iints-sdk-python35 0.1.7__tar.gz

iints_sdk_python35-0.1.7/LICENSE

@@ -0,0 +1,28 @@
+MIT License
+
+Copyright (c) 2026 IINTS-AF Contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+ACADEMIC USE DISCLAIMER:
+This software is intended for academic research purposes only. It is not 
+intended for clinical use or as a medical device. Users must comply with 
+all applicable regulations and obtain proper approvals before any clinical 
+application. The authors disclaim any responsibility for clinical use of 
+this software.

iints_sdk_python35-0.1.7/PKG-INFO

@@ -0,0 +1,122 @@
+Metadata-Version: 2.4
+Name: iints-sdk-python35
+Version: 0.1.7
+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
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Development Status :: 3 - Alpha
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: fpdf2>=2.8.0
+Requires-Dist: matplotlib>=3.5.0
+Requires-Dist: numpy>=1.24.0
+Requires-Dist: openpyxl>=3.0.0
+Requires-Dist: pandas>=2.0.0
+Requires-Dist: pydantic>=2.0.0
+Requires-Dist: PyYAML
+Requires-Dist: rich>=12.0.0
+Requires-Dist: scipy>=1.9.0
+Requires-Dist: seaborn>=0.11.0
+Requires-Dist: typer[all]
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: pandas-stubs; extra == "dev"
+Requires-Dist: types-PyYAML; extra == "dev"
+Requires-Dist: types-psutil; extra == "dev"
+Provides-Extra: torch
+Requires-Dist: torch>=1.9.0; extra == "torch"
+Dynamic: license-file
+
+# IINTS-AF SDK (v0.1.5)
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/python35/IINTS-SDK/blob/main/examples/notebooks/00_Quickstart.ipynb)
+[![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)
+
+## Intelligent Insulin Titration System for Artificial Pancreas
+
+IINTS-AF is a **safety-first simulation and validation platform** for insulin dosing algorithms. It lets you test AI or classical controllers on virtual patients, enforce deterministic safety constraints, and generate audit-ready clinical reports before anything touches a real patient.
+
+**In one session you can**:
+* Run a clinic-safe preset and compare against PID and standard pump baselines
+* Import real-world CGM CSV into a standard schema + scenario JSON
+* Use the bundled demo CGM data pack (zero setup)
+* Export a clean PDF report plus full audit trail (JSONL/CSV)
+* Stress-test sensor noise, pump limits, and human-in-the-loop interventions
+* Generate patient profiles with ISF/ICR + dawn phenomenon
+
+**Who it’s for**:
+* Diabetes researchers and clinicians validating new control strategies
+* ML engineers benchmarking AI controllers with medical safety rails
+* Developers building decision-support systems for closed-loop insulin delivery
+
+### Quick Start (CLI)
+```bash
+iints quickstart --project-name iints_quickstart
+cd iints_quickstart
+iints presets run --name baseline_t1d --algo algorithms/example_algorithm.py
+```
+
+One-line full run (CSV + audit + PDF + baseline):
+```bash
+iints run-full --algo algorithms/example_algorithm.py \
+  --scenario-path scenarios/clinic_safe_baseline.json \
+  --output-dir results/run_full
+```
+
+Import real-world CGM data:
+```bash
+iints import-data --input-csv data/my_cgm.csv --output-dir results/imported
+```
+
+Try the bundled demo data pack:
+```bash
+iints import-demo --output-dir results/demo_import
+```
+
+Or run the full demo workflow (import + run + report) in one script:
+```bash
+python3 examples/demo_quickstart_flow.py
+```
+
+### Quick Start (Python)
+```python
+import iints
+from iints.core.algorithms.pid_controller import PIDController
+
+outputs = iints.run_simulation(
+    algorithm=PIDController(),
+    scenario="scenarios/example_scenario.json",
+    patient_config="default_patient",
+    duration_minutes=720,
+    seed=42,
+    output_dir="results/quick_run",
+)
+```
+
+### Notebook Guide
+Hands-on Jupyter notebooks live in `examples/notebooks/` and cover the full workflow (each is Colab-ready):
+
+* Quickstart end-to-end run
+* Presets + scenario validation
+* Safety supervisor behavior
+* Audit trail + PDF report export
+* Baseline comparison + clinical metrics
+* Sensor/pump models + human-in-the-loop
+* Optional Torch/LSTM usage
+* Ablation study (with/without Supervisor)
+
+### Documentation
+* Product manual: `SDK_COMPREHENSIVE_GUIDE.md`
+* Notebook index: `examples/notebooks/README.md`
+* Technical README: `TECHNICAL_README.md`
+* API Stability: `API_STABILITY.md`
+
+### Ethics & Safety
+This SDK is for **research and validation**. It is not a medical device and does not provide clinical dosing advice.
+
+> “Code shouldn’t be a secret when it’s managing a life.” — Bobbaers Rune

