iints-sdk-python35 0.1.17__tar.gz → 0.1.19__tar.gz

{iints_sdk_python35-0.1.17 → iints_sdk_python35-0.1.19}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: iints-sdk-python35
-Version: 0.1.17
+Version: 0.1.19
 Summary: A pre-clinical Edge-AI SDK for diabetes management validation.
 Author-email: Rune Bobbaers <rune.bobbaers@gmail.com>
 Project-URL: Homepage, https://github.com/python35/IINTS-SDK
@@ -42,6 +42,8 @@ Provides-Extra: research
 Requires-Dist: torch>=2.0.0; extra == "research"
 Requires-Dist: pyarrow>=12.0.0; extra == "research"
 Requires-Dist: h5py>=3.10.0; extra == "research"
+Requires-Dist: onnx>=1.16.0; extra == "research"
+Requires-Dist: onnxscript>=0.1.0; extra == "research"
 Dynamic: license-file
 
 # IINTS-AF SDK
@@ -50,6 +52,7 @@ Dynamic: license-file
 [![Python Package CI](https://github.com/python35/IINTS-SDK/actions/workflows/python-package.yml/badge.svg)](https://github.com/python35/IINTS-SDK/actions/workflows/python-package.yml)
 [![Coverage](https://raw.githubusercontent.com/python35/IINTS-SDK/main/badges/coverage.svg)](https://github.com/python35/IINTS-SDK/actions/workflows/health-badges.yml)
 [![Docs Coverage](https://raw.githubusercontent.com/python35/IINTS-SDK/main/badges/docs.svg)](https://github.com/python35/IINTS-SDK/actions/workflows/health-badges.yml)
+[![Site](https://img.shields.io/badge/site-IINTS--AF-0a66c2?style=flat&logo=firefox-browser&logoColor=white)](https://python35.github.io/IINTS-Site/index.html)
 
 <div style="text-align:center;">
   <img src="Ontwerp zonder titel.png" alt="" style="display:block; margin:0 auto;">

{iints_sdk_python35-0.1.17 → iints_sdk_python35-0.1.19}/README.md

@@ -4,6 +4,7 @@
 [![Python Package CI](https://github.com/python35/IINTS-SDK/actions/workflows/python-package.yml/badge.svg)](https://github.com/python35/IINTS-SDK/actions/workflows/python-package.yml)
 [![Coverage](https://raw.githubusercontent.com/python35/IINTS-SDK/main/badges/coverage.svg)](https://github.com/python35/IINTS-SDK/actions/workflows/health-badges.yml)
 [![Docs Coverage](https://raw.githubusercontent.com/python35/IINTS-SDK/main/badges/docs.svg)](https://github.com/python35/IINTS-SDK/actions/workflows/health-badges.yml)
+[![Site](https://img.shields.io/badge/site-IINTS--AF-0a66c2?style=flat&logo=firefox-browser&logoColor=white)](https://python35.github.io/IINTS-Site/index.html)
 
 <div style="text-align:center;">
   <img src="Ontwerp zonder titel.png" alt="" style="display:block; margin:0 auto;">

{iints_sdk_python35-0.1.17 → iints_sdk_python35-0.1.19}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "iints-sdk-python35" 
-version = "0.1.17"
+version = "0.1.19"
 authors = [
   { name="Rune Bobbaers", email="rune.bobbaers@gmail.com" },
 ]
@@ -55,6 +55,8 @@ research = [
   "torch>=2.0.0",
   "pyarrow>=12.0.0",
   "h5py>=3.10.0",
+  "onnx>=1.16.0",
+  "onnxscript>=0.1.0",
 ]
 
 [project.scripts]

{iints_sdk_python35-0.1.17 → iints_sdk_python35-0.1.19}/src/iints/__init__.py

@@ -3,7 +3,7 @@
 import pandas as pd # Required for type hints like pd.DataFrame
 from typing import Optional
 
-__version__ = "0.1.17"
+__version__ = "0.1.19"
 
