Fix pyproject.toml: explicit package discovery to resolve flat-layout error"

pyproject.toml

@@ -8,23 +8,25 @@ dependencies = [
     "polars>=1.0",
     "duckdb>=1.0",
     "aiohttp>=3.9",
-    "asyncio-throttle>=1.0",
     "jinja2>=3.1",
-    "chromadb>=0.5",
-    "outlines>=0.1",
     "openai>=1.0",
     "numpy>=1.26",
     "scikit-learn>=1.4",
+    "scipy>=1.12",
     "rich>=13.0",
-    "langfuse>=2.0",
 ]
 
 [project.optional-dependencies]
+rag = ["chromadb>=0.5"]
+local-sim = ["yfinance>=0.2"]
 dev = ["pytest>=8.0", "pytest-asyncio>=0.23", "ruff>=0.4"]
-local-sim = ["vectorbt>=0.26", "yfinance>=0.2"]
+all = ["chromadb>=0.5", "yfinance>=0.2", "langfuse>=2.0"]
 
 [project.scripts]
 alpha-factory = "alpha_factory.run:main"
 
+[tool.setuptools.packages.find]
+include = ["alpha_factory*"]
+
 [tool.ruff]
 line-length = 100