iints-sdk-python35 1.5.22__tar.gz → 1.5.24__tar.gz

{iints_sdk_python35-1.5.22/src/iints_sdk_python35.egg-info → iints_sdk_python35-1.5.24}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: iints-sdk-python35
-Version: 1.5.22
+Version: 1.5.24
 Summary: A pre-clinical Edge-AI SDK for diabetes management validation.
 Author-email: Rune Bobbaers <rune.bobbaers@gmail.com>
 License-Expression: Apache-2.0
@@ -71,6 +71,8 @@ Requires-Dist: cryptography<50.0.0,>=42.0.0; extra == "mdmp"
 Provides-Extra: desktop
 Requires-Dist: pyinstaller<7.0.0,>=6.11.0; extra == "desktop"
 Requires-Dist: setuptools<81.0.0,>=77.0.0; extra == "desktop"
+Requires-Dist: PySide6<7.0.0,>=6.7.0; extra == "desktop"
+Requires-Dist: plotly<7.0.0,>=5.18.0; extra == "desktop"
 Provides-Extra: desktop-qt
 Requires-Dist: pyinstaller<7.0.0,>=6.11.0; extra == "desktop-qt"
 Requires-Dist: setuptools<81.0.0,>=77.0.0; extra == "desktop-qt"
@@ -115,7 +117,12 @@ Current beta downloads:
 | macOS | [`.dmg`](https://github.com/python35/IINTS-SDK/releases/download/desktop-beta-latest/IINTS-AF-Desktop-Beta-macos.dmg) |
 | Linux | [executable](https://github.com/python35/IINTS-SDK/releases/download/desktop-beta-latest/IINTS-AF-Desktop-Beta-linux-x64) |
 
+Python install, including the PySide6 desktop runtime:
 
+```bash
+python -m pip install -U "iints-sdk-python35[full,desktop,mdmp]"
+iints-desktop
+```
 
 ## License
 

{iints_sdk_python35-1.5.22 → iints_sdk_python35-1.5.24}/README.md

@@ -31,7 +31,12 @@ Current beta downloads:
 | macOS | [`.dmg`](https://github.com/python35/IINTS-SDK/releases/download/desktop-beta-latest/IINTS-AF-Desktop-Beta-macos.dmg) |
 | Linux | [executable](https://github.com/python35/IINTS-SDK/releases/download/desktop-beta-latest/IINTS-AF-Desktop-Beta-linux-x64) |
 
+Python install, including the PySide6 desktop runtime:
 
+```bash
+python -m pip install -U "iints-sdk-python35[full,desktop,mdmp]"
+iints-desktop
+```
 
 ## License
 

{iints_sdk_python35-1.5.22 → iints_sdk_python35-1.5.24}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "iints-sdk-python35" 
-version = "1.5.22"
+version = "1.5.24"
 authors = [
   { name="Rune Bobbaers", email="rune.bobbaers@gmail.com" },
 ]
@@ -88,6 +88,8 @@ mdmp = [
 desktop = [
   "pyinstaller>=6.11.0,<7.0.0",
   "setuptools>=77.0.0,<81.0.0",
+  "PySide6>=6.7.0,<7.0.0",
+  "plotly>=5.18.0,<7.0.0",
 ]
 desktop-qt = [
   "pyinstaller>=6.11.0,<7.0.0",
@@ -125,6 +127,9 @@ where = ["src"]
 
 [tool.setuptools.package-data]
 iints_desktop = [
+  "assets/*.icns",
+  "assets/*.ico",
+  "assets/*.png",
   "assets/alphafold/*.png",
   "assets/alphafold/*.cif",
 ]

{iints_sdk_python35-1.5.22 → iints_sdk_python35-1.5.24}/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__ = "1.5.22"
+    __version__ = "1.5.24"
 
 # 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_python35-1.5.22 → iints_sdk_python35-1.5.24}/src/iints/core/patient/bergman_model.py

@@ -63,6 +63,11 @@ class BergmanParameters:
     k_a_glucagon: float = 0.05    # 1/min
     S_glucagon: float = 0.02      # sensitivity
 
