iints-sdk-python35 0.1.22__tar.gz → 1.1.0__tar.gz

iints_sdk_python35-1.1.0/PKG-INFO

@@ -0,0 +1,207 @@
+Metadata-Version: 2.4
+Name: iints-sdk-python35
+Version: 1.1.0
+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: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Development Status :: 5 - Production/Stable
+Requires-Python: >=3.10
+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: pillow>=12.1.1
+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: 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: mdmp-protocol>=0.3.0; 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)
+[![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)
+
+IINTS-AF is a safety-first SDK for insulin-algorithm research.
+It lets you simulate, validate, and report results with reproducible artifacts.
+
+Docs (GitHub Pages): [python35.github.io/IINTS-SDK](https://python35.github.io/IINTS-SDK/)
+
+## What You Can Do
+- Run virtual patient simulations.
+- Test algorithm safety gates (deterministic supervisor).
+- Add optional AI glucose forecasting.
+- Validate datasets before training/evaluation.
+- Generate audit-ready CSV/JSON/PDF/HTML outputs.
+
+## Quick Start
+```bash
+python3 -m venv .venv
+source .venv/bin/activate
+python -m pip install -U pip
+pip install iints-sdk-python35
+```
+
+```bash
+iints doctor --smoke-run
+iints quickstart --project-name iints_quickstart
+cd iints_quickstart
+iints presets run --name baseline_t1d --algo algorithms/example_algorithm.py
+```
+
+## AI Assistant (Ministral via Ollama)
+
+The SDK now includes a research-only AI assistant layer for explanations and run summaries.
+It is gated by MDMP verification before any LLM call is allowed.
+
+Use an active virtual environment for the full flow:
+
+```bash
+python3 -m venv .venv
+source .venv/bin/activate
+python -m pip install -U pip
+python -m pip install -e ".[mdmp]"
+```
+
+Run Ministral locally with Ollama:
+
+```bash
+ollama pull mistral/ministral-8b-instruct
+iints ai local-check --model ministral
+```
+
+Example commands:
+
+```bash
+iints ai explain results/step.json \
+  --mdmp-cert results/report.signed.mdmp
+
+iints ai report results/simulation_run.json \
+  --mdmp-cert results/report.signed.mdmp \
+  --output results/ai_report.md
+```
+
+Notes:
+- AI analysis is blocked if the MDMP artifact is invalid.
+- Minimum required MDMP grade defaults to `research_grade`.
+- Large JSON payloads are clipped automatically before prompt generation to keep local inference stable.
+- Output is research-only and not medical advice.
+
+## MDMP (Short)
+MDMP is the data-quality protocol used by IINTS.
+
+- `Contract`: defines expected columns, types, units, and bounds.
+- `Validation`: checks a dataset against the contract.
+- `Fingerprint + Grade`: writes deterministic hashes and a grade (`draft`, `research_grade`, `clinical_grade`).
+- `Visualizer`: builds a single-file HTML report for audits.
+
+Use the dedicated namespace:
+
+```bash
+iints mdmp template --output-path mdmp_contract.yaml