 # Note to developers: this SDK is currently maintained by a single author.
 # Please report bugs via GitHub issues and feel free to contribute fixes via PRs.
@@ -20,6 +20,7 @@ from .api.base_algorithm import (
 # Core Simulation Components
 from .core.simulator import Simulator, StressEvent, SimulationLimitError
 from .core.patient.models import PatientModel
+from .core.patient.patient_factory import PatientFactory
 from .core.patient.profile import PatientProfile
 try:
     from .core.device_manager import DeviceManager
@@ -33,7 +34,12 @@ except Exception:  # pragma: no cover - fallback if torch/device manager import
 from .core.safety import SafetyConfig, SafetySupervisor
 from .core.devices.models import SensorModel, PumpModel
 from .core.algorithms.standard_pump_algo import StandardPumpAlgorithm
-from .core.algorithms.mock_algorithms import ConstantDoseAlgorithm, RandomDoseAlgorithm
+from .core.algorithms.mock_algorithms import (
+    ConstantDoseAlgorithm,
+    RandomDoseAlgorithm,
+    RunawayAIAlgorithm,
+    StackingAIAlgorithm,
+)
 
 # Data Handling
 from .data.ingestor import DataIngestor
@@ -52,6 +58,7 @@ from .data.nightscout import NightscoutConfig, import_nightscout
 from .data.tidepool import TidepoolClient, load_openapi_spec
 from .analysis.metrics import generate_benchmark_metrics # Added for benchmark
 from .analysis.reporting import ClinicalReportGenerator
+from .analysis.edge_efficiency import EnergyEstimate, estimate_energy_per_decision
 from .highlevel import run_simulation, run_full, run_population
 from .scenarios import ScenarioGeneratorConfig, generate_random_scenario
 
@@ -124,6 +131,7 @@ __all__ = [
     "InsulinAlgorithm", "AlgorithmInput", "AlgorithmResult", "AlgorithmMetadata", "WhyLogEntry",
     # Core
     "Simulator", "StressEvent", "PatientModel", "DeviceManager",
+    "PatientFactory",
     "PatientProfile",
     "SimulationLimitError",
     "SafetySupervisor",
@@ -133,6 +141,8 @@ __all__ = [
     "StandardPumpAlgorithm",
     "ConstantDoseAlgorithm",
     "RandomDoseAlgorithm",
+    "RunawayAIAlgorithm",
+    "StackingAIAlgorithm",
     # Data
     "DataIngestor",
     "ImportResult",
@@ -151,6 +161,8 @@ __all__ = [
     # Analysis Metrics
     "generate_benchmark_metrics",
     "ClinicalReportGenerator",
+    "EnergyEstimate",
+    "estimate_energy_per_decision",
     # Reporting
     "generate_report",
     "generate_quickstart_report",

iints_sdk_python35-0.1.19/src/iints/analysis/edge_efficiency.py

@@ -0,0 +1,33 @@
+from __future__ import annotations
+
+from dataclasses import dataclass
+
+
+@dataclass(frozen=True)
+class EnergyEstimate:
+    energy_joules: float
+    energy_microjoules: float
+    decisions_per_day: int
+    energy_joules_per_day: float
+    energy_millijoules_per_day: float
+
+
+def estimate_energy_per_decision(power_watts: float, latency_ms: float, decisions_per_day: int = 288) -> EnergyEstimate:
+    """
+    Estimate energy cost per decision on any device.
+
+    Energy (J) = Power (W) * Time (s)
+
+    decisions_per_day default: 288 (5-minute control loop)
+    """
+    latency_s = max(latency_ms, 0.0) / 1000.0
+    energy_j = max(power_watts, 0.0) * latency_s
+    energy_uj = energy_j * 1_000_000.0
+    energy_day_j = energy_j * max(int(decisions_per_day), 1)
+    return EnergyEstimate(
+        energy_joules=energy_j,
+        energy_microjoules=energy_uj,
+        decisions_per_day=max(int(decisions_per_day), 1),
+        energy_joules_per_day=energy_day_j,
+        energy_millijoules_per_day=energy_day_j * 1_000.0,
+    )

{iints_sdk_python35-0.1.17 → iints_sdk_python35-0.1.19}/src/iints/analysis/population_report.py

