iints-sdk-python35 1.5.0__tar.gz → 1.5.2__tar.gz

iints_sdk_python35-1.5.2/PKG-INFO

@@ -0,0 +1,120 @@
+Metadata-Version: 2.4
+Name: iints-sdk-python35
+Version: 1.5.2
+Summary: A pre-clinical Edge-AI SDK for diabetes management validation.
+Author-email: Rune Bobbaers <rune.bobbaers@gmail.com>
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/python35/IINTS-SDK
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Operating System :: OS Independent
+Classifier: Development Status :: 5 - Production/Stable
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE
+License-File: LICENSE-MIT-IINTS-LEGACY
+Requires-Dist: fastapi>=0.115.0
+Requires-Dist: numpy>=1.24.0
+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: typer[all]
+Requires-Dist: uvicorn>=0.30.0
+Provides-Extra: edge
+Provides-Extra: reports
+Requires-Dist: fpdf2>=2.8.0; extra == "reports"
+Requires-Dist: matplotlib>=3.5.0; extra == "reports"
+Requires-Dist: openpyxl>=3.0.0; extra == "reports"
+Requires-Dist: pillow>=12.1.1; extra == "reports"
+Requires-Dist: seaborn>=0.11.0; extra == "reports"
+Provides-Extra: full
+Requires-Dist: fpdf2>=2.8.0; extra == "full"
+Requires-Dist: matplotlib>=3.5.0; extra == "full"
+Requires-Dist: openpyxl>=3.0.0; extra == "full"
+Requires-Dist: pillow>=12.1.1; extra == "full"
+Requires-Dist: seaborn>=0.11.0; extra == "full"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: hypothesis>=6.0.0; 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"
+Provides-Extra: nightscout
+Requires-Dist: py-nightscout; extra == "nightscout"
+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"
+Provides-Extra: mdmp
+Requires-Dist: cryptography>=42.0.0; extra == "mdmp"
+Dynamic: license-file
+
+# IINTS-AF SDK
+[![PyPI version](https://badge.fury.io/py/iints-sdk-python35.svg)](https://badge.fury.io/py/iints-sdk-python35)
+[![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)
+[![Docs](https://img.shields.io/badge/docs-IINTS--AF-0a66c2?style=flat&logo=firefox-browser&logoColor=white)](https://python35.github.io/IINTS-SDK/)
+
+One platform for insulin-algorithm research.
+
+IINTS-AF combines three layers in one SDK:
+- **Simulate** insulin algorithms on virtual patients
+- **Certify** the data and outputs with built-in trust grading
+- **Understand** results with reports, posters, and local AI review
+
+Docs: [python35.github.io/IINTS-SDK](https://python35.github.io/IINTS-SDK/)
+
+## Install
+```bash
+python3 -m venv .venv
+source .venv/bin/activate
+python -m pip install -U pip
+python -m pip install -U "iints-sdk-python35[full,mdmp]"
+```
+
+For Raspberry Pi or UNO Q edge rigs, use `iints-sdk-python35[edge,mdmp]` and follow `docs/EDGE_HARDWARE.md`.
+
+Edge workflow:
+```bash
+iints edge setup --output-dir iints_edge_demo --board raspberry_pi
+iints edge status --workspace iints_edge_demo/patient_runtime
+iints edge bundle --workspace iints_edge_demo/patient_runtime --output results/edge_runtime_bundle.zip
+```
+
+Sanity check:
+```bash
+iints doctor --smoke-run
+```
+
+## Quick Flow
+```bash
+iints quickstart --project-name iints_quickstart
+cd iints_quickstart
+iints presets run --name baseline_t1d --algo algorithms/example_algorithm.py
+iints data certify contracts/clinical_mdmp_contract.yaml results/<run_id>/results.csv --output-json results/<run_id>/certification.json
+iints ai report results/<run_id>
+```
+
+## Read Next
+- Start here: `docs/GETTING_STARTED.md`
+- Installation and paths: `docs/INSTALLATION.md`
+- Edge hardware profiles: `docs/EDGE_HARDWARE.md`
+- Raspberry Pi digital patient: `docs/DIGITAL_PATIENT_PI.md`
+- Study analysis: `docs/STUDY_ANALYSIS.md`
+- AI assistant: `docs/AI_ASSISTANT.md`
+- Data certification: `docs/MDMP_QUICKSTART.md`
+- Full manual: `docs/manuals/IINTS-AF_SDK_Manual.md`
+
+## Important
+IINTS-AF is research software. It is not a medical device and does not provide clinical treatment advice.

