Run all repositories for maximum output

benchmarks/results/hbcm_20251125_145434.json

@@ -0,0 +1,157 @@
+{
+  "timestamp": "2025-11-25T14:54:34.374584",
+  "benchmark_suite": "HBCM Performance",
+  "results": [
+    {
+      "test_name": "HBCM Single Step",
+      "duration_s": 0.01442199200002392,
+      "iterations": 10000,
+      "mean_latency_ms": 0.0012409382,
+      "median_latency_ms": 0.00122,
+      "p95_latency_ms": 0.001327,
+      "p99_latency_ms": 0.001873,
+      "min_latency_ms": 0.001036,
+      "max_latency_ms": 0.014447,
+      "throughput_ops_per_sec": 693385.4907133088,
+      "memory_mb": 0.0,
+      "metadata": {
+        "dt": 0.001,
+        "state_size": 4
+      }
+    },
+    {
+      "test_name": "HBCM Short Simulation (100 steps)",
+      "duration_s": 0.017287748000000006,
+      "iterations": 100,
+      "mean_latency_ms": 0.17287748,
+      "median_latency_ms": 0.164737,
+      "p95_latency_ms": 0.197652,
+      "p99_latency_ms": 0.345699,
+      "min_latency_ms": 0.161277,
+      "max_latency_ms": 0.345699,
+      "throughput_ops_per_sec": 5784.4434104430475,
+      "memory_mb": 0.0,
+      "metadata": {
+        "steps": 100,
+        "simulated_time_s": 0.1
+      }
+    },
+    {
+      "test_name": "HBCM Long Simulation (10,000 steps)",
+      "duration_s": 0.21427981399999999,
+      "iterations": 10,
+      "mean_latency_ms": 21.4279814,
+      "median_latency_ms": 20.903914,
+      "p95_latency_ms": 26.940432,
+      "p99_latency_ms": 26.940432,
+      "min_latency_ms": 18.785698,
+      "max_latency_ms": 26.940432,
+      "throughput_ops_per_sec": 46.667951653159456,
+      "memory_mb": 0.0,
+      "metadata": {
+        "steps": 10000,
+        "simulated_time_s": 10.0
+      }
+    },
+    {
+      "test_name": "Real-Time Capability (1000 Hz)",
+      "duration_s": 0.015861716999978626,
+      "iterations": 10000,
+      "mean_latency_ms": 0.0013879299,
+      "median_latency_ms": 0.001358,
+      "p95_latency_ms": 0.001571,
+      "p99_latency_ms": 0.001757,
+      "min_latency_ms": 0.001097,
+      "max_latency_ms": 0.011467,
+      "throughput_ops_per_sec": 630448.7717195733,
+      "memory_mb": 0.0,
+      "metadata": {
+        "target_hz": 1000,
+        "target_dt_ms": 1.0,
+        "simulated_time_s": 10.0,
+        "realtime_factor": 630.4487717195733,
+        "can_run_realtime": true
+      }
+    },
+    {
