Version History
|
||||
|
||||
| Version | Date | Changes |
|
||||
|---------|------|---------|
|
||||
| 1.0 | 2026-01-06 | Initial release - Dashboard integration |
|
||||
Reference in New Issue
Block a user