iints_sdk_python35-1.5.2/README.md

@@ -0,0 +1,57 @@
+# IINTS-AF SDK
+[![PyPI version](https://badge.fury.io/py/iints-sdk-python35.svg)](https://badge.fury.io/py/iints-sdk-python35)
+[![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)
+[![Docs](https://img.shields.io/badge/docs-IINTS--AF-0a66c2?style=flat&logo=firefox-browser&logoColor=white)](https://python35.github.io/IINTS-SDK/)
+
+One platform for insulin-algorithm research.
+
+IINTS-AF combines three layers in one SDK:
+- **Simulate** insulin algorithms on virtual patients
+- **Certify** the data and outputs with built-in trust grading
+- **Understand** results with reports, posters, and local AI review
+
+Docs: [python35.github.io/IINTS-SDK](https://python35.github.io/IINTS-SDK/)
+
+## Install
+```bash
+python3 -m venv .venv
+source .venv/bin/activate
+python -m pip install -U pip
+python -m pip install -U "iints-sdk-python35[full,mdmp]"
+```
+
+For Raspberry Pi or UNO Q edge rigs, use `iints-sdk-python35[edge,mdmp]` and follow `docs/EDGE_HARDWARE.md`.
+
+Edge workflow:
+```bash
+iints edge setup --output-dir iints_edge_demo --board raspberry_pi
+iints edge status --workspace iints_edge_demo/patient_runtime
+iints edge bundle --workspace iints_edge_demo/patient_runtime --output results/edge_runtime_bundle.zip
+```
+
+Sanity check:
+```bash
+iints doctor --smoke-run
+```
+
+## Quick Flow
+```bash
+iints quickstart --project-name iints_quickstart
+cd iints_quickstart
+iints presets run --name baseline_t1d --algo algorithms/example_algorithm.py
+iints data certify contracts/clinical_mdmp_contract.yaml results/<run_id>/results.csv --output-json results/<run_id>/certification.json
+iints ai report results/<run_id>
+```
+
+## Read Next
+- Start here: `docs/GETTING_STARTED.md`
+- Installation and paths: `docs/INSTALLATION.md`
+- Edge hardware profiles: `docs/EDGE_HARDWARE.md`
+- Raspberry Pi digital patient: `docs/DIGITAL_PATIENT_PI.md`
+- Study analysis: `docs/STUDY_ANALYSIS.md`
+- AI assistant: `docs/AI_ASSISTANT.md`
+- Data certification: `docs/MDMP_QUICKSTART.md`
+- Full manual: `docs/manuals/IINTS-AF_SDK_Manual.md`
+
+## Important
+IINTS-AF is research software. It is not a medical device and does not provide clinical treatment advice.

{iints_sdk_python35-1.5.0 → iints_sdk_python35-1.5.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "iints-sdk-python35" 
-version = "1.5.0"
+version = "1.5.2"
 authors = [
   { name="Rune Bobbaers", email="rune.bobbaers@gmail.com" },
 ]
@@ -23,21 +23,33 @@ classifiers = [
     "Development Status :: 5 - Production/Stable",
 ]
 dependencies = [
-    "fpdf2>=2.8.0",
-    "matplotlib>=3.5.0",
+    "fastapi>=0.115.0",
     "numpy>=1.24.0",
-    "openpyxl>=3.0.0",
     "pandas>=2.0.0",
-    "pillow>=12.1.1",
     "pydantic>=2.0.0",
     "PyYAML",
     "rich>=12.0.0",
     "scipy>=1.9.0",
-    "seaborn>=0.11.0",
     "typer[all]",
+    "uvicorn>=0.30.0",
 ]
 
