iints-sdk-python35 1.1.0__tar.gz → 1.1.2__tar.gz

{iints_sdk_python35-1.1.0/src/iints_sdk_python35.egg-info → iints_sdk_python35-1.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: iints-sdk-python35
-Version: 1.1.0
+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
@@ -81,7 +81,7 @@ cd iints_quickstart
 iints presets run --name baseline_t1d --algo algorithms/example_algorithm.py
 ```
 
-## AI Assistant (Ministral via Ollama)
+## AI Assistant (Ministral 3 Open-Weight 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.
@@ -95,30 +95,59 @@ python -m pip install -U pip
 python -m pip install -e ".[mdmp]"
 ```
 
-Run Ministral locally with Ollama:
+Run the open local Mistral model locally with Ollama:
 
 ```bash
-ollama pull mistral/ministral-8b-instruct
-iints ai local-check --model ministral
+python -m pip install -e ".[mdmp]"
+ollama pull ministral-3:8b
+iints ai models
+```
+
+Recommended first-time setup:
+
+```bash
+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:
 - AI analysis is blocked if the MDMP artifact is invalid.
 - Minimum required MDMP grade defaults to `research_grade`.
+- 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_python35-1.1.0 → iints_sdk_python35-1.1.2}/README.md

@@ -30,7 +30,7 @@ cd iints_quickstart
 iints presets run --name baseline_t1d --algo algorithms/example_algorithm.py
 ```
 
-## AI Assistant (Ministral via Ollama)
+## AI Assistant (Ministral 3 Open-Weight 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.
@@ -44,30 +44,59 @@ python -m pip install -U pip
 python -m pip install -e ".[mdmp]"
 ```
 
-Run Ministral locally with Ollama:
+Run the open local Mistral model locally with Ollama:
 
 ```bash
-ollama pull mistral/ministral-8b-instruct
-iints ai local-check --model ministral
+python -m pip install -e ".[mdmp]"
+ollama pull ministral-3:8b
+iints ai models
+```
+
+Recommended first-time setup:
+
+```bash
+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:
 - AI analysis is blocked if the MDMP artifact is invalid.
 - Minimum required MDMP grade defaults to `research_grade`.
+- 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_python35-1.1.0 → iints_sdk_python35-1.1.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "iints-sdk-python35" 
-version = "1.1.0"
+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_python35-1.1.0 → 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_python35-1.1.0 → iints_sdk_python35-1.1.2}/src/iints/ai/__init__.py

@@ -1,6 +1,8 @@
 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",
@@ -10,4 +12,7 @@ __all__ = [
     "OllamaBackend",
     "GuardResult",
     "MDMPGuard",
+    "LocalMistralModelProfile",
+    "list_local_mistral_models",
+    "prepare_ai_ready_artifacts",
 ]

{iints_sdk_python35-1.1.0 → iints_sdk_python35-1.1.2}/src/iints/ai/backends/mistral_api.py

@@ -13,5 +13,5 @@ class MistralAPIBackend:
     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."
+            "Use mode='local' with Ollama for the open Ministral 3 model."
         )

{iints_sdk_python35-1.1.0 → iints_sdk_python35-1.1.2}/src/iints/ai/backends/ollama.py

@@ -6,12 +6,19 @@ from urllib import error, request
 
 
 DEFAULT_OLLAMA_HOST = "http://127.0.0.1:11434"
-DEFAULT_MINISTRAL_MODEL = "mistral/ministral-8b-instruct"
+DEFAULT_MINISTRAL_MODEL = "ministral-3:8b"
+LEGACY_MINISTRAL_MODEL = "mistral/ministral-8b-instruct"
+MIN_OLLAMA_VERSION_FOR_MINISTRAL_3 = (0, 13, 1)
 MINISTRAL_MODEL_ALIASES = (
     DEFAULT_MINISTRAL_MODEL,
+    "ministral-3",
+    "ministral-3:latest",
+    "ministral-3:8b",
+    "ministral-3:8b-instruct",
     "ministral",
     "ministral-8b",
     "ministral-8b-instruct",
+    LEGACY_MINISTRAL_MODEL,
 )
 
 
@@ -23,7 +30,7 @@ class OllamaBackend:
         *,
         model_name: str = DEFAULT_MINISTRAL_MODEL,
         base_url: str | None = None,
-        timeout_seconds: float = 60.0,
+        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("/")
@@ -33,6 +40,28 @@ class OllamaBackend:
     def _pull_hint(self) -> str:
         return f"ollama pull {self.model_name}"
 
