iints-sdk-python35 1.3.2__tar.gz → 1.4.0__tar.gz

iints_sdk_python35-1.4.0/LICENSE

@@ -0,0 +1,173 @@
+Apache License
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+any Contribution intentionally submitted for inclusion in the Work
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iints_sdk_python35-1.3.2/LICENSE → iints_sdk_python35-1.4.0/LICENSE-MIT-IINTS-LEGACY

@@ -19,10 +19,3 @@ 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_python35-1.4.0/NOTICE

@@ -0,0 +1,17 @@
+IINTS-AF SDK
+Copyright (c) 2026 IINTS-AF Contributors
+
+This distribution now bundles MDMP components directly inside the SDK source tree,
+including `mdmp_core`, `mdmp_ai`, `mdmp_flavors`, and `mdmp_integrations`.
+
+Bundled MDMP code originates from the MDMP project and is included here under
+the Apache License, Version 2.0.
+
+The original IINTS-AF SDK was previously distributed under the MIT License.
+The preserved MIT notice for legacy IINTS-origin portions is included in:
+
+`LICENSE-MIT-IINTS-LEGACY`
+
+Research-use notice:
+This software is intended for academic and pre-clinical research purposes only.
+It is not a medical device and does not provide clinical dosing advice.

{iints_sdk_python35-1.3.2/src/iints_sdk_python35.egg-info → iints_sdk_python35-1.4.0}/PKG-INFO

@@ -1,20 +1,22 @@
 Metadata-Version: 2.4
 Name: iints-sdk-python35
-Version: 1.3.2
+Version: 1.4.0
 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: 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
+License-File: NOTICE
+License-File: LICENSE-MIT-IINTS-LEGACY
 Requires-Dist: fpdf2>=2.8.0
 Requires-Dist: matplotlib>=3.5.0
 Requires-Dist: numpy>=1.24.0
@@ -46,7 +48,7 @@ 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"
+Requires-Dist: cryptography>=42.0.0; extra == "mdmp"
 Dynamic: license-file
 
 # IINTS-AF SDK
@@ -83,6 +85,8 @@ iints presets run --name baseline_t1d --algo algorithms/example_algorithm.py
 
 If you want the clearest install/path rules first, read:
 - `docs/INSTALLATION.md`
+- `docs/AI_ASSISTANT.md` for the small Ollama setup and SDK linking flow
+- `docs/EVIDENCE_BASE.md` for the full medical + technical source legend
 
 Short rule:
 - installed `iints ...` commands can run from any folder
@@ -160,6 +164,12 @@ ollama pull ministral-3:8b
 iints ai models
 ```
 
+If you want the short "install Ollama + link it to the SDK" guide, read:
+- `docs/AI_ASSISTANT.md`
+
+If you want the full legend of medical, dataset, runtime, and emulator references used across the project docs:
+- `docs/EVIDENCE_BASE.md`
+
 Recommended first-time setup:
 
 ```bash
@@ -345,13 +355,13 @@ iints mdmp validate mdmp_contract.yaml data/my_cgm.csv --output-json results/mdm
 iints mdmp visualizer results/mdmp_report.json --output-html results/mdmp_dashboard.html
 ```
 
-Use standalone MDMP backend (optional):
+Use bundled `mdmp_core` backend (optional):
 
 ```bash
 export IINTS_MDMP_BACKEND=mdmp_core
 ```
 
-Staleness / lineage checks (standalone MDMP CLI):
+Staleness / lineage checks via the bundled `mdmp` CLI:
 
 ```bash
 mdmp fingerprint-record data/my_cgm.csv --output-json results/fingerprint.json --expires-days 365
@@ -361,21 +371,17 @@ 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`
+## Bundled MDMP
 
-Local helper scripts:
-- `tools/dev/dual_repo_status.sh`
-- `tools/dev/dual_repo_commit_push.sh`
+MDMP now ships inside the SDK, so the SDK no longer depends on a separate public MDMP repository checkout.
 