+    # --- Stem Cell Graft (Research) ---
+    stem_cell_engraftment_percent: float = 0.0 # 0 for T1D, 100 for cure
+    stem_cell_subq_fraction: float = 0.0       # 0.0 = PV (immediate), 1.0 = subQ (delayed via S1)
+    immune_rejection_rate: float = 0.0         # 1/min decay of graft mass
+
     # --- Gut absorption ---
     tau_meal: float = 40.0  # min    — gastric emptying time constant
     k_abs: float = 0.05     # 1/min  — intestinal absorption rate constant
@@ -96,6 +101,7 @@ class BergmanPatientModel:
         carb_absorption_duration_minutes: float = 240.0,
         max_glucose_rate_mgdl_per_min: float = 3.0,
         bergman_params: Optional[BergmanParameters] = None,
+        **kwargs
     ) -> None:
         # Store clinical knobs (for ratio queries and compatibility)
         self.basal_insulin_rate = basal_insulin_rate
@@ -121,6 +127,10 @@ class BergmanPatientModel:
             Gb=gb_default,
             tau_meal=max(45.0, min(float(carb_absorption_duration_minutes) / 3.0, 100.0)),
             k_abs=max(0.015, min(float(glucose_absorption_rate), 0.035)),
+            stem_cell_engraftment_percent=kwargs.get('stem_cell_engraftment_percent', 0.0),
+            stem_cell_subq_fraction=kwargs.get('stem_cell_subq_fraction', 0.0),
+            immune_rejection_rate=kwargs.get('immune_rejection_rate', 0.0),
+            gamma=0.005 if kwargs.get('stem_cell_engraftment_percent', 0.0) > 0 else 0.0
         )
 
         # Exercise book-keeping
@@ -159,6 +169,7 @@ class BergmanPatientModel:
             0.0,                   # 10: Gamma (pg/mL) - Plasma Glucagon
             0.0,                   # 11: x_gluc (1) - Glucagon action on EGP
             0.0,                   # 12: HAAF (1) - Memory
+            (self.params.stem_cell_engraftment_percent / 100.0),  # 13: M_graft (1) - Graft Mass
         ], dtype=np.float64)
 
         self.reset()
@@ -183,7 +194,7 @@ class BergmanPatientModel:
         """Reset to initial conditions."""
         self._state = np.array([
             self.initial_glucose, 0.0, self.params.Ib, 0.0, 0.0, 0.0, 0.0, 0.0,
-            0.0, 0.0, 0.0, 0.0, 0.0
+            0.0, 0.0, 0.0, 0.0, 0.0, (self.params.stem_cell_engraftment_percent / 100.0)
         ], dtype=np.float64)
         self.current_glucose = self.initial_glucose
         self.insulin_on_board = 0.0
@@ -369,22 +380,27 @@ class BergmanPatientModel:
             # Handle legacy snapshot coercions to 13-state vector
             if ode_state.size == 4:
                 ode_state = np.array(
-                    [ode_state[0], ode_state[1], ode_state[2], 0.0, 0.0, ode_state[3], 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+                    [ode_state[0], ode_state[1], ode_state[2], 0.0, 0.0, ode_state[3], 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, (self.params.stem_cell_engraftment_percent / 100.0)],
                     dtype=np.float64,
                 )
             elif ode_state.size == 5:
                 ode_state = np.array(
-                    [ode_state[0], ode_state[1], ode_state[2], ode_state[3], 0.0, ode_state[4], 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+                    [ode_state[0], ode_state[1], ode_state[2], ode_state[3], 0.0, ode_state[4], 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, (self.params.stem_cell_engraftment_percent / 100.0)],
                     dtype=np.float64,
                 )
             elif ode_state.size == 7:
                 ode_state = np.array(
-                    [ode_state[0], ode_state[1], ode_state[2], ode_state[3], 0.0, ode_state[4], ode_state[5], ode_state[6], 0.0, 0.0, 0.0, 0.0, 0.0],
+                    [ode_state[0], ode_state[1], ode_state[2], ode_state[3], 0.0, ode_state[4], ode_state[5], ode_state[6], 0.0, 0.0, 0.0, 0.0, 0.0, (self.params.stem_cell_engraftment_percent / 100.0)],
                     dtype=np.float64,
                 )
             elif ode_state.size == 8:
                 ode_state = np.array(
-                    [ode_state[0], ode_state[1], ode_state[2], ode_state[3], ode_state[4], ode_state[5], ode_state[6], ode_state[7], 0.0, 0.0, 0.0, 0.0, 0.0],
+                    [ode_state[0], ode_state[1], ode_state[2], ode_state[3], ode_state[4], ode_state[5], ode_state[6], ode_state[7], 0.0, 0.0, 0.0, 0.0, 0.0, (self.params.stem_cell_engraftment_percent / 100.0)],
+                    dtype=np.float64,
+                )
+            elif ode_state.size == 13:
+                ode_state = np.array(
+                    list(ode_state) + [(self.params.stem_cell_engraftment_percent / 100.0)],
                     dtype=np.float64,
                 )
             self._state = ode_state
@@ -415,7 +431,7 @@ class BergmanPatientModel:
         u_glucagon_pg_per_min: float,
         current_time: float,
     ) -> np.ndarray:
-        G, X, I, Q_sto1, Q_sto2, Q_gut, S1, S2, Y1, Y2, Gamma, x_gluc, HAAF = y
+        G, X, I, Q_sto1, Q_sto2, Q_gut, S1, S2, Y1, Y2, Gamma, x_gluc, HAAF, M_graft = y
         p = self.params
 