 [project.optional-dependencies]
+edge = []
+reports = [
+  "fpdf2>=2.8.0",
+  "matplotlib>=3.5.0",
+  "openpyxl>=3.0.0",
+  "pillow>=12.1.1",
+  "seaborn>=0.11.0",
+]
+full = [
+  "fpdf2>=2.8.0",
+  "matplotlib>=3.5.0",
+  "openpyxl>=3.0.0",
+  "pillow>=12.1.1",
+  "seaborn>=0.11.0",
+]
 dev = [
   "pytest>=7.0.0",
   "hypothesis>=6.0.0",
@@ -67,7 +79,6 @@ mdmp = [
 [project.scripts]
 iints = "iints.cli.cli:app"
 iints-sdk-doctor = "iints_sdk_python35_doctor:main"
-mdmp = "mdmp_core.cli:app"
 
 [project.entry-points."iints.algorithms"]
 "PID Controller" = "iints.core.algorithms.pid_controller:PIDController"
@@ -87,6 +98,8 @@ where = ["src"]
 iints = [
   "templates/*.py",
   "templates/scenarios/*.json",
+  "templates/uno_q/*.ino",
+  "templates/uno_q/*.md",
   "assets/*.png",
   "data/*.json",
   "data/virtual_patients/*.yaml",

{iints_sdk_python35-1.5.0 → iints_sdk_python35-1.5.2}/src/iints/__init__.py

@@ -11,11 +11,18 @@ except ImportError:  # pragma: no cover - Python < 3.8 fallback
 try:
     __version__ = version("iints-sdk-python35")
 except PackageNotFoundError:  # pragma: no cover - source tree fallback
-    __version__ = "1.5.0"
+    __version__ = "1.5.2"
 
 # 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.
 
+
+def _missing_reports_dependency(feature: str, exc: Exception) -> None:
+    raise ImportError(
+        f"{feature} requires the optional reporting stack. Install "
+        f"'iints-sdk-python35[reports]' or 'iints-sdk-python35[full]'."
+    ) from exc
+
 # API Components for Algorithm Development
 from .api.base_algorithm import (
     InsulinAlgorithm,
@@ -70,16 +77,60 @@ from .data.nightscout import NightscoutConfig, import_nightscout
 from .data.tidepool import TidepoolClient, load_openapi_spec
 from .data.guardians import mdmp_gate, MDMPGateError
 from .data.synthetic_mirror import generate_synthetic_mirror, SyntheticMirrorArtifact
+from .data.study_corruption import AVAILABLE_STUDY_CORRUPTIONS, apply_study_corruptions, write_corrupted_study_csv
 from .analysis.metrics import generate_benchmark_metrics # Added for benchmark
-from .analysis.booth_demo import build_booth_demo
-from .analysis.carelink_workbench import build_carelink_workbench
-from .analysis.poster import generate_results_poster
-from .analysis.reporting import ClinicalReportGenerator
+from .analysis.study_protocol import build_study_protocol_payload, render_study_protocol_markdown, write_study_protocol_bundle
 from .analysis.edge_efficiency import EnergyEstimate, estimate_energy_per_decision
 from .ai import AIResponse, IINTSAssistant, MDMPGuard
+from .live_patient import (
+    create_edge_bundle,
+    export_edge_setup,
+    LivePatientDaemon,
+    PatientRuntimeConfig,
+    create_patient_app,
+    export_uno_q_bridge,
+    get_runtime_scenario_profile,
+    list_runtime_scenario_profiles,
+    run_edge_benchmark,
+    summarize_edge_workspace,
+    write_edge_update_script,
+)
 from .highlevel import run_simulation, run_full, run_population
 from .scenarios import ScenarioGeneratorConfig, generate_random_scenario
 