-Full process: `docs/DUAL_REPO_WORKFLOW.md`
+That means:
+- `iints mdmp ...` stays available
+- the bundled `mdmp` CLI can still be used
+- local AI signing and verification can still use `mdmp_core`
 
-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`).
+Reference:
+- `docs/DUAL_REPO_WORKFLOW.md`
 
 ## Tools Layout
 

{iints_sdk_python35-1.3.2 → iints_sdk_python35-1.4.0}/README.md

@@ -32,6 +32,8 @@ iints presets run --name baseline_t1d --algo algorithms/example_algorithm.py
 
 If you want the clearest install/path rules first, read:
 - `docs/INSTALLATION.md`
+- `docs/AI_ASSISTANT.md` for the small Ollama setup and SDK linking flow
+- `docs/EVIDENCE_BASE.md` for the full medical + technical source legend
 
 Short rule:
 - installed `iints ...` commands can run from any folder
@@ -109,6 +111,12 @@ ollama pull ministral-3:8b
 iints ai models
 ```
 
+If you want the short "install Ollama + link it to the SDK" guide, read:
+- `docs/AI_ASSISTANT.md`
+
+If you want the full legend of medical, dataset, runtime, and emulator references used across the project docs:
+- `docs/EVIDENCE_BASE.md`
+
 Recommended first-time setup:
 
 ```bash
@@ -294,13 +302,13 @@ iints mdmp validate mdmp_contract.yaml data/my_cgm.csv --output-json results/mdm
 iints mdmp visualizer results/mdmp_report.json --output-html results/mdmp_dashboard.html
 ```
 
-Use standalone MDMP backend (optional):
+Use bundled `mdmp_core` backend (optional):
 
 ```bash
 export IINTS_MDMP_BACKEND=mdmp_core
 ```
 
-Staleness / lineage checks (standalone MDMP CLI):
+Staleness / lineage checks via the bundled `mdmp` CLI:
 
 ```bash
 mdmp fingerprint-record data/my_cgm.csv --output-json results/fingerprint.json --expires-days 365
@@ -310,21 +318,17 @@ 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`
+## Bundled MDMP
 
-Local helper scripts:
-- `tools/dev/dual_repo_status.sh`
-- `tools/dev/dual_repo_commit_push.sh`
+MDMP now ships inside the SDK, so the SDK no longer depends on a separate public MDMP repository checkout.
 
-Full process: `docs/DUAL_REPO_WORKFLOW.md`
+That means:
+- `iints mdmp ...` stays available
+- the bundled `mdmp` CLI can still be used
+- local AI signing and verification can still use `mdmp_core`
 
-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`).
+Reference:
+- `docs/DUAL_REPO_WORKFLOW.md`
 
 ## Tools Layout
 

{iints_sdk_python35-1.3.2 → iints_sdk_python35-1.4.0}/pyproject.toml

@@ -1,15 +1,17 @@
 [build-system]
-requires = ["setuptools>=61.0"]
+requires = ["setuptools>=77.0.0"]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "iints-sdk-python35" 
-version = "1.3.2"
+version = "1.4.0"
 authors = [
   { name="Rune Bobbaers", email="rune.bobbaers@gmail.com" },
 ]
 description = "A pre-clinical Edge-AI SDK for diabetes management validation."
 readme = "README.md"
+license = "Apache-2.0"
+license-files = ["LICENSE", "NOTICE", "LICENSE-MIT-IINTS-LEGACY"]
 requires-python = ">=3.10"
 classifiers = [
     "Programming Language :: Python :: 3",
@@ -17,7 +19,6 @@ classifiers = [
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
-    "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
     "Development Status :: 5 - Production/Stable",
 ]
@@ -60,12 +61,13 @@ research = [
   "onnxscript>=0.1.0",
 ]
 mdmp = [
-  "mdmp-protocol>=0.3.0",
+  "cryptography>=42.0.0",
 ]
 
 [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"
@@ -92,3 +94,7 @@ iints = [
   "presets/*.json",
   "presets/*.yaml",
 ]
+mdmp_core = [
+  "keys/*.pem",
+  "data/conformance/vectors/*.json",
+]

{iints_sdk_python35-1.3.2 → iints_sdk_python35-1.4.0}/src/iints/__init__.py

@@ -11,7 +11,7 @@ except ImportError:  # pragma: no cover - Python < 3.8 fallback
 try:
     __version__ = version("iints-sdk-python35")
 except PackageNotFoundError:  # pragma: no cover - source tree fallback
-    __version__ = "1.3.2"
+    __version__ = "1.4.0"
 