         Vg_abs = p.Vg * p.body_weight_kg   # dL
@@ -484,16 +500,28 @@ class BergmanPatientModel:
         # --- dX/dt ---
         dXdt = -p.p2 * X + p3_eff * max(I - p.Ib, 0.0)
 
+        # --- Stem Cell / Islet Secretion ---
+        # Gamma acts as base secretion rate for a 100% functional pancreas
+        # M_graft acts as the survival fraction multiplier.
+        total_secretion = p.gamma * M_graft * max(G - p.h, 0.0)
+        
+        secretion_subq = total_secretion * p.stem_cell_subq_fraction
+        secretion_plasma = total_secretion * (1.0 - p.stem_cell_subq_fraction)
+
         # --- dS1/dt, dS2/dt (Subcutaneous Insulin Absorption) ---
-        dS1dt = u_insulin_mu_per_min - p.k_a * S1
+        # Any SubQ implanted islet cells release into S1
+        dS1dt = u_insulin_mu_per_min + secretion_subq - p.k_a * S1
         dS2dt = p.k_a * S1 - p.k_a * S2
 
         # Rate of appearance of insulin into plasma (mU/min)
         Ra_I = p.k_a * S2
 
         # --- dI/dt ---
-        secretion = p.gamma * max(G - p.h, 0.0)
-        dIdt = -p.n * (I - p.Ib) + secretion + Ra_I / Vi_abs
+        # Any PV/Hepatic implanted islet cells release directly into plasma
+        dIdt = -p.n * (I - p.Ib) + secretion_plasma + Ra_I / Vi_abs
+        
+        # --- dM_graft/dt ---
+        dM_graft_dt = -p.immune_rejection_rate * M_graft
 
         # --- Dalla Man Multi-compartment Meal Kinetcs ---
         gastric_emptying_rate = 1.0 / max(float(p.tau_meal), 1.0)
@@ -502,4 +530,4 @@ class BergmanPatientModel:
         dQ_sto2_dt = solid_to_liquid_rate * Q_sto1 - gastric_emptying_rate * Q_sto2
         dQ_gut_dt = gastric_emptying_rate * Q_sto2 - p.k_abs * Q_gut
 
-        return np.array([dGdt, dXdt, dIdt, dQ_sto1_dt, dQ_sto2_dt, dQ_gut_dt, dS1dt, dS2dt, dY1_dt, dY2_dt, dGamma_dt, dx_gluc_dt, dHAAF_dt])
+        return np.array([dGdt, dXdt, dIdt, dQ_sto1_dt, dQ_sto2_dt, dQ_gut_dt, dS1dt, dS2dt, dY1_dt, dY2_dt, dGamma_dt, dx_gluc_dt, dHAAF_dt, dM_graft_dt])