iints_sdk_python35-0.1.7/README.md

@@ -0,0 +1,87 @@
+# IINTS-AF SDK (v0.1.5)
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/python35/IINTS-SDK/blob/main/examples/notebooks/00_Quickstart.ipynb)
+[![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)
+
+## Intelligent Insulin Titration System for Artificial Pancreas
+
+IINTS-AF is a **safety-first simulation and validation platform** for insulin dosing algorithms. It lets you test AI or classical controllers on virtual patients, enforce deterministic safety constraints, and generate audit-ready clinical reports before anything touches a real patient.
+
+**In one session you can**:
+* Run a clinic-safe preset and compare against PID and standard pump baselines
+* Import real-world CGM CSV into a standard schema + scenario JSON
+* Use the bundled demo CGM data pack (zero setup)
+* Export a clean PDF report plus full audit trail (JSONL/CSV)
+* Stress-test sensor noise, pump limits, and human-in-the-loop interventions
+* Generate patient profiles with ISF/ICR + dawn phenomenon
+
+**Who it’s for**:
+* Diabetes researchers and clinicians validating new control strategies
+* ML engineers benchmarking AI controllers with medical safety rails
+* Developers building decision-support systems for closed-loop insulin delivery
+
+### Quick Start (CLI)
+```bash
+iints quickstart --project-name iints_quickstart
+cd iints_quickstart
+iints presets run --name baseline_t1d --algo algorithms/example_algorithm.py
+```
+
+One-line full run (CSV + audit + PDF + baseline):
+```bash
+iints run-full --algo algorithms/example_algorithm.py \
+  --scenario-path scenarios/clinic_safe_baseline.json \
+  --output-dir results/run_full
+```
+
+Import real-world CGM data:
+```bash
+iints import-data --input-csv data/my_cgm.csv --output-dir results/imported
+```
+
+Try the bundled demo data pack:
+```bash
+iints import-demo --output-dir results/demo_import
+```
+
+Or run the full demo workflow (import + run + report) in one script:
+```bash
+python3 examples/demo_quickstart_flow.py
+```
+
+### Quick Start (Python)
+```python
+import iints
+from iints.core.algorithms.pid_controller import PIDController
+
+outputs = iints.run_simulation(
+    algorithm=PIDController(),
+    scenario="scenarios/example_scenario.json",
+    patient_config="default_patient",
+    duration_minutes=720,
+    seed=42,
+    output_dir="results/quick_run",
+)
+```
+
+### Notebook Guide
+Hands-on Jupyter notebooks live in `examples/notebooks/` and cover the full workflow (each is Colab-ready):
+
+* Quickstart end-to-end run
+* Presets + scenario validation
+* Safety supervisor behavior
+* Audit trail + PDF report export
+* Baseline comparison + clinical metrics
+* Sensor/pump models + human-in-the-loop
+* Optional Torch/LSTM usage
+* Ablation study (with/without Supervisor)
+
+### Documentation
+* Product manual: `SDK_COMPREHENSIVE_GUIDE.md`
+* Notebook index: `examples/notebooks/README.md`
+* Technical README: `TECHNICAL_README.md`
+* API Stability: `API_STABILITY.md`
+
+### Ethics & Safety
+This SDK is for **research and validation**. It is not a medical device and does not provide clinical dosing advice.
+
+> “Code shouldn’t be a secret when it’s managing a life.” — Bobbaers Rune

iints_sdk_python35-0.1.7/pyproject.toml

@@ -0,0 +1,60 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "iints-sdk-python35" 
+version = "0.1.7"
+authors = [
+  { name="Rune Bobbaers", email="rune.bobbaers@gmail.com" },
+]
+description = "A pre-clinical Edge-AI SDK for diabetes management validation."
+readme = "README.md"
+requires-python = ">=3.8"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Development Status :: 3 - Alpha",
+]
+dependencies = [
+    "fpdf2>=2.8.0",
+    "matplotlib>=3.5.0",
+    "numpy>=1.24.0",
+    "openpyxl>=3.0.0",
+    "pandas>=2.0.0",
+    "pydantic>=2.0.0",
+    "PyYAML",
+    "rich>=12.0.0",
+    "scipy>=1.9.0",
+    "seaborn>=0.11.0",
+    "typer[all]",
+]
+
+[project.optional-dependencies]
+dev = [
+  "pytest>=7.0.0",
+  "flake8",
+  "mypy",
+  "pandas-stubs",
+  "types-PyYAML",
+  "types-psutil",
+]
+torch = [
+  "torch>=1.9.0",
+]
+
+[project.scripts]
+iints = "iints.cli.cli:app"
+
+[project.urls]
+"Homepage" = "https://github.com/python35/IINTS-SDK"
+
+[tool.setuptools.package-data]
+iints = [
+  "templates/*.py",
+  "templates/scenarios/*.json",
+  "data/virtual_patients/*.yaml",
+  "data/demo/*.csv",
+  "presets/*.json",
+]