 # 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.

{iints_sdk_python35-1.3.2 → iints_sdk_python35-1.4.0}/src/iints/ai/backends/ollama.py

@@ -2,9 +2,11 @@ from __future__ import annotations
 
 import json
 import os
+from ipaddress import ip_address
 from http.client import IncompleteRead, RemoteDisconnected
 from time import sleep
 from urllib import error, request
+from urllib.parse import urlparse
 
 
 DEFAULT_OLLAMA_HOST = "http://127.0.0.1:11434"
@@ -35,10 +37,38 @@ class OllamaBackend:
         timeout_seconds: float = 120.0,
     ) -> None:
         self.model_name = model_name
-        self.base_url = (base_url or os.getenv("OLLAMA_HOST") or DEFAULT_OLLAMA_HOST).rstrip("/")
+        raw_base_url = base_url or os.getenv("OLLAMA_HOST") or DEFAULT_OLLAMA_HOST
+        self.base_url = self._validate_base_url(raw_base_url)
         self.timeout_seconds = timeout_seconds
         self.resolved_model_name: str | None = None
 
+    @staticmethod
+    def _is_loopback_host(hostname: str) -> bool:
+        if hostname == "localhost":
+            return True
+        try:
+            return ip_address(hostname).is_loopback
+        except ValueError:
+            return False
+
+    @classmethod
+    def _validate_base_url(cls, raw_base_url: str) -> str:
+        parsed = urlparse(raw_base_url)
+        if parsed.scheme not in {"http", "https"}:
+            raise ValueError(
+                "OLLAMA_HOST/base_url must use http or https. Other URL schemes are blocked."
+            )
+        if not parsed.hostname:
+            raise ValueError("OLLAMA_HOST/base_url must include a hostname.")
+        if parsed.path not in {"", "/"}:
+            raise ValueError("OLLAMA_HOST/base_url must not include a path component.")
+        if not cls._is_loopback_host(parsed.hostname) and os.getenv("IINTS_ALLOW_REMOTE_OLLAMA") != "1":
+            raise ValueError(
+                "Remote Ollama endpoints are disabled by default. "
+                "Use localhost/127.0.0.1 or set IINTS_ALLOW_REMOTE_OLLAMA=1 explicitly."
+            )
+        return raw_base_url.rstrip("/")
+
     def _pull_hint(self) -> str:
         return f"ollama pull {self.model_name}"
 
@@ -102,7 +132,7 @@ class OllamaBackend:
             headers["Content-Type"] = "application/json"
         req = request.Request(url, data=body, headers=headers, method=method)
         try:
-            with request.urlopen(req, timeout=self.timeout_seconds) as response:
+            with request.urlopen(req, timeout=self.timeout_seconds) as response:  # nosec B310 - base_url is scheme/host validated
                 text = response.read().decode("utf-8")
         except error.HTTPError as exc:
             detail = exc.read().decode("utf-8", errors="replace").strip()

{iints_sdk_python35-1.3.2 → iints_sdk_python35-1.4.0}/src/iints/ai/mdmp_guard.py

@@ -14,9 +14,8 @@ def _load_mdmp_verifier() -> type[Any]:
         module = importlib.import_module("mdmp_core")
     except Exception as exc:
         raise ImportError(
-            "MDMP verification requires the optional standalone package.\n"
-            "Install with: pip install iints-sdk-python35[mdmp]\n"
-            "or: pip install 'mdmp-protocol>=0.3.0'"
+            "MDMP verification requires the bundled MDMP crypto support.\n"
+            "Install with: pip install iints-sdk-python35[mdmp]"
         ) from exc
     verifier_cls = getattr(module, "MDMPVerifier", None)
     if verifier_cls is None:

{iints_sdk_python35-1.3.2 → iints_sdk_python35-1.4.0}/src/iints/ai/prepare.py

@@ -245,7 +245,7 @@ def _load_mdmp_signer_tools() -> tuple[type[Any], Any]:
         module = importlib.import_module("mdmp_core")
     except Exception as exc:
         raise ImportError(
-            "Local AI certification requires the optional standalone MDMP package.\n"
+            "Local AI certification requires the bundled MDMP crypto support.\n"
             "Install with: pip install 'iints-sdk-python35[mdmp]'"
         ) from exc
 

{iints_sdk_python35-1.3.2 → iints_sdk_python35-1.4.0}/src/iints/analysis/clinical_metrics.py

@@ -144,6 +144,12 @@ class ClinicalMetricsCalculator:
         """
         self.target_range = target_range
         self.tight_range = tight_range
+
+    @staticmethod
+    def _percentage(mask: pd.Series) -> float:
+        if len(mask) == 0:
+            return 0.0
+        return float(mask.sum()) / float(len(mask)) * 100.0
         
     def calculate_tir(self, 
                       glucose: pd.Series, 
@@ -169,13 +175,13 @@ class ClinicalMetricsCalculator:
     def calculate_all_tir_metrics(self, glucose: pd.Series) -> Dict[str, float]:
         """Calculate all TIR-related metrics"""
         return {
-            'tir_70_180': self.calculate_tir(glucose, 70, 180),
-            'tir_70_140': self.calculate_tir(glucose, 70, 140),
-            'tir_70_110': self.calculate_tir(glucose, 70, 110),
-            'tir_below_70': self.calculate_tir(glucose, 0, 70),
-            'tir_below_54': self.calculate_tir(glucose, 0, 54),
-            'tir_above_180': self.calculate_tir(glucose, 180, 600),
-            'tir_above_250': self.calculate_tir(glucose, 250, 600)
+            'tir_70_180': self._percentage((glucose >= 70) & (glucose <= 180)),
+            'tir_70_140': self._percentage((glucose >= 70) & (glucose <= 140)),
+            'tir_70_110': self._percentage((glucose >= 70) & (glucose <= 110)),
+            'tir_below_70': self._percentage(glucose < 70),
+            'tir_below_54': self._percentage(glucose < 54),
+            'tir_above_180': self._percentage(glucose > 180),
+            'tir_above_250': self._percentage(glucose > 250)
         }
     
     def calculate_gmi(self, glucose: pd.Series) -> float:

{iints_sdk_python35-1.3.2 → iints_sdk_python35-1.4.0}/src/iints/analysis/validator.py

@@ -4,6 +4,12 @@ from typing import Dict, List, Tuple, Optional, Any
 from dataclasses import dataclass
 from enum import Enum
 
+from iints.core.safety.config import (
+    SENSOR_GLUCOSE_MAX_MGDL,
+    SENSOR_GLUCOSE_MIN_MGDL,
+    SENSOR_MAX_GLUCOSE_RATE_PER_MIN_MGDL,
+)
+
 class ReliabilityLevel(Enum):
     HIGH = "high"
     MEDIUM = "medium" 
@@ -22,9 +28,9 @@ class DataIntegrityValidator:
     """Validates data integrity for reverse engineering analysis."""
     
     def __init__(self):
-        # Physiological limits
-        self.max_glucose_rate = 10  # mg/dL per minute
-        self.glucose_range = (20, 600)  # Physiologically possible range
+        # Broad CGM/sensor fail-soft limits
+        self.max_glucose_rate = SENSOR_MAX_GLUCOSE_RATE_PER_MIN_MGDL
+        self.glucose_range = (SENSOR_GLUCOSE_MIN_MGDL, SENSOR_GLUCOSE_MAX_MGDL)
         self.max_insulin_per_step = 5.0  # Units per 5-min step
         
     def validate_glucose_data(self, glucose_values: List[float], timestamps: List[float]) -> ValidationResult:
@@ -270,4 +276,4 @@ class ReverseEngineeringValidator:
             "issues": all_issues,
             "warnings": all_warnings,
             "category_scores": {category: result.reliability_score for category, result in validation_results.items()}
-        }
+        }

{iints_sdk_python35-1.3.2 → iints_sdk_python35-1.4.0}/src/iints/core/patient/bergman_model.py