+iints mdmp validate mdmp_contract.yaml data/my_cgm.csv --output-json results/mdmp_report.json
+iints mdmp visualizer results/mdmp_report.json --output-html results/mdmp_dashboard.html
+```
+
+Use standalone MDMP backend (optional):
+
+```bash
+export IINTS_MDMP_BACKEND=mdmp_core
+```
+
+Staleness / lineage checks (standalone MDMP CLI):
+
+```bash
+mdmp fingerprint-record data/my_cgm.csv --output-json results/fingerprint.json --expires-days 365
+mdmp fingerprint-check results/fingerprint.json data/my_cgm.csv
+mdmp lineage-card-refresh results/mdmp_model_card.yaml
+mdmp registry init --registry registry/mdmp_registry.json
+mdmp registry push --registry registry/mdmp_registry.json --report results/mdmp_report.json
+```
+
+## Dual Repo Workflow
+- SDK repo: `python35/IINTS-SDK`
+- MDMP repo: `python35/MDMP`
+
+Local helper scripts:
+- `tools/dev/dual_repo_status.sh`
+- `tools/dev/dual_repo_commit_push.sh`
+
+Full process: `docs/DUAL_REPO_WORKFLOW.md`
+
+MDMP sync CI gate:
+- `.github/workflows/mdmp-sync.yml`
+- Uses private-repo checkout when `MDMP_REPO_TOKEN` is configured.
+- Falls back to `mdmp-protocol` from PyPI when checkout is unavailable.
+- Auto dependency updates for MDMP are handled via Dependabot (`.github/dependabot.yml`).
+
+## Tools Layout
+
+Repository helpers are now grouped by purpose:
+
+- `scripts/`: simple user-facing shortcuts like test, lint, and demo entrypoints
+- `tools/ci/`: CI gates and policy checks
+- `tools/dev/`: maintainer workflows and multi-repo helpers
+- `tools/docs/`: manual and documentation builders
+- `tools/data/`: dataset import and conversion utilities
+- `tools/analysis/`: plotting, diagnostics, and report helpers
+- `tools/assets/`: branding and asset generation helpers
+
+Reference: `tools/README.md`
+
+## Typical Workflow
+1. Prepare or import data.
+2. Validate data with MDMP.
+3. Run simulation or forecast evaluation.
+4. Review report artifacts and metrics.
+
+## Key Commands
+```bash
+iints run-full --algo algorithms/example_algorithm.py --scenario-path scenarios/clinic_safe_baseline.json --output-dir results/run_full
+iints scorecard --algo algorithms/example_algorithm.py --profile research_default --output-dir results/scorecard
+iints study-ready --algo algorithms/example_algorithm.py --output-dir results/study_ready
+iints sources --output-json results/source_manifest.json
+```
+
+## Documentation
+- Docs site: [python35.github.io/IINTS-SDK](https://python35.github.io/IINTS-SDK/)
+- Plain guide: [docs/PLAIN_LANGUAGE_GUIDE.md](https://github.com/python35/IINTS-SDK/blob/main/docs/PLAIN_LANGUAGE_GUIDE.md)
+- Comprehensive guide: [docs/COMPREHENSIVE_GUIDE.md](https://github.com/python35/IINTS-SDK/blob/main/docs/COMPREHENSIVE_GUIDE.md)
+- MDMP draft: [docs/MDMP.md](https://github.com/python35/IINTS-SDK/blob/main/docs/MDMP.md)
+- Demos: [examples/demos](https://github.com/python35/IINTS-SDK/tree/main/examples/demos)
+- Notebooks: [examples/notebooks](https://github.com/python35/IINTS-SDK/tree/main/examples/notebooks)
+
+## Safety Notice
+For research use only. Not a medical device. No clinical dosing advice.