iints_sdk_python35-0.1.7/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

iints_sdk_python35-0.1.7/src/iints/__init__.py

@@ -0,0 +1,134 @@
+# src/iints/__init__.py
+
+import pandas as pd # Required for type hints like pd.DataFrame
+from typing import Optional
+
+__version__ = "0.1.5"
+
+# API Components for Algorithm Development
+from .api.base_algorithm import (
+    InsulinAlgorithm,
+    AlgorithmInput,
+    AlgorithmResult,
+    AlgorithmMetadata,
+    WhyLogEntry,
+)
+
+# Core Simulation Components
+from .core.simulator import Simulator, StressEvent, SimulationLimitError
+from .core.patient.models import PatientModel
+from .core.patient.profile import PatientProfile
+try:
+    from .core.device_manager import DeviceManager
+except Exception:  # pragma: no cover - fallback if torch/device manager import fails
+    class DeviceManager:  # type: ignore
+        def __init__(self):
+            self._device = "cpu"
+
+        def get_device(self):
+            return self._device
+from .core.safety import SafetySupervisor
+from .core.devices.models import SensorModel, PumpModel
+from .core.algorithms.standard_pump_algo import StandardPumpAlgorithm
+from .core.algorithms.mock_algorithms import ConstantDoseAlgorithm, RandomDoseAlgorithm
+
+# Data Handling
+from .data.ingestor import DataIngestor
+from .data.importer import (
+    ImportResult,
+    export_demo_csv,
+    export_standard_csv,
+    guess_column_mapping,
+    import_cgm_csv,
+    import_cgm_dataframe,
+    load_demo_dataframe,
+    scenario_from_csv,
+    scenario_from_dataframe,
+)
+from .analysis.metrics import generate_benchmark_metrics # Added for benchmark
+from .analysis.reporting import ClinicalReportGenerator
+from .highlevel import run_simulation, run_full
+
+# Placeholder for Reporting/Analysis
+# This will be further developed in a dedicated module (e.g., iints.analysis.reporting)
+def generate_report(simulation_results: 'pd.DataFrame', output_path: Optional[str] = None, safety_report: Optional[dict] = None) -> Optional[str]:
+    """
+    Generate a clinical PDF report from simulation results.
+    """
+    if output_path is None:
+        return None
+    generator = ClinicalReportGenerator()
+    return generator.generate_pdf(simulation_results, safety_report or {}, output_path)
+
+def generate_quickstart_report(
+    simulation_results: 'pd.DataFrame',
+    output_path: Optional[str] = None,
+    safety_report: Optional[dict] = None,
+) -> Optional[str]:
+    """
+    Generate a concise Quickstart PDF report from simulation results.
+    """
+    if output_path is None:
+        return None
+    generator = ClinicalReportGenerator()
+    return generator.generate_pdf(
+        simulation_results,
+        safety_report or {},
+        output_path,
+        title="IINTS-AF Quickstart Report",
+    )
+
+def generate_demo_report(
+    simulation_results: 'pd.DataFrame',
+    output_path: Optional[str] = None,
+    safety_report: Optional[dict] = None,
+) -> Optional[str]:
+    """
+    Generate a demo-friendly PDF with big visuals (Maker Faire style).
+    """
+    if output_path is None:
+        return None
+    generator = ClinicalReportGenerator()
+    return generator.generate_demo_pdf(
+        simulation_results,
+        safety_report or {},
+        output_path,
+        title="IINTS-AF Demo Report",
+    )
+
+# You can also define __all__ to explicitly control what gets imported with `from iints import *`
+__all__ = [
+    # API
+    "InsulinAlgorithm", "AlgorithmInput", "AlgorithmResult", "AlgorithmMetadata", "WhyLogEntry",
+    # Core
+    "Simulator", "StressEvent", "PatientModel", "DeviceManager",
+    "PatientProfile",
+    "SimulationLimitError",
+    "SafetySupervisor",
+    "SensorModel",
+    "PumpModel",
+    "StandardPumpAlgorithm",
+    "ConstantDoseAlgorithm",
+    "RandomDoseAlgorithm",
+    # Data
+    "DataIngestor",
+    "ImportResult",
+    "export_demo_csv",
+    "export_standard_csv",
+    "guess_column_mapping",
+    "import_cgm_csv",
+    "import_cgm_dataframe",
+    "load_demo_dataframe",
+    "scenario_from_csv",
+    "scenario_from_dataframe",
+    # Analysis Metrics
+    "generate_benchmark_metrics",
+    "ClinicalReportGenerator",
+    # Reporting
+    "generate_report",
+    "generate_quickstart_report",
+    "generate_demo_report",
+    # High-level API
+    "run_simulation",
+    "run_full",
+]

iints_sdk_python35-0.1.7/src/iints/analysis/__init__.py

@@ -0,0 +1,12 @@
+from .clinical_metrics import ClinicalMetricsCalculator, ClinicalMetricsResult
+from .baseline import compute_metrics, run_baseline_comparison, write_baseline_comparison
+from .reporting import ClinicalReportGenerator
+
+__all__ = [
+    "ClinicalMetricsCalculator",
+    "ClinicalMetricsResult",
+    "ClinicalReportGenerator",
+    "compute_metrics",
+    "run_baseline_comparison",
+    "write_baseline_comparison",
+]