@@ -46,7 +46,7 @@ class BergmanParameters:
     n: float = 0.23         # 1/min  — fractional insulin degradation
     Ib: float = 7.0         # mU/L   — basal plasma insulin
     Vi: float = 0.05        # L/kg   — insulin distribution volume
-    gamma: float = 0.004    # (mU/L)/(mg/dL)/min — endogenous secretion gain
+    gamma: float = 0.0      # (mU/L)/(mg/dL)/min — endogenous secretion gain (0 for T1D default)
     h: float = 80.0         # mg/dL  — secretion glucose threshold
 
     # --- Gut absorption ---
@@ -330,7 +330,8 @@ class BergmanPatientModel:
         dXdt = -p.p2 * X + p.p3 * max(I - p.Ib, 0.0)
 
         # --- dI/dt ---
-        # Endogenous pancreatic secretion (blunted in T1D, but kept for generality)
+        # T1D defaults keep endogenous secretion disabled (gamma=0). Override
+        # gamma explicitly if you intentionally want residual beta-cell function.
         secretion = p.gamma * max(G - p.h, 0.0)
         dIdt = -p.n * (I - p.Ib) + secretion + u_insulin_mu_per_min / Vi_abs
 

{iints_sdk_python35-1.3.2 → iints_sdk_python35-1.4.0}/src/iints/core/patient/models.py

@@ -14,7 +14,7 @@ class CustomPatientModel:
     This model is intended for educational and stress-testing purposes, not for clinical accuracy.
     """
     def __init__(self, basal_insulin_rate: float = 0.8, insulin_sensitivity: float = 50.0,
-                 carb_factor: float = 10.0, glucose_decay_rate: float = 0.002,
+                 carb_factor: float = 10.0, glucose_decay_rate: float = 0.05,
                  initial_glucose: float = 120.0, glucose_absorption_rate: float = 0.03,
                  basal_glucose_target: Optional[float] = None,
                  insulin_action_duration: float = 300.0, # minutes, e.g., 5 hours

{iints_sdk_python35-1.3.2 → iints_sdk_python35-1.4.0}/src/iints/core/patient/patient_factory.py

@@ -63,14 +63,14 @@ class PatientFactory:
         """Get a diverse set of patients for population studies."""
         if not SIMGLUCOSE_AVAILABLE:
             # Create diverse custom patients with different parameters
-            return [
-                CustomPatientModel(initial_glucose=120, insulin_sensitivity=40),  # High sensitivity
-                CustomPatientModel(initial_glucose=120, insulin_sensitivity=60),  # Low sensitivity
-                CustomPatientModel(initial_glucose=120, carb_factor=8),          # Fast carb absorption
-                CustomPatientModel(initial_glucose=120, carb_factor=12),         # Slow carb absorption
-                CustomPatientModel(initial_glucose=120, glucose_decay_rate=0.0015), # Slow metabolism
-                CustomPatientModel(initial_glucose=120, glucose_decay_rate=0.0035), # Fast metabolism
-            ]
+                return [
+                    CustomPatientModel(initial_glucose=120, insulin_sensitivity=40),  # High sensitivity
+                    CustomPatientModel(initial_glucose=120, insulin_sensitivity=60),  # Low sensitivity
+                    CustomPatientModel(initial_glucose=120, carb_factor=8),          # Fast carb absorption
+                    CustomPatientModel(initial_glucose=120, carb_factor=12),         # Slow carb absorption
+                    CustomPatientModel(initial_glucose=120, glucose_decay_rate=0.03), # Slower homeostatic drift
+                    CustomPatientModel(initial_glucose=120, glucose_decay_rate=0.07), # Faster homeostatic drift
+                ]
         else:
             # Use FDA-approved virtual patients
             selected_patients = [

{iints_sdk_python35-1.3.2 → iints_sdk_python35-1.4.0}/src/iints/core/patient/profile.py

@@ -18,7 +18,7 @@ class PatientProfile:
     dawn_end_hour: float = 8.0
 
     # Advanced knobs (optional)
-    glucose_decay_rate: float = 0.002
+    glucose_decay_rate: float = 0.05
     glucose_absorption_rate: float = 0.03
     insulin_action_duration: float = 300.0
     insulin_peak_time: float = 75.0