iints_sdk_python35-1.1.0/README.md

@@ -0,0 +1,156 @@
+# 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)
+[![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)
+
+IINTS-AF is a safety-first SDK for insulin-algorithm research.
+It lets you simulate, validate, and report results with reproducible artifacts.
+
+Docs (GitHub Pages): [python35.github.io/IINTS-SDK](https://python35.github.io/IINTS-SDK/)
+
+## What You Can Do
+- Run virtual patient simulations.
+- Test algorithm safety gates (deterministic supervisor).
+- Add optional AI glucose forecasting.
+- Validate datasets before training/evaluation.
+- Generate audit-ready CSV/JSON/PDF/HTML outputs.
+
+## Quick Start
+```bash
+python3 -m venv .venv
+source .venv/bin/activate
+python -m pip install -U pip
+pip install iints-sdk-python35
+```
+
+```bash
+iints doctor --smoke-run
+iints quickstart --project-name iints_quickstart
+cd iints_quickstart
+iints presets run --name baseline_t1d --algo algorithms/example_algorithm.py
+```
+
+## AI Assistant (Ministral via Ollama)
+
+The SDK now includes a research-only AI assistant layer for explanations and run summaries.
+It is gated by MDMP verification before any LLM call is allowed.
+
+Use an active virtual environment for the full flow:
+
+```bash
+python3 -m venv .venv
+source .venv/bin/activate
+python -m pip install -U pip
+python -m pip install -e ".[mdmp]"
+```
+
+Run Ministral locally with Ollama:
+
+```bash
+ollama pull mistral/ministral-8b-instruct
+iints ai local-check --model ministral
+```
+
+Example commands:
+
+```bash
+iints ai explain results/step.json \
+  --mdmp-cert results/report.signed.mdmp
+
+iints ai report results/simulation_run.json \
+  --mdmp-cert results/report.signed.mdmp \
+  --output results/ai_report.md
+```
+
+Notes:
+- AI analysis is blocked if the MDMP artifact is invalid.
+- Minimum required MDMP grade defaults to `research_grade`.
+- Large JSON payloads are clipped automatically before prompt generation to keep local inference stable.
+- Output is research-only and not medical advice.
+
+## MDMP (Short)
+MDMP is the data-quality protocol used by IINTS.
+
+- `Contract`: defines expected columns, types, units, and bounds.
+- `Validation`: checks a dataset against the contract.
+- `Fingerprint + Grade`: writes deterministic hashes and a grade (`draft`, `research_grade`, `clinical_grade`).
+- `Visualizer`: builds a single-file HTML report for audits.
+
+Use the dedicated namespace:
+
+```bash
+iints mdmp template --output-path mdmp_contract.yaml
+iints mdmp validate mdmp_contract.yaml data/my_cgm.csv --output-json results/mdmp_report.json
+iints mdmp visualizer results/mdmp_report.json --output-html results/mdmp_dashboard.html
+```
+
+Use standalone MDMP backend (optional):
+
+```bash
+export IINTS_MDMP_BACKEND=mdmp_core
+```
+
+Staleness / lineage checks (standalone MDMP CLI):
+
+```bash
+mdmp fingerprint-record data/my_cgm.csv --output-json results/fingerprint.json --expires-days 365
+mdmp fingerprint-check results/fingerprint.json data/my_cgm.csv
+mdmp lineage-card-refresh results/mdmp_model_card.yaml
+mdmp registry init --registry registry/mdmp_registry.json
+mdmp registry push --registry registry/mdmp_registry.json --report results/mdmp_report.json
+```
+
+## Dual Repo Workflow
+- SDK repo: `python35/IINTS-SDK`
+- MDMP repo: `python35/MDMP`
+
+Local helper scripts:
+- `tools/dev/dual_repo_status.sh`
+- `tools/dev/dual_repo_commit_push.sh`
+
+Full process: `docs/DUAL_REPO_WORKFLOW.md`
+
+MDMP sync CI gate:
+- `.github/workflows/mdmp-sync.yml`
+- Uses private-repo checkout when `MDMP_REPO_TOKEN` is configured.
+- Falls back to `mdmp-protocol` from PyPI when checkout is unavailable.
+- Auto dependency updates for MDMP are handled via Dependabot (`.github/dependabot.yml`).
+
+## Tools Layout
+
+Repository helpers are now grouped by purpose:
+
+- `scripts/`: simple user-facing shortcuts like test, lint, and demo entrypoints
+- `tools/ci/`: CI gates and policy checks
+- `tools/dev/`: maintainer workflows and multi-repo helpers
+- `tools/docs/`: manual and documentation builders
+- `tools/data/`: dataset import and conversion utilities
+- `tools/analysis/`: plotting, diagnostics, and report helpers
+- `tools/assets/`: branding and asset generation helpers
+
+Reference: `tools/README.md`
+
+## Typical Workflow
+1. Prepare or import data.
+2. Validate data with MDMP.
+3. Run simulation or forecast evaluation.
+4. Review report artifacts and metrics.
+
+## Key Commands
+```bash
+iints run-full --algo algorithms/example_algorithm.py --scenario-path scenarios/clinic_safe_baseline.json --output-dir results/run_full
+iints scorecard --algo algorithms/example_algorithm.py --profile research_default --output-dir results/scorecard
+iints study-ready --algo algorithms/example_algorithm.py --output-dir results/study_ready
+iints sources --output-json results/source_manifest.json
+```
+
+## Documentation
+- Docs site: [python35.github.io/IINTS-SDK](https://python35.github.io/IINTS-SDK/)
+- Plain guide: [docs/PLAIN_LANGUAGE_GUIDE.md](https://github.com/python35/IINTS-SDK/blob/main/docs/PLAIN_LANGUAGE_GUIDE.md)
+- Comprehensive guide: [docs/COMPREHENSIVE_GUIDE.md](https://github.com/python35/IINTS-SDK/blob/main/docs/COMPREHENSIVE_GUIDE.md)
+- MDMP draft: [docs/MDMP.md](https://github.com/python35/IINTS-SDK/blob/main/docs/MDMP.md)
+- Demos: [examples/demos](https://github.com/python35/IINTS-SDK/tree/main/examples/demos)
+- Notebooks: [examples/notebooks](https://github.com/python35/IINTS-SDK/tree/main/examples/notebooks)
+
+## Safety Notice
+For research use only. Not a medical device. No clinical dosing advice.