@@ -171,9 +171,10 @@ class PopulationReportGenerator:
         if hypo_cols:
             path = str(output_dir / "_plot_hypo_risk.png")
             fig, ax = plt.subplots(figsize=(6, 4))
-            data = [df[c].dropna().values for c in hypo_cols]
+            data = [df[c].dropna().astype(float).to_numpy() for c in hypo_cols]
             labels = ["TBR <70 mg/dL (%)", "TBR <54 mg/dL (%)"][:len(data)]
-            bp = ax.boxplot(data, labels=labels, patch_artist=True)
+            bp = ax.boxplot(data, patch_artist=True)
+            ax.set_xticklabels(labels)
             for patch, color in zip(bp["boxes"], [IINTS_BLUE, IINTS_RED]):
                 patch.set_facecolor(color)
                 patch.set_alpha(0.6)

{iints_sdk_python35-0.1.17 → iints_sdk_python35-0.1.19}/src/iints/analysis/safety_index.py

@@ -96,7 +96,7 @@ def _interpret(score: float, penalties: Dict[str, float], weights: Dict[str, flo
 
     # Identify the top penalty contributor
     weighted = {k: weights[k] * _norm(v, NORM_SCALES[k]) for k, v in penalties.items()}
-    top_key = max(weighted, key=weighted.get)
+    top_key = max(weighted, key=lambda k: weighted[k])
     key_labels = {
         "w_below54":    "time critically below 54 mg/dL",
         "w_below70":    "time below 70 mg/dL",
@@ -167,8 +167,8 @@ def _compute_hypo_episode_duration(glucose: pd.Series, time_step_minutes: float)
     An episode starts when glucose drops below 70 mg/dL and ends when it
     rises back above 70 mg/dL.  Returns 0.0 if no episodes.
     """
-    below = (glucose < 70.0).values
-    if not below.any():
+    below = (glucose < 70.0).to_numpy(dtype=bool)
+    if not np.any(below):
         return 0.0
 
     episode_lengths: list[int] = []
@@ -228,7 +228,8 @@ def compute_safety_index(
         weights = dict(weights)  # defensive copy
     _validate_weights(weights)
 
-    glucose = results_df["glucose_actual_mgdl"].astype(float)
+    glucose_series = results_df["glucose_actual_mgdl"].astype(float)
+    glucose = glucose_series.to_numpy(dtype=float)
     n = max(len(glucose), 1)
 
     # --- Component 1: TBR critical < 54 mg/dL (%) ---
@@ -243,10 +244,10 @@ def compute_safety_index(
     supervisor_rate = interventions / duration_hours
 
     # --- Component 4: Mean hypo episode duration (hours) ---
-    mean_episode_hr = _compute_hypo_episode_duration(glucose, time_step_minutes) / 60.0
+    mean_episode_hr = _compute_hypo_episode_duration(glucose_series, time_step_minutes) / 60.0
 
     # --- Component 5: Tail-risk binary (1 if any glucose < 54, else 0) ---
-    tail_risk = 1.0 if (glucose < 54.0).any() else 0.0
+    tail_risk = 1.0 if np.any(glucose < 54.0) else 0.0
 
