Replace Python numerical kernels with native C execution

tests/test_dependency_constraints.py

@@ -25,9 +25,7 @@ VERIFY_ENVIRONMENT_VARIABLE = "SYSTEM_SIMULATION_VERIFY_LOCKED_ENV"
 REFERENCE_DIRECT_VERSIONS = {
     "fastapi": "0.141.1",
     "lxml": "6.1.1",
-    "numpy": "2.5.2",
     "pydantic": "2.13.4",
-    "scipy": "1.18.0",
     "uvicorn": "0.52.3",
 }
 REFERENCE_LOCKED_VERSIONS = {
@@ -40,12 +38,10 @@ REFERENCE_LOCKED_VERSIONS = {
     "httptools": "0.8.0",
     "idna": "3.18",
     "lxml": "6.1.1",
-    "numpy": "2.5.2",
     "pydantic": "2.13.4",
     "pydantic-core": "2.46.4",
     "python-dotenv": "1.2.3",
     "pyyaml": "6.0.3",
-    "scipy": "1.18.0",
     "starlette": "1.6.0",
     "typing-extensions": "4.16.0",
     "typing-inspection": "0.4.4",