iints_sdk_python35-1.5.24/src/iints/research/stem_cell_optimizer.py

@@ -0,0 +1,85 @@
+import numpy as np
+import pandas as pd
+from typing import Dict, Any, List, Optional
+from iints.core.simulator import Simulator
+from iints.core.patient.bergman_model import BergmanPatientModel, BergmanParameters
+from iints.core.algorithms.pid_controller import PIDController
+from iints.core.devices.models import SensorModel, PumpModel
+
+class StemCellOptimizer:
+    """
+    Research optimization module for stem cell / islet cell graft simulations.
+    Runs batch simulations to evaluate graft survival and kinetics for T1D cures.
+    """
+    
+    def __init__(self, duration_minutes: int = 1440, time_step: int = 5):
+        self.duration_minutes = duration_minutes
+        self.time_step = time_step
+        
+    def evaluate_graft_configuration(
+        self, 
+        engraftment_percent: float, 
+        subq_fraction: float, 
+        immune_decay: float,
+        meal_schedule: List[Dict[str, float]],
+        seed: int = 42
+    ) -> Dict[str, Any]:
+        """
+        Runs a simulation for a specific stem cell graft configuration.
+        """
+        # Create bergman parameters with stem cell settings
+        params = BergmanParameters(
+            stem_cell_engraftment_percent=engraftment_percent,
+            stem_cell_subq_fraction=subq_fraction,
+            immune_rejection_rate=immune_decay,
+            gamma=0.005 # Baseline healthy beta cell secretion rate
+        )
+        
+        patient = BergmanPatientModel(
+            initial_glucose=100.0,
+            bergman_params=params
+        )
+        
+        # We use a dummy controller since the patient is autonomously producing insulin
+        controller = PIDController()
+        sensor = SensorModel(noise_std=1.0, seed=seed)
+        pump = PumpModel()
+        
+        from iints.validation import build_stress_events
+        
+        simulator = Simulator(
+            patient_model=patient,  # type: ignore
+            algorithm=controller,
+            sensor_model=sensor,
+            pump_model=pump,
+        )
+        for event in build_stress_events(meal_schedule):
+            simulator.add_stress_event(event)
+        
+        df, stats = simulator.run_batch(duration_minutes=self.duration_minutes)
+        
+        # Calculate TIR
+        if not df.empty:
+            bg_col = "bg" if "bg" in df.columns else "CGM" if "CGM" in df.columns else "glucose" if "glucose" in df.columns else df.columns[1]
+            tir_mask = (df[bg_col] >= 70) & (df[bg_col] <= 180)
+            tir = tir_mask.mean() * 100.0
+            
+            hypo_mask = df[bg_col] < 70
+            hypo = hypo_mask.mean() * 100.0
+            
+            hyper_mask = df[bg_col] > 180
+            hyper = hyper_mask.mean() * 100.0
+        else:
+            tir, hypo, hyper = 0.0, 0.0, 0.0
+            
+        return {
+            "tir_percent": tir,
+            "hypo_percent": hypo,
+            "hyper_percent": hyper,
+            "max_glucose": df[bg_col].max() if not df.empty else 0.0,
+            "min_glucose": df[bg_col].min() if not df.empty else 0.0,
+            "engraftment_percent": engraftment_percent,
+            "subq_fraction": subq_fraction,
+            "immune_decay": immune_decay,
+            "df": df
+        }

{iints_sdk_python35-1.5.22 → iints_sdk_python35-1.5.24}/src/iints_desktop/app.py

@@ -5,6 +5,7 @@ import sys
 import threading
 import tkinter as tk
 import webbrowser
+from importlib import resources
 from pathlib import Path
 from tkinter import filedialog, messagebox, ttk
 
@@ -26,6 +27,7 @@ class IINTSDesktopApp:
         self.root.title("IINTS-AF Desktop")
         self.root.geometry("980x720")
         self.root.minsize(860, 620)
+        self._apply_app_icon()
 
         self.presets = list_desktop_presets()
         self.preset_by_title = {preset.title: preset for preset in self.presets}
@@ -42,6 +44,15 @@ class IINTSDesktopApp:
         self._build_ui()
         self.root.after(200, self._poll_messages)
 
+    def _apply_app_icon(self) -> None:
+        try:
+            icon_ref = resources.files("iints_desktop").joinpath("assets", "app_icon.png")
+            if icon_ref.is_file():
+                self._window_icon = tk.PhotoImage(file=str(icon_ref))
+                self.root.iconphoto(True, self._window_icon)
+        except Exception:
+            pass
+
     def _build_ui(self) -> None:
         self._configure_style()
 

{iints_sdk_python35-1.5.22 → iints_sdk_python35-1.5.24}/src/iints_desktop/cocoa_app.py

@@ -3,6 +3,7 @@ from __future__ import annotations
 import queue
 import sys
 import threading
+from importlib import resources
 from pathlib import Path
 from typing import Any
 
@@ -40,6 +41,7 @@ def main() -> int:
             NSMakeRect,
             NSMiniaturizableWindowMask,
             NSModalResponseOK,
+            NSImage,
             NSOpenPanel,
             NSPopUpButton,
             NSResizableWindowMask,
@@ -67,6 +69,7 @@ def main() -> int:
         last_result: DesktopRunResult | None
 
         def applicationDidFinishLaunching_(self, _notification: Any) -> None:
+            self._apply_app_icon()
             self.presets = list_desktop_presets()
             self.messages = queue.Queue()
             self.last_result = None
@@ -80,6 +83,17 @@ def main() -> int:
         def applicationShouldTerminateAfterLastWindowClosed_(self, _sender: Any) -> bool:
             return True
 