+try:
+    from .analysis.booth_demo import build_booth_demo
+except Exception as exc:  # pragma: no cover - optional reports stack
+    _build_booth_demo_exc = exc
+
+    def build_booth_demo(*args, **kwargs):  # type: ignore[misc,no-redef]
+        _missing_reports_dependency("build_booth_demo()", _build_booth_demo_exc)
+
+try:
+    from .analysis.carelink_workbench import build_carelink_workbench
+except Exception as exc:  # pragma: no cover - optional reports stack
+    _build_carelink_workbench_exc = exc
+
+    def build_carelink_workbench(*args, **kwargs):  # type: ignore[misc,no-redef]
+        _missing_reports_dependency("build_carelink_workbench()", _build_carelink_workbench_exc)
+
+try:
+    from .analysis.poster import generate_results_poster
+except Exception as exc:  # pragma: no cover - optional reports stack
+    _generate_results_poster_exc = exc
+
+    def generate_results_poster(*args, **kwargs):  # type: ignore[misc,no-redef]
+        _missing_reports_dependency("generate_results_poster()", _generate_results_poster_exc)
+
+try:
+    from .analysis.reporting import ClinicalReportGenerator
+except Exception as exc:  # pragma: no cover - optional reports stack
+    _clinical_report_generator_exc = exc
+
+    class ClinicalReportGenerator:  # type: ignore[no-redef]
+        def __init__(self, *args, **kwargs):
+            _missing_reports_dependency("ClinicalReportGenerator", _clinical_report_generator_exc)
+
 # Population testing
 from .population import (
     PopulationGenerator,
@@ -184,16 +235,33 @@ __all__ = [
     "MDMPGateError",
     "generate_synthetic_mirror",
     "SyntheticMirrorArtifact",
+    "AVAILABLE_STUDY_CORRUPTIONS",
+    "apply_study_corruptions",
+    "write_corrupted_study_csv",
     # Analysis Metrics
     "generate_benchmark_metrics",
     "build_booth_demo",
     "build_carelink_workbench",
+    "build_study_protocol_payload",
+    "render_study_protocol_markdown",
+    "write_study_protocol_bundle",
     "ClinicalReportGenerator",
     "EnergyEstimate",
     "estimate_energy_per_decision",
     "AIResponse",
     "IINTSAssistant",
     "MDMPGuard",
+    "create_edge_bundle",
+    "export_edge_setup",
+    "LivePatientDaemon",
+    "PatientRuntimeConfig",
+    "create_patient_app",
+    "export_uno_q_bridge",
+    "get_runtime_scenario_profile",
+    "list_runtime_scenario_profiles",
+    "run_edge_benchmark",
+    "summarize_edge_workspace",
+    "write_edge_update_script",
     # Reporting
     "generate_report",
     "generate_quickstart_report",

{iints_sdk_python35-1.5.0 → iints_sdk_python35-1.5.2}/src/iints/ai/cli.py

@@ -70,6 +70,15 @@ def _resolve_cli_inputs(
 
     if input_path.is_dir():
         ai_dir = input_path / "ai"
+        if (
+            not ai_dir.exists()
+            or not any((ai_dir / candidate).is_file() for candidate in ("report_payload.json", "trends_payload.json", "anomalies_payload.json", "step_riskiest.json", "review_payload.json"))
+            or (resolved_cert is None and not (ai_dir / "report.signed.mdmp").is_file())
+        ):
+            prepare_ai_ready_artifacts(
+                input_path,
+                create_dev_mdmp_cert=resolved_cert is None,
+            )
         resolved_input = _default_prepared_payload(task, ai_dir)
         if resolved_cert is None:
             candidate_cert = ai_dir / "report.signed.mdmp"