     penalties: Dict[str, float] = {
         "w_below54":    tbr_critical,

{iints_sdk_python35-0.1.17 → iints_sdk_python35-0.1.19}/src/iints/cli/cli.py

@@ -226,7 +226,7 @@ def evaluate(
     output_dir: Annotated[Optional[Path], typer.Option(help="Output directory")] = None,
     max_workers: Annotated[Optional[int], typer.Option(help="Max parallel workers (default: all cores)")] = None,
     seed: Annotated[Optional[int], typer.Option(help="Random seed for reproducibility")] = None,
-    patient_model: Annotated[str, typer.Option("--patient-model", help="Patient model type: 'custom' or 'bergman'")] = "custom",
+    patient_model: Annotated[str, typer.Option("--patient-model", help="Patient model: auto, bergman, custom, simglucose")] = "auto",
 ):
     """
     Run a Monte Carlo population evaluation of an algorithm.
@@ -361,11 +361,15 @@ def init(
             algo_content = files("iints.templates").joinpath("default_algorithm.py").read_text()
             scenario_content = files("iints.templates.scenarios").joinpath("example_scenario.json").read_text()
             exercise_content = files("iints.templates.scenarios").joinpath("exercise_stress.json").read_text()
+            stacking_content = files("iints.templates.scenarios").joinpath("chaos_insulin_stacking.json").read_text()
+            runaway_content = files("iints.templates.scenarios").joinpath("chaos_runaway_ai.json").read_text()
         else:
             from importlib import resources
             algo_content = resources.read_text("iints.templates", "default_algorithm.py")
             scenario_content = resources.read_text("iints.templates.scenarios", "example_scenario.json")
             exercise_content = resources.read_text("iints.templates.scenarios", "exercise_stress.json")
+            stacking_content = resources.read_text("iints.templates.scenarios", "chaos_insulin_stacking.json")
+            runaway_content = resources.read_text("iints.templates.scenarios", "chaos_runaway_ai.json")
     except Exception as e:
         console.print(f"[bold red]Error reading template files: {e}[/bold red]")
         raise typer.Exit(code=1)
@@ -381,6 +385,10 @@ def init(
         f.write(scenario_content)
     with open(project_path / "scenarios" / "exercise_stress.json", "w") as f:
         f.write(exercise_content)
+    with open(project_path / "scenarios" / "chaos_insulin_stacking.json", "w") as f:
+        f.write(stacking_content)
+    with open(project_path / "scenarios" / "chaos_runaway_ai.json", "w") as f:
+        f.write(runaway_content)
         
     # Create README
     readme_content = f"""# {project_name}
@@ -573,6 +581,11 @@ def presets_run(
     output_dir: Annotated[Optional[Path], typer.Option(help="Directory to save outputs")] = None,
     compare_baselines: Annotated[bool, typer.Option(help="Run PID and standard pump baselines in the background")] = True,
     seed: Annotated[Optional[int], typer.Option(help="Random seed for deterministic runs")] = None,
+    patient_model_type: Annotated[str, typer.Option("--patient-model", help="Patient model: auto, bergman, custom, simglucose")] = "auto",
+    sensor_noise_std: Annotated[Optional[float], typer.Option("--sensor-noise-std", help="CGM noise std (mg/dL)")] = None,
+    sensor_lag_minutes: Annotated[Optional[int], typer.Option("--sensor-lag-minutes", help="CGM lag (minutes)")] = None,
+    sensor_dropout_prob: Annotated[Optional[float], typer.Option("--sensor-dropout-prob", help="CGM dropout probability (0-1)")] = None,
+    sensor_bias: Annotated[Optional[float], typer.Option("--sensor-bias", help="CGM bias (mg/dL)")] = None,
     safety_min_glucose: Annotated[Optional[float], typer.Option("--safety-min-glucose", help="Min plausible glucose (mg/dL)")] = None,
     safety_max_glucose: Annotated[Optional[float], typer.Option("--safety-max-glucose", help="Max plausible glucose (mg/dL)")] = None,
     safety_max_glucose_delta_per_5_min: Annotated[Optional[float], typer.Option("--safety-max-glucose-delta-per-5-min", help="Max glucose delta per 5 min (mg/dL)")] = None,
@@ -605,7 +618,7 @@ def presets_run(
     try:
         patient_config_name = preset.get("patient_config", "default_patient")
         validated_patient_params = load_patient_config_by_name(patient_config_name).model_dump()
-        patient_model = iints.PatientModel(**validated_patient_params)
+        patient_model = iints.PatientFactory.create_patient(patient_type=patient_model_type, **validated_patient_params)
     except ValidationError as e:
         console.print("[bold red]Patient config validation failed:[/bold red]")
         for line in format_validation_error(e):
@@ -634,12 +647,32 @@ def presets_run(
         critical_glucose_duration_minutes=safety_critical_glucose_duration_minutes,
     )
 
