iints-sdk-python35 1.1.1__tar.gz → 1.1.2__tar.gz

{iints_sdk_python35-1.1.1 → iints_sdk_python35-1.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: iints-sdk-python35
-Version: 1.1.1
+Version: 1.1.2
 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
@@ -110,15 +110,21 @@ ollama pull ministral-3:8b
 iints ai local-check --model ministral-3:8b
 ```
 
-Example commands:
+Recommended flow:
+
+```bash
+iints quickstart --project-name iints_quickstart
+cd iints_quickstart
+iints presets run --name baseline_t1d --algo algorithms/example_algorithm.py
+iints ai prepare results/<run_id>
+iints ai report results/<run_id>
+```
+
+Direct JSON mode still works if you already have your own payloads and signed MDMP artifact:
 
 ```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:
@@ -127,8 +133,21 @@ Notes:
 - The SDK now targets the open local `Ministral 3` Ollama model by default.
 - Users can choose a larger or smaller local Mistral-family model with `--model ...`.
 - Large JSON payloads are clipped automatically before prompt generation to keep local inference stable.
+- `iints ai prepare <run_dir>` now creates AI-ready JSON payloads and, when MDMP is installed, a local development certificate plus keypair in `<run_dir>/ai/`.
+- After `iints ai prepare`, you can point `iints ai explain|trends|anomalies|report` directly at the run directory.
 - Output is research-only and not medical advice.
 
+Troubleshooting:
+- If `iints ai ...` says `No such command 'ai'`, your environment usually still has a legacy `iints` package installed alongside `iints-sdk-python35`.
+- Run `iints-sdk-doctor` first.
+- If it reports a conflict, repair the environment with:
+
+```bash
+python -m pip uninstall -y iints iints-sdk-python35
+python -m pip install -U "iints-sdk-python35[mdmp]==1.1.2"
+hash -r
+```
+
 ## MDMP (Short)
 MDMP is the data-quality protocol used by IINTS.
 

{iints_sdk_python35-1.1.1 → iints_sdk_python35-1.1.2}/README.md

@@ -59,15 +59,21 @@ ollama pull ministral-3:8b
 iints ai local-check --model ministral-3:8b
 ```
 
-Example commands:
+Recommended flow:
+
+```bash
+iints quickstart --project-name iints_quickstart
+cd iints_quickstart
+iints presets run --name baseline_t1d --algo algorithms/example_algorithm.py
+iints ai prepare results/<run_id>
+iints ai report results/<run_id>
+```
+
+Direct JSON mode still works if you already have your own payloads and signed MDMP artifact:
 
 ```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:
@@ -76,8 +82,21 @@ Notes:
 - The SDK now targets the open local `Ministral 3` Ollama model by default.
 - Users can choose a larger or smaller local Mistral-family model with `--model ...`.
 - Large JSON payloads are clipped automatically before prompt generation to keep local inference stable.
+- `iints ai prepare <run_dir>` now creates AI-ready JSON payloads and, when MDMP is installed, a local development certificate plus keypair in `<run_dir>/ai/`.
+- After `iints ai prepare`, you can point `iints ai explain|trends|anomalies|report` directly at the run directory.
 - Output is research-only and not medical advice.
 
+Troubleshooting:
+- If `iints ai ...` says `No such command 'ai'`, your environment usually still has a legacy `iints` package installed alongside `iints-sdk-python35`.
+- Run `iints-sdk-doctor` first.
+- If it reports a conflict, repair the environment with:
+
+```bash
+python -m pip uninstall -y iints iints-sdk-python35
+python -m pip install -U "iints-sdk-python35[mdmp]==1.1.2"
+hash -r
+```
+
 ## MDMP (Short)
 MDMP is the data-quality protocol used by IINTS.
 

{iints_sdk_python35-1.1.1 → iints_sdk_python35-1.1.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "iints-sdk-python35" 
-version = "1.1.1"
+version = "1.1.2"
 authors = [
   { name="Rune Bobbaers", email="rune.bobbaers@gmail.com" },
 ]
@@ -65,6 +65,7 @@ mdmp = [
 
 [project.scripts]
 iints = "iints.cli.cli:app"
+iints-sdk-doctor = "iints_sdk_python35_doctor:main"
 
 [project.entry-points."iints.algorithms"]
 "PID Controller" = "iints.core.algorithms.pid_controller:PIDController"

