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Run all repositories for maximum output (#25)
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‎COMPREHENSIVE_RUN_SUMMARY.md‎

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‎benchmarks/results/hbcm_20251125_145434.json‎

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

‎benchmarks/results/plp_vs_pid_validation.json‎

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"disturbance_rejection_time": 0.0,
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"noise_amplification": 0.24693005316107844,
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"control_effort": 1.9646503563061755,
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"computation_time_us": 6.768041399999999,
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"computation_time_us": 6.8092844,
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"stability_margin": 0.20406070310891564,
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"max_control_value": 0.21381508940429902
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},
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"disturbance_rejection_time": 0.0,
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"noise_amplification": 0.37800948291826,
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"control_effort": 8.311934466214723,
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"computation_time_us": 4.0539564,
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"computation_time_us": 4.0034568,
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"stability_margin": 0.37160875122898035,
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"max_control_value": 1.0
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}

‎pytest_output.log‎

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

‎run_tests_simple.py‎

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

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