{iints_sdk_python35-0.1.22 → iints_sdk_python35-1.1.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "iints-sdk-python35" 
-version = "0.1.22"
+version = "1.1.0"
 authors = [
   { name="Rune Bobbaers", email="rune.bobbaers@gmail.com" },
 ]
@@ -19,7 +19,7 @@ classifiers = [
     "Programming Language :: Python :: 3.13",
     "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
-    "Development Status :: 3 - Alpha",
+    "Development Status :: 5 - Production/Stable",
 ]
 dependencies = [
     "fpdf2>=2.8.0",
@@ -59,6 +59,9 @@ research = [
   "onnx>=1.16.0",
   "onnxscript>=0.1.0",
 ]
+mdmp = [
+  "mdmp-protocol>=0.3.0",
+]
 
 [project.scripts]
 iints = "iints.cli.cli:app"

{iints_sdk_python35-0.1.22 → iints_sdk_python35-1.1.0}/src/iints/__init__.py

@@ -61,6 +61,7 @@ from .data.synthetic_mirror import generate_synthetic_mirror, SyntheticMirrorArt
 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 .ai import AIResponse, IINTSAssistant, MDMPGuard
 from .highlevel import run_simulation, run_full, run_population
 from .scenarios import ScenarioGeneratorConfig, generate_random_scenario
 
@@ -169,6 +170,9 @@ __all__ = [
     "ClinicalReportGenerator",
     "EnergyEstimate",
     "estimate_energy_per_decision",
+    "AIResponse",
+    "IINTSAssistant",
+    "MDMPGuard",
     # Reporting
     "generate_report",
     "generate_quickstart_report",

iints_sdk_python35-1.1.0/src/iints/ai/__init__.py

@@ -0,0 +1,13 @@
+from .assistant import AIResponse, IINTSAssistant
+from .backends import DEFAULT_MINISTRAL_MODEL, DEFAULT_OLLAMA_HOST, OllamaBackend
+from .mdmp_guard import GuardResult, MDMPGuard
+
+__all__ = [
+    "AIResponse",
+    "IINTSAssistant",
+    "DEFAULT_MINISTRAL_MODEL",
+    "DEFAULT_OLLAMA_HOST",
+    "OllamaBackend",
+    "GuardResult",
+    "MDMPGuard",
+]