+    sensor_model = None
+    if any(v is not None for v in (sensor_noise_std, sensor_lag_minutes, sensor_dropout_prob, sensor_bias)):
+        sensor_model = iints.SensorModel(
+            noise_std=float(sensor_noise_std or 0.0),
+            lag_minutes=int(sensor_lag_minutes or 0),
+            dropout_prob=float(sensor_dropout_prob or 0.0),
+            bias=float(sensor_bias or 0.0),
+            seed=resolved_seed,
+        )
+    elif patient_model_type == "auto":
+        sensor_model = iints.SensorModel(
+            noise_std=7.0,
+            lag_minutes=10,
+            dropout_prob=0.0,
+            bias=0.0,
+            seed=resolved_seed,
+        )
+
     simulator_kwargs: Dict[str, Any] = {
         "patient_model": patient_model,
         "algorithm": algorithm_instance,
         "time_step": time_step,
         "safety_config": safety_config,
     }
+    if sensor_model is not None:
+        simulator_kwargs["sensor_model"] = sensor_model
     simulator_kwargs["seed"] = resolved_seed
     if safety_config is None:
         safety_config = SafetyConfig()
@@ -973,6 +1006,11 @@ def run(
     output_dir: Annotated[Optional[Path], typer.Option(help="Directory to save simulation results")] = None,
     compare_baselines: Annotated[bool, typer.Option(help="Run PID and standard pump baselines in the background")] = True,
     seed: Annotated[Optional[int], typer.Option(help="Random seed for deterministic runs")] = None,
+    patient_model_type: Annotated[str, typer.Option("--patient-model", help="Patient model: auto, bergman, custom, simglucose")] = "auto",
+    sensor_noise_std: Annotated[Optional[float], typer.Option("--sensor-noise-std", help="CGM noise std (mg/dL)")] = None,
+    sensor_lag_minutes: Annotated[Optional[int], typer.Option("--sensor-lag-minutes", help="CGM lag (minutes)")] = None,
+    sensor_dropout_prob: Annotated[Optional[float], typer.Option("--sensor-dropout-prob", help="CGM dropout probability (0-1)")] = None,
+    sensor_bias: Annotated[Optional[float], typer.Option("--sensor-bias", help="CGM bias (mg/dL)")] = None,
     safety_min_glucose: Annotated[Optional[float], typer.Option("--safety-min-glucose", help="Min plausible glucose (mg/dL)")] = None,
     safety_max_glucose: Annotated[Optional[float], typer.Option("--safety-max-glucose", help="Max plausible glucose (mg/dL)")] = None,
     safety_max_glucose_delta_per_5_min: Annotated[Optional[float], typer.Option("--safety-max-glucose-delta-per-5-min", help="Max glucose delta per 5 min (mg/dL)")] = None,
@@ -1052,8 +1090,11 @@ def run(
             validated_patient_params = load_patient_config_by_name(patient_config_name).model_dump()
             patient_label = patient_config_name
 
-        patient_model = iints.PatientModel(**validated_patient_params)
-        console.print(f"Using patient model: {patient_model.__class__.__name__} with config [cyan]{patient_label}[/cyan]")
+        patient_model = iints.PatientFactory.create_patient(patient_type=patient_model_type, **validated_patient_params)
+        console.print(
+            f"Using patient model: {patient_model.__class__.__name__} "
+            f"({patient_model_type}) with config [cyan]{patient_label}[/cyan]"
+        )
     except ValidationError as e:
         console.print("[bold red]Patient config validation failed:[/bold red]")
         for line in format_validation_error(e):
@@ -1117,12 +1158,31 @@ def run(
     output_dir = resolve_output_dir(output_dir, run_id)
 
     effective_safety_config = safety_config or SafetyConfig()
+    sensor_model = None
+    if any(v is not None for v in (sensor_noise_std, sensor_lag_minutes, sensor_dropout_prob, sensor_bias)):
+        sensor_model = iints.SensorModel(
+            noise_std=float(sensor_noise_std or 0.0),
+            lag_minutes=int(sensor_lag_minutes or 0),
+            dropout_prob=float(sensor_dropout_prob or 0.0),
+            bias=float(sensor_bias or 0.0),
+            seed=resolved_seed,
+        )
+    elif patient_model_type == "auto":
+        sensor_model = iints.SensorModel(
+            noise_std=7.0,
+            lag_minutes=10,
+            dropout_prob=0.0,
+            bias=0.0,
+            seed=resolved_seed,
+        )
+
     simulator = iints.Simulator(
         patient_model=patient_model,
         algorithm=algorithm_instance,
         time_step=time_step,
         seed=resolved_seed,
         safety_config=effective_safety_config,
+        sensor_model=sensor_model,
     )
     
     for event in stress_events:
@@ -1725,6 +1785,180 @@ def research_prepare_azt1d(
     console.print(f"[green]Quality report   :[/green] {report}")
 