+        @objc.python_method
+        def _apply_app_icon(self) -> None:
+            try:
+                icon_ref = resources.files("iints_desktop").joinpath("assets", "app_icon.png")
+                if icon_ref.is_file():
+                    image = NSImage.alloc().initWithContentsOfFile_(str(icon_ref))
+                    if image is not None:
+                        NSApplication.sharedApplication().setApplicationIconImage_(image)
+            except Exception:
+                pass
+
         @objc.python_method
         def _label(self, parent: Any, text: str, frame: tuple[float, float, float, float], *, size: float = 13.0, bold: bool = False) -> Any:
             field = NSTextField.alloc().initWithFrame_(NSMakeRect(*frame))

{iints_sdk_python35-1.5.22 → iints_sdk_python35-1.5.24}/src/iints_desktop/launcher.py

@@ -29,7 +29,8 @@ def main() -> int | None:
         return qt_main()
 
     print(
-        "PySide6 is not installed; falling back to the Tkinter desktop app.",
+        "PySide6 is not installed; falling back to the Tkinter desktop app. "
+        'Install the full desktop app with: python -m pip install -U "iints-sdk-python35[full,desktop,mdmp]"',
         file=sys.stderr,
     )
     from iints_desktop.app import main as tk_main

{iints_sdk_python35-1.5.22 → iints_sdk_python35-1.5.24}/src/iints_desktop/local_ai.py

@@ -49,16 +49,17 @@ class LocalAIStartResult:
 SYSTEM_PROMPT = """You are a highly advanced Medical Data Scientist and Computational Biologist analyzing output from the IINTS-AF closed-loop insulin simulator.
 
 CRITICAL INSTRUCTIONS:
-1. Speak with absolute professional authority and scientific rigor. Do NOT sound like an AI assistant. Do NOT use vague conversational filler.
-2. Analyze the provided clinical simulation data. Extract meaningful physiological insights, glycemic control patterns (Time in Range, Coefficient of Variation), and algorithmic behaviors (e.g. basal suspension aggressiveness, insulin resistance masking).
-3. Do not include boilerplate legal disclaimers at the beginning of your text. If necessary, include a single sentence limitation at the very end.
-4. Structure your response explicitly using these exact headers:
+1. Speak with absolute professional authority and scientific rigor. Do NOT sound like an AI assistant.
+2. PROHIBITED PHRASES: "Here is an analysis", "As an AI", "In conclusion", "I can help with that". Start immediately with the facts.
+3. Analyze the provided clinical simulation data. Extract meaningful physiological insights, glycemic control patterns (Time in Range, Coefficient of Variation), and algorithmic behaviors.
+4. Structure your response explicitly using these exact headers (do not use other headers):
   Clinical Overview
   Biomathematical Observations
   Algorithmic Behavior
   Conclusions
-5. Use highly specific scientific terminology (e.g., exogenous insulin kinetics, hepatic glucose production, PI3K/AKT pathway attenuation).
-6. Acknowledge that the IINTS-AF simulator is for research and education only. It is Not a medical device. Do not provide diagnosis, insulin dosing, or treatment advice.
+5. Use highly specific scientific terminology (e.g., exogenous insulin kinetics, hepatic glucose production).
+6. Present findings in dense, hard-hitting bullet points. Do not write fluffy paragraphs.
+7. Acknowledge that the IINTS-AF simulator is for research and education only. It is Not a medical device. Do not provide diagnosis, insulin dosing, or treatment advice.
 """
 
 
@@ -284,7 +285,7 @@ def format_ai_answer(text: str) -> str:
             "algorithmic behavior", 
             "conclusions"
         }:
-            line = line.rstrip(":").title()
+            line = f"\n=== {line.rstrip(':').upper()} ==="
         lines.append(line)
     return "\n".join(lines).strip()
 
@@ -302,7 +303,7 @@ def ask_local_ai(
     backend = OllamaBackend(
         model_name=model,
         base_url=host,
-        timeout_seconds=180.0,
+        timeout_seconds=900.0,
         temperature=0.1,
         top_p=0.8,
         num_predict=1000,