iints_sdk_python35-1.1.0/src/iints/ai/assistant.py

@@ -0,0 +1,124 @@
+from __future__ import annotations
+
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Any
+
+from .backends import DEFAULT_MINISTRAL_MODEL, CompletionBackend, MistralAPIBackend, OllamaBackend
+from .mdmp_guard import GuardResult, MDMPGuard
+from .prompts import TaskName, build_prompt
+
+
+@dataclass(frozen=True)
+class AIResponse:
+    task: str
+    text: str
+    backend: str
+    model: str
+    certification: GuardResult
+
+    def to_dict(self) -> dict[str, Any]:
+        return {
+            "task": self.task,
+            "text": self.text,
+            "backend": self.backend,
+            "model": self.model,
+            "certification": self.certification.to_dict(),
+        }
+
+
+class IINTSAssistant:
+    """Research-only LLM assistant gated by MDMP certification."""
+
+    def __init__(
+        self,
+        mdmp_cert: str | Path,
+        *,
+        mode: str = "auto",
+        model: str = DEFAULT_MINISTRAL_MODEL,
+        minimum_grade: str = "research_grade",
+        public_key_path: str | Path | None = None,
+        trust_store_path: str | Path | None = None,
+        ollama_host: str | None = None,
+        timeout_seconds: float = 120.0,
+        backend: CompletionBackend | None = None,
+        guard: MDMPGuard | None = None,
+    ) -> None:
+        self.guard = guard or MDMPGuard(
+            mdmp_cert,
+            minimum_grade=minimum_grade,
+            public_key_path=public_key_path,
+            trust_store_path=trust_store_path,
+        )
+        self.backend = backend or self._detect_backend(
+            mode=mode,
+            model=model,
+            ollama_host=ollama_host,
+            timeout_seconds=timeout_seconds,
+        )
+
+    def _detect_backend(
+        self,
+        *,
+        mode: str,
+        model: str,
+        ollama_host: str | None,
+        timeout_seconds: float,
+    ) -> CompletionBackend:
+        requested = mode.strip().lower()
+        if requested in {"auto", "local", "ollama"}:
+            ollama_backend = OllamaBackend(
+                model_name=model,
+                base_url=ollama_host,
+                timeout_seconds=timeout_seconds,
+            )
+            local_backend: CompletionBackend = ollama_backend
+            if not ollama_backend.available():
+                raise RuntimeError(
+                    "No local Ollama backend is available. "
+                    f"Could not reach {ollama_backend.base_url}. "
+                    "Start Ollama and try again."
+                )
+            ollama_backend.ensure_model_ready()
+            return local_backend
+        if requested == "api":
+            api_backend: CompletionBackend = MistralAPIBackend()
+            if api_backend.available():
+                return api_backend
+            raise RuntimeError(
+                "Cloud API fallback is not enabled in this SDK build yet. "
+                "Use mode='local' with Ollama."
+            )
+        raise ValueError(f"Unsupported AI mode: {mode}")
+
+    def _run_task(self, task: TaskName, payload: Any) -> AIResponse:
+        certification = self.guard.check()
+        system_prompt, user_prompt = build_prompt(task, payload)
+        text = self.guard.wrap(
+            self.backend.complete(system_prompt=system_prompt, user_prompt=user_prompt)
+        )
+        resolved_model = getattr(self.backend, "resolved_model_name", None)
+        response_model = (
+            str(resolved_model)
+            if isinstance(resolved_model, str) and resolved_model.strip()
+            else str(getattr(self.backend, "model_name", DEFAULT_MINISTRAL_MODEL))
+        )
+        return AIResponse(
+            task=task,
+            text=text,
+            backend=getattr(self.backend, "backend_name", type(self.backend).__name__),
+            model=response_model,
+            certification=certification,
+        )
+
+    def explain_decision(self, step: dict[str, Any]) -> AIResponse:
+        return self._run_task("explain_decision", step)
+
+    def analyze_trends(self, glucose_payload: list[Any] | dict[str, Any]) -> AIResponse:
+        return self._run_task("analyze_trends", glucose_payload)
+
+    def detect_anomalies(self, results: dict[str, Any]) -> AIResponse:
+        return self._run_task("detect_anomalies", results)
+
+    def generate_report(self, run: dict[str, Any]) -> AIResponse:
+        return self._run_task("generate_report", run)

iints_sdk_python35-1.1.0/src/iints/ai/backends/__init__.py

@@ -0,0 +1,11 @@
+from .base import CompletionBackend
+from .mistral_api import MistralAPIBackend
+from .ollama import DEFAULT_MINISTRAL_MODEL, DEFAULT_OLLAMA_HOST, OllamaBackend
+
+__all__ = [
+    "CompletionBackend",
+    "DEFAULT_MINISTRAL_MODEL",
+    "DEFAULT_OLLAMA_HOST",
+    "OllamaBackend",
+    "MistralAPIBackend",
+]

iints_sdk_python35-1.1.0/src/iints/ai/backends/base.py

@@ -0,0 +1,14 @@
+from __future__ import annotations
+
+from typing import Protocol
+
+
+class CompletionBackend(Protocol):
+    backend_name: str
+    model_name: str
+
+    def available(self) -> bool:
+        ...
+
+    def complete(self, *, system_prompt: str, user_prompt: str) -> str:
+        ...

iints_sdk_python35-1.1.0/src/iints/ai/backends/mistral_api.py

@@ -0,0 +1,17 @@
+from __future__ import annotations
+
+
+class MistralAPIBackend:
+    backend_name = "mistral_api"
+
+    def __init__(self, *args, **kwargs) -> None:
+        self.model_name = "mistral_api_unconfigured"
+
+    def available(self) -> bool:
+        return False
+
+    def complete(self, *, system_prompt: str, user_prompt: str) -> str:
+        raise RuntimeError(
+            "Cloud fallback is not enabled in this SDK build yet. "
+            "Use mode='local' with Ollama for Ministral."
+        )