{iints_sdk_python35-1.1.1 → iints_sdk_python35-1.1.2}/src/iints/__init__.py

@@ -3,7 +3,15 @@
 import pandas as pd # Required for type hints like pd.DataFrame
 from typing import Optional
 
-__version__ = "0.1.22"
+try:
+    from importlib.metadata import PackageNotFoundError, version
+except ImportError:  # pragma: no cover - Python < 3.8 fallback
+    from importlib_metadata import PackageNotFoundError, version  # type: ignore
+
+try:
+    __version__ = version("iints-sdk-python35")
+except PackageNotFoundError:  # pragma: no cover - source tree fallback
+    __version__ = "1.1.2"
 
 # 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.

{iints_sdk_python35-1.1.1 → iints_sdk_python35-1.1.2}/src/iints/ai/__init__.py

@@ -2,6 +2,7 @@ from .assistant import AIResponse, IINTSAssistant
 from .backends import DEFAULT_MINISTRAL_MODEL, DEFAULT_OLLAMA_HOST, OllamaBackend
 from .mdmp_guard import GuardResult, MDMPGuard
 from .model_catalog import LocalMistralModelProfile, list_local_mistral_models
+from .prepare import prepare_ai_ready_artifacts
 
 __all__ = [
     "AIResponse",
@@ -13,4 +14,5 @@ __all__ = [
     "MDMPGuard",
     "LocalMistralModelProfile",
     "list_local_mistral_models",
+    "prepare_ai_ready_artifacts",
 ]

{iints_sdk_python35-1.1.1 → iints_sdk_python35-1.1.2}/src/iints/ai/cli.py

@@ -13,6 +13,7 @@ from typing_extensions import Annotated
 from .assistant import AIResponse, IINTSAssistant
 from .backends import DEFAULT_MINISTRAL_MODEL, OllamaBackend
 from .model_catalog import list_local_mistral_models
+from .prepare import prepare_ai_ready_artifacts
 
 
 app = typer.Typer(help="Research-only AI assistant commands gated by MDMP certification.")
@@ -36,6 +37,57 @@ def _load_json_payload(path: Path, label: str) -> Any:
     return payload
 
 
+def _default_prepared_payload(task: str, ai_dir: Path) -> Path:
+    candidates = {
+        "explain": ["step_riskiest.json", "step_latest.json"],
+        "trends": ["trends_payload.json"],
+        "anomalies": ["anomalies_payload.json"],
+        "report": ["report_payload.json"],
+    }.get(task, [])
+    for filename in candidates:
+        candidate = ai_dir / filename
+        if candidate.is_file():
+            return candidate
+    expected = ", ".join(candidates) if candidates else "prepared payload"
+    raise typer.BadParameter(
+        f"No prepared AI payload found in {ai_dir}. Expected one of: {expected}. "
+        "Run `iints ai prepare <run_dir>` first."
+    )
+
+
+def _resolve_cli_inputs(
+    *,
+    task: str,
+    input_path: Path,
+    mdmp_cert: Path | None,
+    public_key: Path | None,
+    trust_store: Path | None,
+) -> tuple[Path, Path, Path | None]:
+    resolved_input = input_path
+    resolved_cert = mdmp_cert
+    resolved_public_key = public_key
+
+    if input_path.is_dir():
+        ai_dir = input_path / "ai"
+        resolved_input = _default_prepared_payload(task, ai_dir)
+        if resolved_cert is None:
+            candidate_cert = ai_dir / "report.signed.mdmp"
+            if candidate_cert.is_file():
+                resolved_cert = candidate_cert
+        if resolved_public_key is None and trust_store is None:
+            candidate_public_key = ai_dir / "keys" / "mdmp_pub_v1.pem"
+            if candidate_public_key.is_file():
+                resolved_public_key = candidate_public_key
+
+    if resolved_cert is None:
+        raise typer.BadParameter(
+            "No MDMP certificate provided. Pass --mdmp-cert or run "
+            "`iints ai prepare <run_dir>` to generate a local development certificate."
+        )
+
+    return resolved_input, resolved_cert, resolved_public_key
+
+
 def _write_output(path: Path | None, response: AIResponse) -> None:
     if path is None:
         return
@@ -117,6 +169,47 @@ def models() -> None:
     )
 
