refactor: Reorganize code structure and create tests directory

- Consolidate surrogates module to processors/surrogates/
- Move ensemble_surrogate.py to proper location
- Add deprecation shim for old import path
- Create tests/ directory with pytest structure
- Move test files from archive/test_scripts/
- Add conftest.py with shared fixtures

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

optimization_engine/processors/surrogates/__init__.py

@@ -59,6 +59,15 @@ def __getattr__(name):
     elif name == 'create_exporter_from_config':
         from .training_data_exporter import create_exporter_from_config
         return create_exporter_from_config
+    elif name == 'EnsembleSurrogate':
+        from .ensemble_surrogate import EnsembleSurrogate
+        return EnsembleSurrogate
+    elif name == 'OODDetector':
+        from .ensemble_surrogate import OODDetector
+        return OODDetector
+    elif name == 'create_and_train_ensemble':
+        from .ensemble_surrogate import create_and_train_ensemble
+        return create_and_train_ensemble
 
     raise AttributeError(f"module 'optimization_engine.processors.surrogates' has no attribute '{name}'")
 
@@ -76,4 +85,7 @@ __all__ = [
     'AutoTrainer',
     'TrainingDataExporter',
     'create_exporter_from_config',
+    'EnsembleSurrogate',
+    'OODDetector',
+    'create_and_train_ensemble',
 ]

optimization_engine/surrogates/__init__.py

@@ -1,19 +1,26 @@
 """
-Surrogate models for FEA acceleration.
+DEPRECATED: This module has been moved to optimization_engine.processors.surrogates
 
-Available surrogates:
+Please update your imports:
-- EnsembleSurrogate: Multiple MLPs with uncertainty quantification
+    from optimization_engine.processors.surrogates import EnsembleSurrogate
-- OODDetector: Out-of-distribution detection
+
+This module will be removed in a future version.
 """
 
-from .ensemble_surrogate import (
+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__ = [
+__all__ = ['EnsembleSurrogate', 'OODDetector', 'create_and_train_ensemble']
-    'EnsembleSurrogate',
-    'OODDetector',
-    'create_and_train_ensemble'
-]

tests/conftest.py

@@ -0,0 +1,32 @@
+"""
+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"}
+        ]
+    }