{iints_sdk_python35-1.5.0 → iints_sdk_python35-1.5.2}/src/iints/ai/prompts.py

@@ -63,10 +63,11 @@ TASK_TEMPLATES: dict[TaskName, str] = {
         "Be conservative and do not overclaim. If the payload is incomplete, say so clearly.\n"
         "Respond in markdown with these sections:\n"
         "1. Overall realism verdict (Likely realistic / Needs review / Likely unrealistic)\n"
-        "2. Strong realism signals\n"
-        "3. Questionable or unrealistic patterns\n"
-        "4. Concrete feedback points the SDK developer can improve\n"
-        "5. Suggested follow-up validation checks\n\n"
+        "2. What looks realistic\n"
+        "3. What looks suspicious\n"
+        "4. Priority fixes\n"
+        "5. What to improve next\n"
+        "6. Suggested follow-up validation checks\n\n"
         "Focus on glycemic ranges, excursion patterns, insulin behavior, safety overrides, and whether the data looks internally coherent.\n\n"
         "Input JSON:\n{data}"
     ),

iints_sdk_python35-1.5.2/src/iints/analysis/__init__.py

@@ -0,0 +1,95 @@
+from .clinical_metrics import ClinicalMetricsCalculator, ClinicalMetricsResult
+from .baseline import compute_metrics, run_baseline_comparison, write_baseline_comparison
+from .study_protocol import (
+    build_study_protocol_payload,
+    render_study_protocol_markdown,
+    write_study_protocol_bundle,
+)
+from .study_analysis import (
+    analyze_run_directory,
+    analyze_study_directory,
+    compare_studies,
+    load_study_summary,
+    quality_badges_for_metrics,
+    StudyComparison,
+    StudyRunSummary,
+    StudySummary,
+)
+
+
+def _missing_reports_dependency(feature: str, exc: Exception) -> None:
+    raise ImportError(
+        f"{feature} requires the optional reporting stack. Install "
+        f"'iints-sdk-python35[reports]' or 'iints-sdk-python35[full]'."
+    ) from exc
+
+
+try:
+    from .booth_demo import build_booth_demo
+except Exception as exc:  # pragma: no cover - optional reports stack
+    _build_booth_demo_exc = exc
+
+    def build_booth_demo(*args, **kwargs):  # type: ignore[misc,no-redef]
+        _missing_reports_dependency("build_booth_demo()", _build_booth_demo_exc)
+
+
+try:
+    from .carelink_workbench import build_carelink_workbench
+except Exception as exc:  # pragma: no cover - optional reports stack
+    _build_carelink_workbench_exc = exc
+
+    def build_carelink_workbench(*args, **kwargs):  # type: ignore[misc,no-redef]
+        _missing_reports_dependency("build_carelink_workbench()", _build_carelink_workbench_exc)
+
+
+try:
+    from .poster import generate_results_poster
+except Exception as exc:  # pragma: no cover - optional reports stack
+    _generate_results_poster_exc = exc
+
+    def generate_results_poster(*args, **kwargs):  # type: ignore[misc,no-redef]
+        _missing_reports_dependency("generate_results_poster()", _generate_results_poster_exc)
+
+
+try:
+    from .reporting import ClinicalReportGenerator
+except Exception as exc:  # pragma: no cover - optional reports stack
+    _clinical_report_generator_exc = exc
+
+    class ClinicalReportGenerator:  # type: ignore[no-redef]
+        def __init__(self, *args, **kwargs):
+            _missing_reports_dependency("ClinicalReportGenerator", _clinical_report_generator_exc)
+
+
+try:
+    from .study_poster import generate_study_poster
+except Exception as exc:  # pragma: no cover - optional reports stack
+    _generate_study_poster_exc = exc
+
+    def generate_study_poster(*args, **kwargs):  # type: ignore[misc,no-redef]
+        _missing_reports_dependency("generate_study_poster()", _generate_study_poster_exc)
+
+
+__all__ = [
+    "analyze_run_directory",
+    "analyze_study_directory",
+    "build_booth_demo",
+    "build_carelink_workbench",
+    "ClinicalMetricsCalculator",
+    "ClinicalMetricsResult",
+    "ClinicalReportGenerator",
+    "compute_metrics",
+    "compare_studies",
+    "generate_results_poster",
+    "generate_study_poster",
+    "build_study_protocol_payload",
+    "render_study_protocol_markdown",
+    "write_study_protocol_bundle",
+    "load_study_summary",
+    "quality_badges_for_metrics",
+    "run_baseline_comparison",
+    "StudyComparison",
+    "StudyRunSummary",
+    "StudySummary",
+    "write_baseline_comparison",
+]