+      "test_name": "Parameter Scaling (dt=0.0001s)",
+      "duration_s": 0.0012714360000000001,
+      "iterations": 1000,
+      "mean_latency_ms": 0.001271436,
+      "median_latency_ms": 0.001222,
+      "p95_latency_ms": 0.001351,
+      "p99_latency_ms": 0.001549,
+      "min_latency_ms": 0.001071,
+      "max_latency_ms": 0.021118,
+      "throughput_ops_per_sec": 786512.2585800622,
+      "memory_mb": 0.0,
+      "metadata": {
+        "dt": 0.0001
+      }
+    },
+    {
+      "test_name": "Parameter Scaling (dt=0.0005s)",
+      "duration_s": 0.0012715989999999985,
+      "iterations": 1000,
+      "mean_latency_ms": 0.001271599,
+      "median_latency_ms": 0.00124,
+      "p95_latency_ms": 0.001336,
+      "p99_latency_ms": 0.001403,
+      "min_latency_ms": 0.00114,
+      "max_latency_ms": 0.011554,
+      "throughput_ops_per_sec": 786411.4394553638,
+      "memory_mb": 0.0,
+      "metadata": {
+        "dt": 0.0005
+      }
+    },
+    {
+      "test_name": "Parameter Scaling (dt=0.001s)",
+      "duration_s": 0.0012477389999999994,
+      "iterations": 1000,
+      "mean_latency_ms": 0.001247739,
+      "median_latency_ms": 0.001241,
+      "p95_latency_ms": 0.001334,
+      "p99_latency_ms": 0.001412,
+      "min_latency_ms": 0.001076,
+      "max_latency_ms": 0.004644,
+      "throughput_ops_per_sec": 801449.6621488953,
+      "memory_mb": 0.0,
+      "metadata": {
+        "dt": 0.001
+      }
+    },
+    {
+      "test_name": "Parameter Scaling (dt=0.005s)",
+      "duration_s": 0.001226551999999999,
+      "iterations": 1000,
+      "mean_latency_ms": 0.001226552,
+      "median_latency_ms": 0.001217,
+      "p95_latency_ms": 0.001326,
+      "p99_latency_ms": 0.00145,
+      "min_latency_ms": 0.001063,
+      "max_latency_ms": 0.003936,
+      "throughput_ops_per_sec": 815293.6035325048,
+      "memory_mb": 0.0,
+      "metadata": {
+        "dt": 0.005
+      }
+    },
+    {
+      "test_name": "Parameter Scaling (dt=0.01s)",
+      "duration_s": 0.00127227,
+      "iterations": 1000,
+      "mean_latency_ms": 0.00127227,
+      "median_latency_ms": 0.001262,
+      "p95_latency_ms": 0.00137,
+      "p99_latency_ms": 0.001494,
+      "min_latency_ms": 0.001082,
+      "max_latency_ms": 0.008907,
+      "throughput_ops_per_sec": 785996.6830939973,
+      "memory_mb": 0.0,
+      "metadata": {
+        "dt": 0.01
+      }
+    }
+  ]
+}

