iints-sdk-python35 1.5.1__tar.gz → 1.5.3__tar.gz

{iints_sdk_python35-1.5.1/src/iints_sdk_python35.egg-info → iints_sdk_python35-1.5.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: iints-sdk-python35
-Version: 1.5.1
+Version: 1.5.3
 Summary: A pre-clinical Edge-AI SDK for diabetes management validation.
 Author-email: Rune Bobbaers <rune.bobbaers@gmail.com>
 License-Expression: Apache-2.0
@@ -17,22 +17,35 @@ 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: fastapi>=0.115.0
 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]
+Requires-Dist: uvicorn>=0.30.0
+Provides-Extra: edge
+Requires-Dist: pyserial>=3.5; 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: pyserial>=3.5; 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: httpx>=0.27.0; extra == "dev"
 Requires-Dist: mypy; extra == "dev"
 Requires-Dist: pandas-stubs; extra == "dev"
 Requires-Dist: types-PyYAML; extra == "dev"
@@ -70,7 +83,16 @@ Docs: [python35.github.io/IINTS-SDK](https://python35.github.io/IINTS-SDK/)
 python3 -m venv .venv
 source .venv/bin/activate
 python -m pip install -U pip
-python -m pip install -U "iints-sdk-python35[mdmp]"
+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:
@@ -90,6 +112,8 @@ 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`

{iints_sdk_python35-1.5.1 → iints_sdk_python35-1.5.3}/README.md

@@ -17,7 +17,16 @@ Docs: [python35.github.io/IINTS-SDK](https://python35.github.io/IINTS-SDK/)
 python3 -m venv .venv
 source .venv/bin/activate
 python -m pip install -U pip
-python -m pip install -U "iints-sdk-python35[mdmp]"
+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:
@@ -37,6 +46,8 @@ 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`

{iints_sdk_python35-1.5.1 → iints_sdk_python35-1.5.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "iints-sdk-python35" 
-version = "1.5.1"
+version = "1.5.3"
 authors = [
   { name="Rune Bobbaers", email="rune.bobbaers@gmail.com" },
 ]
@@ -23,25 +23,41 @@ 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 = [
+  "pyserial>=3.5",
+]
+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",
+  "pyserial>=3.5",
+  "pillow>=12.1.1",
+  "seaborn>=0.11.0",
+]
 dev = [
   "pytest>=7.0.0",
   "hypothesis>=6.0.0",
   "flake8",
+  "httpx>=0.27.0",
   "mypy",
   "pandas-stubs",
   "types-PyYAML",
@@ -86,6 +102,8 @@ 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_python35-1.5.1 → iints_sdk_python35-1.5.3}/src/iints/__init__.py

@@ -1,7 +1,7 @@
 # src/iints/__init__.py
 
 import pandas as pd # Required for type hints like pd.DataFrame
-from typing import Optional
+from typing import Any, Optional
 
 try:
     from importlib.metadata import PackageNotFoundError, version
@@ -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__ = "1.5.1"
+    __version__ = "1.5.3"
 
 # 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,
@@ -72,16 +79,75 @@ 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 .highlevel import run_simulation, run_full, run_population
+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 .scenarios import ScenarioGeneratorConfig, generate_random_scenario
 
+
+def run_simulation(*args: Any, **kwargs: Any) -> Any:
+    from .highlevel import run_simulation as _run_simulation
+
+    return _run_simulation(*args, **kwargs)
+
+
+def run_full(*args: Any, **kwargs: Any) -> Any:
+    from .highlevel import run_full as _run_full
+
+    return _run_full(*args, **kwargs)
+
+
+def run_population(*args: Any, **kwargs: Any) -> Any:
+    from .highlevel import run_population as _run_population
+
+    return _run_population(*args, **kwargs)
+
+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,
@@ -202,6 +268,17 @@ __all__ = [
     "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_python35-1.5.3/src/iints/analysis/__init__.py

@@ -0,0 +1,129 @@
+from .clinical_metrics import ClinicalMetricsCalculator, ClinicalMetricsResult
+from .baseline import compute_metrics, run_baseline_comparison, write_baseline_comparison
+from .study_engine import (
+    StudyAlgorithmSpec,
+    StudyArmSpec,
+    StudyDesignPayload,
+    StudyMatrixRow,
+    StudyProfileSpec,
+    build_algorithm_registry,
+    build_study_design_payload,
+    resolve_profile_specs,
+)
+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,
+)
+from .eucys_results import (
+    build_eucys_abstract_draft_markdown,
+    build_eucys_filled_abstract_markdown,
+    build_eucys_jury_qa_markdown,
+    build_eucys_limitations_and_ethics_markdown,
+    build_eucys_poster_outline_markdown,
+    generate_eucys_main_figure,
+    generate_eucys_results_bundle,
+)
+
+
+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",
+    "build_eucys_abstract_draft_markdown",
+    "build_eucys_filled_abstract_markdown",
+    "build_eucys_jury_qa_markdown",
+    "build_eucys_limitations_and_ethics_markdown",
+    "build_eucys_poster_outline_markdown",
+    "generate_eucys_main_figure",
+    "resolve_profile_specs",
+    "generate_eucys_results_bundle",
+    "generate_results_poster",
+    "generate_study_poster",
+    "build_algorithm_registry",
+    "build_study_design_payload",
+    "build_study_protocol_payload",
+    "render_study_protocol_markdown",
+    "write_study_protocol_bundle",
+    "load_study_summary",
+    "quality_badges_for_metrics",
+    "run_baseline_comparison",
+    "StudyAlgorithmSpec",
+    "StudyArmSpec",
+    "StudyComparison",
+    "StudyDesignPayload",
+    "StudyMatrixRow",
+    "StudyProfileSpec",
+    "StudyRunSummary",
+    "StudySummary",
+    "write_baseline_comparison",
+]

{iints_sdk_python35-1.5.1 → iints_sdk_python35-1.5.3}/src/iints/analysis/baseline.py

@@ -12,6 +12,7 @@ from iints.core.algorithms.pid_controller import PIDController
 from iints.core.algorithms.standard_pump_algo import StandardPumpAlgorithm
 from iints.core.patient.models import PatientModel
 from iints.core.simulator import Simulator
+from iints.utils.csv_safety import sanitize_csv_dataframe
 from iints.validation import build_stress_events
 
 
@@ -88,5 +89,5 @@ def write_baseline_comparison(comparison: Dict[str, Any], output_dir: Path) -> D
     json_path = output_dir / "baseline_comparison.json"
     csv_path = output_dir / "baseline_comparison.csv"
     json_path.write_text(json.dumps(comparison, indent=2))
-    pd.DataFrame(comparison.get("rows", [])).to_csv(csv_path, index=False)
+    sanitize_csv_dataframe(pd.DataFrame(comparison.get("rows", []))).to_csv(csv_path, index=False)
     return {"json": str(json_path), "csv": str(csv_path)}