 
+@research_app.command("prepare-ohio")
+def research_prepare_ohio(
+    input_dir: Annotated[Path, typer.Option(help="Root directory containing OhioT1DM patient_* folders")] = Path("data_packs/public/ohio_t1dm"),
+    output: Annotated[Path, typer.Option(help="Output dataset path (CSV or Parquet)")] = Path("data_packs/public/ohio_t1dm/processed/ohio_t1dm_merged.csv"),
+    report: Annotated[Path, typer.Option(help="Quality report output path")] = Path("data_packs/public/ohio_t1dm/quality_report.json"),
+    time_step: Annotated[int, typer.Option(help="Expected CGM sample interval (minutes)")] = 5,
+    max_gap_multiplier: Annotated[float, typer.Option(help="Segment-break gap multiplier")] = 2.5,
+    dia_minutes: Annotated[float, typer.Option(help="Insulin action duration (minutes)")] = 240.0,
+    peak_minutes: Annotated[float, typer.Option(help="IOB peak time (minutes, OpenAPS bilinear)")] = 75.0,
+    carb_absorb_minutes: Annotated[float, typer.Option(help="Carb absorption duration (minutes)")] = 120.0,
+    max_insulin: Annotated[float, typer.Option(help="Clip insulin units above this")] = 30.0,
+    max_carbs: Annotated[float, typer.Option(help="Clip carb grams above this")] = 200.0,
+    icr_default: Annotated[float, typer.Option(help="Fallback ICR (g/U)")] = 10.0,
+    isf_default: Annotated[float, typer.Option(help="Fallback ISF (mg/dL per U)")] = 50.0,
+    basal_default: Annotated[float, typer.Option(help="Fallback basal rate (U/hr)")] = 0.0,
+    meal_window_min: Annotated[float, typer.Option(help="Meal→insulin matching window (minutes)")] = 30.0,
+    isf_window_min: Annotated[float, typer.Option(help="ISF estimation window (minutes)")] = 60.0,
+    min_meal_carbs: Annotated[float, typer.Option(help="Minimum carbs to consider a meal (g)")] = 5.0,
+    min_bolus: Annotated[float, typer.Option(help="Minimum insulin to consider a bolus (U)")] = 0.1,
+):
+    """
+    Prepare the OhioT1DM dataset for LSTM predictor training.
+
+    Reads per-patient CSVs, derives IOB/COB using the OpenAPS bilinear model,
+    estimates effective ISF/ICR/basal per subject, adds time-of-day features,
+    and writes the merged dataset plus a quality report.
+
+    Example
+    -------
+    iints research prepare-ohio --input-dir data_packs/public/ohio_t1dm --output ohio.parquet
+    """
+    console = Console()
+    if not input_dir.exists():
+        console.print(f"[bold red]Input directory not found: {input_dir}[/bold red]")
+        raise typer.Exit(code=1)
+
+    import subprocess, sys  # noqa: E401
+    cmd = [
+        sys.executable,
+        str(Path(__file__).parent.parent.parent.parent.parent / "research" / "prepare_ohio_t1dm.py"),
+        "--input", str(input_dir),
+        "--output", str(output),
+        "--report", str(report),
+        "--time-step", str(time_step),
+        "--max-gap-multiplier", str(max_gap_multiplier),
+        "--dia-minutes", str(dia_minutes),
+        "--peak-minutes", str(peak_minutes),
+        "--carb-absorb-minutes", str(carb_absorb_minutes),
+        "--max-insulin", str(max_insulin),
+        "--max-carbs", str(max_carbs),
+        "--icr-default", str(icr_default),
+        "--isf-default", str(isf_default),
+        "--basal-default", str(basal_default),
+        "--meal-window-min", str(meal_window_min),
+        "--isf-window-min", str(isf_window_min),
+        "--min-meal-carbs", str(min_meal_carbs),
+        "--min-bolus", str(min_bolus),
+    ]
+    try:
+        import importlib.util as _ilu
+        spec = _ilu.spec_from_file_location(
+            "_prepare_ohio_t1dm",
+            Path(__file__).parent.parent.parent.parent.parent / "research" / "prepare_ohio_t1dm.py",
+        )
+        if spec is not None and spec.loader is not None:
+            import sys as _sys
+            _old_argv = _sys.argv[:]
+            _sys.argv = cmd[1:]
+            try:
+                mod = _ilu.module_from_spec(spec)
+                spec.loader.exec_module(mod)  # type: ignore[union-attr]
+                mod.main()  # type: ignore[attr-defined]
+            finally:
+                _sys.argv = _old_argv
+        else:
+            subprocess.run(cmd, check=True)
+    except Exception as exc:
+        console.print(f"[bold red]prepare-ohio failed: {exc}[/bold red]")
+        raise typer.Exit(code=1)
+
+    console.print(f"[green]Dataset written to:[/green] {output}")
+    console.print(f"[green]Quality report   :[/green] {report}")
+
+
+@research_app.command("prepare-hupa")
+def research_prepare_hupa(
+    input_dir: Annotated[Path, typer.Option(help="Root directory containing HUPA-UCM CSV files")] = Path("data_packs/public/hupa_ucm"),
+    output: Annotated[Path, typer.Option(help="Output dataset path (CSV or Parquet)")] = Path("data_packs/public/hupa_ucm/processed/hupa_ucm_merged.csv"),