benchmarks/results/plp_vs_pid_validation.json

@@ -50022,7 +50022,7 @@
       "disturbance_rejection_time": 0.0,
       "noise_amplification": 0.24693005316107844,
       "control_effort": 1.9646503563061755,
-      "computation_time_us": 6.768041399999999,
+      "computation_time_us": 6.8092844,
       "stability_margin": 0.20406070310891564,
       "max_control_value": 0.21381508940429902
     },
@@ -50034,7 +50034,7 @@
       "disturbance_rejection_time": 0.0,
       "noise_amplification": 0.37800948291826,
       "control_effort": 8.311934466214723,
-      "computation_time_us": 4.0539564,
+      "computation_time_us": 4.0034568,
       "stability_margin": 0.37160875122898035,
       "max_control_value": 1.0
     }

pytest_output.log

@@ -0,0 +1,83 @@
+============================= test session starts ==============================
+platform linux -- Python 3.11.14, pytest-9.0.1, pluggy-1.6.0 -- /root/.local/share/uv/tools/pytest/bin/python
+cachedir: .pytest_cache
+rootdir: /home/user/Multi-Heart-Model
+collecting ... collected 8 items / 6 errors
+
+==================================== ERRORS ====================================
+_____ ERROR collecting tests/integration/test_microprocessor_motorhand.py ______
+ImportError while importing test module '/home/user/Multi-Heart-Model/tests/integration/test_microprocessor_motorhand.py'.
+Hint: make sure your test modules/packages have valid Python names.
+Traceback:
+/usr/lib/python3.11/importlib/__init__.py:126: in import_module
+    return _bootstrap._gcd_import(name[level:], package, level)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+tests/integration/test_microprocessor_motorhand.py:10: in <module>
+    import numpy as np
+E   ModuleNotFoundError: No module named 'numpy'
+___________ ERROR collecting tests/organ_chip/test_drug_toxicity.py ____________
+ImportError while importing test module '/home/user/Multi-Heart-Model/tests/organ_chip/test_drug_toxicity.py'.
+Hint: make sure your test modules/packages have valid Python names.
+Traceback:
+/usr/lib/python3.11/importlib/__init__.py:126: in import_module
+    return _bootstrap._gcd_import(name[level:], package, level)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+tests/organ_chip/test_drug_toxicity.py:18: in <module>
+    import numpy as np
+E   ModuleNotFoundError: No module named 'numpy'
+____________ ERROR collecting tests/organchip/test_drug_toxicity.py ____________
+ImportError while importing test module '/home/user/Multi-Heart-Model/tests/organchip/test_drug_toxicity.py'.
+Hint: make sure your test modules/packages have valid Python names.
+Traceback:
+/usr/lib/python3.11/importlib/__init__.py:126: in import_module
+    return _bootstrap._gcd_import(name[level:], package, level)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+tests/organchip/test_drug_toxicity.py:17: in <module>
+    from organchip.orchestrator import OrganChipSuite, create_default_organ_chip_suite
+E   ModuleNotFoundError: No module named 'organchip.orchestrator'
+_______ ERROR collecting tests/surgical_robotics/test_dvrk_interface.py ________
+ImportError while importing test module '/home/user/Multi-Heart-Model/tests/surgical_robotics/test_dvrk_interface.py'.
+Hint: make sure your test modules/packages have valid Python names.
+Traceback:
+/usr/lib/python3.11/importlib/__init__.py:126: in import_module
+    return _bootstrap._gcd_import(name[level:], package, level)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+tests/surgical_robotics/test_dvrk_interface.py:6: in <module>
+    import numpy as np
+E   ModuleNotFoundError: No module named 'numpy'
+______ ERROR collecting tests/surgical_robotics/test_physio_controller.py ______
+ImportError while importing test module '/home/user/Multi-Heart-Model/tests/surgical_robotics/test_physio_controller.py'.
+Hint: make sure your test modules/packages have valid Python names.
+Traceback:
+/usr/lib/python3.11/importlib/__init__.py:126: in import_module
+    return _bootstrap._gcd_import(name[level:], package, level)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+tests/surgical_robotics/test_physio_controller.py:6: in <module>
+    import numpy as np
+E   ModuleNotFoundError: No module named 'numpy'
+____________________ ERROR collecting tests/test_models.py _____________________
+ImportError while importing test module '/home/user/Multi-Heart-Model/tests/test_models.py'.
+Hint: make sure your test modules/packages have valid Python names.
+Traceback:
+/usr/lib/python3.11/importlib/__init__.py:126: in import_module
+    return _bootstrap._gcd_import(name[level:], package, level)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+tests/test_models.py:3: in <module>
+    from src.cardiac import VanDerPolOscillator
+src/__init__.py:3: in <module>
+    from . import neural, cardiac, coupling  # re-export packages
+    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+src/cardiac/__init__.py:26: in <module>
+    from .luo_rudy import LuoRudyModel, LuoRudyParameters
+src/cardiac/luo_rudy.py:29: in <module>
+    import numpy as np
+E   ModuleNotFoundError: No module named 'numpy'
+=========================== short test summary info ============================
+ERROR tests/integration/test_microprocessor_motorhand.py
+ERROR tests/organ_chip/test_drug_toxicity.py
+ERROR tests/organchip/test_drug_toxicity.py
+ERROR tests/surgical_robotics/test_dvrk_interface.py
+ERROR tests/surgical_robotics/test_physio_controller.py
+ERROR tests/test_models.py
+!!!!!!!!!!!!!!!!!!! Interrupted: 6 errors during collection !!!!!!!!!!!!!!!!!!!!
+============================== 6 errors in 0.65s ===============================