 
+@app.command("prepare")
+def prepare(
+    run_dir: Annotated[Path, typer.Argument(help="Run output directory containing results.csv and run_metadata.json.")],
+    create_dev_mdmp_cert: Annotated[
+        bool,
+        typer.Option(
+            "--create-dev-mdmp-cert/--no-create-dev-mdmp-cert",
+            help="Generate a local development MDMP certificate and keypair for AI commands.",
+        ),
+    ] = True,
+    grade: Annotated[str, typer.Option(help="Grade to embed in the local development MDMP certificate.")] = "research_grade",
+    expires_days: Annotated[int, typer.Option(help="Certificate expiry window in days for local development certs.")] = 30,
+    key_dir: Annotated[Optional[Path], typer.Option(help="Optional directory to store the generated local MDMP keypair.")] = None,
+) -> None:
+    console = Console()
+    try:
+        outputs = prepare_ai_ready_artifacts(
+            run_dir,
+            create_dev_mdmp_cert=create_dev_mdmp_cert,
+            grade=grade,
+            expires_days=expires_days,
+            key_dir=key_dir,
+        )
+    except Exception as exc:
+        console.print(f"[bold red]Error:[/bold red] {exc}")
+        raise typer.Exit(code=1)
+
+    table = Table(title="IINTS AI Prepared Artifacts")
+    table.add_column("Artifact", style="cyan")
+    table.add_column("Path", overflow="fold")
+    for key, value in outputs.items():
+        table.add_row(key, value)
+    console.print(table)
+    console.print("[green]Prepared AI payloads are ready.[/green]")
+    if "mdmp_cert" in outputs:
+        console.print(
+            "[green]You can now run:[/green] "
+            f"`iints ai report {run_dir}` or `iints ai explain {run_dir}`"
+        )
+
+
 def _build_assistant(
     *,
     mdmp_cert: Path,
@@ -169,8 +262,8 @@ def local_check(
 
 @app.command("explain")
 def explain(
-    input_json: Annotated[Path, typer.Argument(help="JSON file with a single simulation step or decision context.")],
-    mdmp_cert: Annotated[Path, typer.Option(help="Signed MDMP artifact required before AI analysis can run.")],
+    input_json: Annotated[Path, typer.Argument(help="Prepared run directory or JSON file with a single simulation step or decision context.")],
+    mdmp_cert: Annotated[Optional[Path], typer.Option(help="Signed MDMP artifact required before AI analysis can run.")] = None,
     mode: Annotated[str, typer.Option(help="AI backend mode. Use 'local' for Ollama/Ministral.")] = "auto",
     model: Annotated[str, typer.Option(help="Ollama model name to use.")] = DEFAULT_MINISTRAL_MODEL,
     minimum_grade: Annotated[str, typer.Option(help="Minimum MDMP grade required to allow analysis.")] = "research_grade",
@@ -182,13 +275,20 @@ def explain(
 ) -> None:
     console = Console()
     try:
-        payload = _load_json_payload(input_json, "Input JSON")
-        assistant = _build_assistant(
+        resolved_input, resolved_cert, resolved_public_key = _resolve_cli_inputs(
+            task="explain",
+            input_path=input_json,
             mdmp_cert=mdmp_cert,
+            public_key=public_key,
+            trust_store=trust_store,
+        )
+        payload = _load_json_payload(resolved_input, "Input JSON")
+        assistant = _build_assistant(
+            mdmp_cert=resolved_cert,
             mode=mode,
             model=model,
             minimum_grade=minimum_grade,
-            public_key=public_key,
+            public_key=resolved_public_key,
             trust_store=trust_store,
             ollama_host=ollama_host,
             timeout_seconds=timeout_seconds,
@@ -203,8 +303,8 @@ def explain(
 
 @app.command("trends")
 def trends(
-    input_json: Annotated[Path, typer.Argument(help="JSON file with glucose trace data or a run payload.")],
-    mdmp_cert: Annotated[Path, typer.Option(help="Signed MDMP artifact required before AI analysis can run.")],
+    input_json: Annotated[Path, typer.Argument(help="Prepared run directory or JSON file with glucose trace data or a run payload.")],
+    mdmp_cert: Annotated[Optional[Path], typer.Option(help="Signed MDMP artifact required before AI analysis can run.")] = None,
     mode: Annotated[str, typer.Option(help="AI backend mode. Use 'local' for Ollama/Ministral.")] = "auto",
     model: Annotated[str, typer.Option(help="Ollama model name to use.")] = DEFAULT_MINISTRAL_MODEL,
     minimum_grade: Annotated[str, typer.Option(help="Minimum MDMP grade required to allow analysis.")] = "research_grade",
@@ -216,13 +316,20 @@ def trends(
 ) -> None:
     console = Console()
     try:
-        payload = _load_json_payload(input_json, "Input JSON")
-        assistant = _build_assistant(
+        resolved_input, resolved_cert, resolved_public_key = _resolve_cli_inputs(
+            task="trends",
+            input_path=input_json,
             mdmp_cert=mdmp_cert,
+            public_key=public_key,
+            trust_store=trust_store,
+        )
+        payload = _load_json_payload(resolved_input, "Input JSON")
+        assistant = _build_assistant(
+            mdmp_cert=resolved_cert,
             mode=mode,
             model=model,
             minimum_grade=minimum_grade,
-            public_key=public_key,
+            public_key=resolved_public_key,
             trust_store=trust_store,
             ollama_host=ollama_host,
             timeout_seconds=timeout_seconds,
@@ -237,8 +344,8 @@ def trends(
 