+    report: Annotated[Path, typer.Option(help="Quality report output path")] = Path("data_packs/public/hupa_ucm/quality_report.json"),
+    time_step: Annotated[int, typer.Option(help="Expected CGM sample interval (minutes)")] = 5,
+    max_gap_multiplier: Annotated[float, typer.Option(help="Segment-break gap multiplier")] = 2.5,
+    dia_minutes: Annotated[float, typer.Option(help="Insulin action duration (minutes)")] = 240.0,
+    peak_minutes: Annotated[float, typer.Option(help="IOB peak time (minutes, OpenAPS bilinear)")] = 75.0,
+    carb_absorb_minutes: Annotated[float, typer.Option(help="Carb absorption duration (minutes)")] = 120.0,
+    max_insulin: Annotated[float, typer.Option(help="Clip insulin units above this")] = 30.0,
+    max_carbs: Annotated[float, typer.Option(help="Clip carb grams above this")] = 200.0,
+    carb_serving_grams: Annotated[float, typer.Option(help="Carb serving size (g) for carb_input")] = 10.0,
+    basal_is_rate: Annotated[bool, typer.Option(help="Treat basal_rate as U/hr (convert to U/step)")] = False,
+    icr_default: Annotated[float, typer.Option(help="Fallback ICR (g/U)")] = 10.0,
+    isf_default: Annotated[float, typer.Option(help="Fallback ISF (mg/dL per U)")] = 50.0,
+    basal_default: Annotated[float, typer.Option(help="Fallback basal rate (U/hr)")] = 0.0,
+    meal_window_min: Annotated[float, typer.Option(help="Meal→insulin matching window (minutes)")] = 30.0,
+    isf_window_min: Annotated[float, typer.Option(help="ISF estimation window (minutes)")] = 60.0,
+    min_meal_carbs: Annotated[float, typer.Option(help="Minimum carbs to consider a meal (g)")] = 5.0,
+    min_bolus: Annotated[float, typer.Option(help="Minimum insulin to consider a bolus (U)")] = 0.1,
+):
+    """
+    Prepare the HUPA-UCM dataset for LSTM predictor training.
+
+    Parses per-patient CSVs, derives IOB/COB, estimates ISF/ICR/basal per
+    subject, and writes the merged dataset plus a quality report.
+
+    Example
+    -------
+    iints research prepare-hupa --input-dir data_packs/public/hupa_ucm --output hupa.parquet
+    """
+    console = Console()
+    if not input_dir.exists():
+        console.print(f"[bold red]Input directory not found: {input_dir}[/bold red]")
+        raise typer.Exit(code=1)
+
+    import subprocess, sys  # noqa: E401
+    cmd = [
+        sys.executable,
+        str(Path(__file__).parent.parent.parent.parent.parent / "research" / "prepare_hupa_ucm.py"),
+        "--input", str(input_dir),
+        "--output", str(output),
+        "--report", str(report),
+        "--time-step", str(time_step),
+        "--max-gap-multiplier", str(max_gap_multiplier),
+        "--dia-minutes", str(dia_minutes),
+        "--peak-minutes", str(peak_minutes),
+        "--carb-absorb-minutes", str(carb_absorb_minutes),
+        "--max-insulin", str(max_insulin),
+        "--max-carbs", str(max_carbs),
+        "--carb-serving-grams", str(carb_serving_grams),
+        "--icr-default", str(icr_default),
+        "--isf-default", str(isf_default),
+        "--basal-default", str(basal_default),
+        "--meal-window-min", str(meal_window_min),
+        "--isf-window-min", str(isf_window_min),
+        "--min-meal-carbs", str(min_meal_carbs),
+        "--min-bolus", str(min_bolus),
+    ]
+    if basal_is_rate:
+        cmd.append("--basal-is-rate")
+    else:
+        cmd.append("--no-basal-is-rate")
+    try:
+        import importlib.util as _ilu
+        spec = _ilu.spec_from_file_location(
+            "_prepare_hupa_ucm",
+            Path(__file__).parent.parent.parent.parent.parent / "research" / "prepare_hupa_ucm.py",
+        )
+        if spec is not None and spec.loader is not None:
+            import sys as _sys
+            _old_argv = _sys.argv[:]
+            _sys.argv = cmd[1:]
+            try:
+                mod = _ilu.module_from_spec(spec)
+                spec.loader.exec_module(mod)  # type: ignore[union-attr]
+                mod.main()  # type: ignore[attr-defined]
+            finally:
+                _sys.argv = _old_argv
+        else:
+            subprocess.run(cmd, check=True)
+    except Exception as exc:
+        console.print(f"[bold red]prepare-hupa failed: {exc}[/bold red]")
+        raise typer.Exit(code=1)
+
+    console.print(f"[green]Dataset written to:[/green] {output}")
+    console.print(f"[green]Quality report   :[/green] {report}")
+
+
 @research_app.command("quality")
 def research_quality(
     report: Annotated[Path, typer.Option(help="Path to quality_report.json produced by prepare-azt1d")] = Path("data_packs/public/azt1d/quality_report.json"),
@@ -1790,6 +2024,35 @@ def research_quality(
     console.print(table)
 