run_tests_simple.py

@@ -0,0 +1,129 @@
+#!/usr/bin/env python3
+"""
+Simple test runner that doesn't require pytest
+Runs basic functionality tests for all models
+"""
+
+import sys
+from pathlib import Path
+
+sys.path.insert(0, str(Path(__file__).parent / 'src'))
+
+def test_van_der_pol():
+    """Test Van der Pol oscillator"""
+    from src.cardiac import VanDerPolOscillator
+
+    model = VanDerPolOscillator(mu=1.5, omega=1.0)
+    state = (1.0, 0.0)
+
+    # Test step
+    new_state = model.step(0.0, state, 0.001)
+    assert len(new_state) == 2
+    assert not any(v != v for v in new_state)  # Check for NaN
+
+    return True
+
+def test_fitzhugh_nagumo():
+    """Test FitzHugh-Nagumo model"""
+    from src.neural import FitzHughNagumo
+
+    model = FitzHughNagumo(stimulus_amplitude=0.5)
+    state = (0.0, 0.0)
+
+    # Test step
+    new_state = model.step(0.0, state, 0.001)
+    assert len(new_state) == 2
+    assert not any(v != v for v in new_state)
+
+    return True
+
+def test_hbcm():
+    """Test Heart-Brain Coupling Model"""
+    from src.cardiac import VanDerPolOscillator
+    from src.neural import FitzHughNagumo
+    from src.coupling import HeartBrainCouplingModel
+
+    neural = FitzHughNagumo()
+    cardiac = VanDerPolOscillator()
+    hbcm = HeartBrainCouplingModel(neural_model=neural, cardiac_model=cardiac)
+
+    # Test simulation
+    trajectory = hbcm.simulate((0.0, 0.0, 1.0, 0.0), (0.0, 1.0), 0.001)
+    assert len(trajectory) > 0
+
+    return True
+
+def test_primal_processor():
+    """Test Primal Logic Processor"""
+    from src.microprocessor import PrimalLogicProcessor
+
+    processor = PrimalLogicProcessor()
+    control, state = processor.compute_control(
+        current_value=30.0,
+        target_value=0.0,
+        timestamp=0.0
+    )
+
+    assert -10.0 <= control <= 10.0
+    assert state.error == 30.0
+
+    return True
+
+def test_organchip():
+    """Test Organ Chip Suite"""
+    from src.organchip.orchestrator import create_default_organ_chip_suite
+
+    suite = create_default_organ_chip_suite()
+    suite.verbose = False
+
+    # Test initialization
+    state = suite.initialize_state(drug_amount_mg=100.0)
+    assert 'circulation' in state
+
+    return True
+
+def main():
+    """Run all tests"""
+    print("=" * 70)
+    print("SIMPLE TEST RUNNER - Multi-Heart-Model")
+    print("=" * 70)
+
+    tests = [
+        ("Van der Pol Oscillator", test_van_der_pol),
+        ("FitzHugh-Nagumo Model", test_fitzhugh_nagumo),
+        ("Heart-Brain Coupling Model", test_hbcm),
+        ("Primal Logic Processor", test_primal_processor),
+        ("Organ Chip Suite", test_organchip),
+    ]
+
+    results = []
+
+    for name, test_func in tests:
+        try:
+            print(f"\nTesting {name}...")
+            result = test_func()
+            print(f"  ✓ PASSED")
+            results.append((name, True))
+        except Exception as e:
+            print(f"  ✗ FAILED: {e}")
+            results.append((name, False))
+
+    print("\n" + "=" * 70)
+    print("TEST SUMMARY")
+    print("=" * 70)
+
+    passed = sum(1 for _, result in results if result)
+    total = len(results)
+
+    for name, result in results:
+        status = "✓ PASS" if result else "✗ FAIL"
+        print(f"  {status}: {name}")
+
+    print("=" * 70)
+    print(f"  Results: {passed}/{total} tests passed ({100*passed/total:.1f}%)")
+    print("=" * 70)
+
+    return 0 if passed == total else 1
+
+if __name__ == "__main__":
+    sys.exit(main())