 @app.command("anomalies")
 def anomalies(
-    input_json: Annotated[Path, typer.Argument(help="JSON file with simulation results or run summary.")],
-    mdmp_cert: Annotated[Path, typer.Option(help="Signed MDMP artifact required before AI analysis can run.")],
+    input_json: Annotated[Path, typer.Argument(help="Prepared run directory or JSON file with simulation results or run summary.")],
+    mdmp_cert: Annotated[Optional[Path], typer.Option(help="Signed MDMP artifact required before AI analysis can run.")] = None,
     mode: Annotated[str, typer.Option(help="AI backend mode. Use 'local' for Ollama/Ministral.")] = "auto",
     model: Annotated[str, typer.Option(help="Ollama model name to use.")] = DEFAULT_MINISTRAL_MODEL,
     minimum_grade: Annotated[str, typer.Option(help="Minimum MDMP grade required to allow analysis.")] = "research_grade",
@@ -250,13 +357,20 @@ def anomalies(
 ) -> None:
     console = Console()
     try:
-        payload = _load_json_payload(input_json, "Input JSON")
-        assistant = _build_assistant(
+        resolved_input, resolved_cert, resolved_public_key = _resolve_cli_inputs(
+            task="anomalies",
+            input_path=input_json,
             mdmp_cert=mdmp_cert,
+            public_key=public_key,
+            trust_store=trust_store,
+        )
+        payload = _load_json_payload(resolved_input, "Input JSON")
+        assistant = _build_assistant(
+            mdmp_cert=resolved_cert,
             mode=mode,
             model=model,
             minimum_grade=minimum_grade,
-            public_key=public_key,
+            public_key=resolved_public_key,
             trust_store=trust_store,
             ollama_host=ollama_host,
             timeout_seconds=timeout_seconds,
@@ -271,8 +385,8 @@ def anomalies(
 
 @app.command("report")
 def report(
-    input_json: Annotated[Path, typer.Argument(help="JSON file with run-level simulation outputs.")],
-    mdmp_cert: Annotated[Path, typer.Option(help="Signed MDMP artifact required before AI analysis can run.")],
+    input_json: Annotated[Path, typer.Argument(help="Prepared run directory or JSON file with run-level simulation outputs.")],
+    mdmp_cert: Annotated[Optional[Path], typer.Option(help="Signed MDMP artifact required before AI analysis can run.")] = None,
     mode: Annotated[str, typer.Option(help="AI backend mode. Use 'local' for Ollama/Ministral.")] = "auto",
     model: Annotated[str, typer.Option(help="Ollama model name to use.")] = DEFAULT_MINISTRAL_MODEL,
     minimum_grade: Annotated[str, typer.Option(help="Minimum MDMP grade required to allow analysis.")] = "research_grade",
@@ -284,13 +398,20 @@ def report(
 ) -> None:
     console = Console()
     try:
-        payload = _load_json_payload(input_json, "Input JSON")
-        assistant = _build_assistant(
+        resolved_input, resolved_cert, resolved_public_key = _resolve_cli_inputs(
+            task="report",
+            input_path=input_json,
             mdmp_cert=mdmp_cert,
+            public_key=public_key,
+            trust_store=trust_store,
+        )
+        payload = _load_json_payload(resolved_input, "Input JSON")
+        assistant = _build_assistant(
+            mdmp_cert=resolved_cert,
             mode=mode,
             model=model,
             minimum_grade=minimum_grade,
-            public_key=public_key,
+            public_key=resolved_public_key,
             trust_store=trust_store,
             ollama_host=ollama_host,
             timeout_seconds=timeout_seconds,