 
+@research_app.command("export-onnx")
+def research_export_onnx(
+    model: Annotated[Path, typer.Option(help="Predictor checkpoint (.pt)")] = Path("models/hupa_finetuned_v2/predictor.pt"),
+    out: Annotated[Path, typer.Option(help="Output ONNX file path")] = Path("models/predictor.onnx"),
+):
+    """
+    Export a trained predictor to ONNX for edge/Jetson deployment.
+    """
+    console = Console()
+    if not model.exists():
+        console.print(f"[bold red]Model not found: {model}[/bold red]")
+        raise typer.Exit(code=1)
+
+    import subprocess, sys  # noqa: E401
+    cmd = [
+        sys.executable,
+        str(Path(__file__).parent.parent.parent.parent.parent / "research" / "export_predictor.py"),
+        "--model", str(model),
+        "--out", str(out),
+    ]
+    try:
+        subprocess.run(cmd, check=True)
+    except Exception as exc:
+        console.print(f"[bold red]export-onnx failed: {exc}[/bold red]")
+        raise typer.Exit(code=1)
+
+    console.print(f"[green]ONNX written to:[/green] {out}")
+
+
 @app.command("import-data")
 def import_data(
     input_csv: Annotated[Path, typer.Option(help="Path to CGM CSV file")],