+    def _requires_ministral_3_runtime(self) -> bool:
+        requested = self.model_name.strip().lower()
+        return requested.startswith("ministral-3") or requested == "ministral"
+
+    @staticmethod
+    def _parse_version(raw_version: str) -> tuple[int, ...] | None:
+        value = raw_version.strip().lower().lstrip("v")
+        numeric_parts: list[int] = []
+        for part in value.split("."):
+            digits = ""
+            for char in part:
+                if char.isdigit():
+                    digits += char
+                else:
+                    break
+            if not digits:
+                break
+            numeric_parts.append(int(digits))
+        if not numeric_parts:
+            return None
+        return tuple(numeric_parts)
+
     def _request_json(
         self,
         path: str,
@@ -79,6 +108,27 @@ class OllamaBackend:
             return False
         return True
 
+    def server_version(self) -> str | None:
+        try:
+            response = self._request_json("/api/version", method="GET")
+        except Exception:
+            return None
+        raw_version = response.get("version")
+        if isinstance(raw_version, str) and raw_version.strip():
+            return raw_version.strip()
+        return None
+
+    def version_supported(self) -> tuple[bool | None, str | None]:
+        version = self.server_version()
+        if version is None:
+            return None, None
+        if not self._requires_ministral_3_runtime():
+            return True, version
+        parsed = self._parse_version(version)
+        if parsed is None:
+            return None, version
+        return parsed >= MIN_OLLAMA_VERSION_FOR_MINISTRAL_3, version
+
     def list_models(self) -> list[str]:
         response = self._request_json("/api/tags", method="GET")
         raw_models = response.get("models", [])
@@ -102,12 +152,24 @@ class OllamaBackend:
             return installed_lookup[self.model_name.lower()]
 
         requested = self.model_name.strip().lower()
-        if requested in {"ministral", "ministral-8b", "ministral-8b-instruct"}:
+        if requested in {
+            "ministral",
+            "ministral-3",
+            "ministral-3:latest",
+            "ministral-3:8b",
+            "ministral-3:8b-instruct",
+            "ministral-8b",
+            "ministral-8b-instruct",
+        }:
             for alias in MINISTRAL_MODEL_ALIASES:
                 resolved = installed_lookup.get(alias.lower())
                 if resolved is not None:
                     return resolved
 
+        for installed_name in installed:
+            lowered = installed_name.lower()
+            if "ministral-3" in lowered and "8b" in lowered:
+                return installed_name
         for installed_name in installed:
             lowered = installed_name.lower()
             if "ministral" in lowered and "8b" in lowered:
@@ -116,6 +178,14 @@ class OllamaBackend:
         return None
 
     def ensure_model_ready(self) -> str:
+        version_ok, version = self.version_supported()
+        if version_ok is False:
+            required_version = ".".join(str(part) for part in MIN_OLLAMA_VERSION_FOR_MINISTRAL_3)
+            raise RuntimeError(
+                "The open Ministral 3 local model requires a newer Ollama runtime.\n"
+                f"Detected Ollama: {version}\n"
+                f"Required Ollama: >= {required_version}"
+            )
         try:
             resolved = self.resolve_model_name()
         except RuntimeError:
@@ -137,6 +207,7 @@ class OllamaBackend:
         return resolved
 
     def healthcheck(self) -> dict[str, object]:
+        version_ok, version = self.version_supported()
         installed = self.list_models()
         resolved = self.resolve_model_name() if installed else None
         return {
@@ -148,6 +219,8 @@ class OllamaBackend:
             "ready": resolved is not None,
             "pull_command": None if resolved is not None else self._pull_hint(),
             "timeout_seconds": self.timeout_seconds,
+            "server_version": version,
+            "version_ok": version_ok,
         }
 
     def complete(self, *, system_prompt: str, user_prompt: str) -> str:

{iints_sdk_python35-1.1.0 → iints_sdk_python35-1.1.2}/src/iints/ai/cli.py

@@ -7,10 +7,13 @@ from typing import Any, Optional
 import typer
 from rich.console import Console
 from rich.panel import Panel
+from rich.table import Table
 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.")
@@ -34,6 +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
@@ -64,6 +118,7 @@ def _render_local_check(console: Console, status: dict[str, object]) -> None:
                     f"Endpoint: {status.get('base_url')}",
                     f"Requested model: {status.get('requested_model')}",
                     f"Resolved local model: {resolved_model}",
+                    f"Server version: {status.get('server_version') or 'unknown'}",
                     f"Timeout (s): {status.get('timeout_seconds')}",
                     f"Installed models: {installed_text}",
                     (
@@ -78,9 +133,81 @@ def _render_local_check(console: Console, status: dict[str, object]) -> None:
         )
     )
     if ready:
-        console.print("[green]Local Ollama backend is ready for Ministral inference.[/green]")
+        console.print("[green]Local Ollama backend is ready for open Ministral 3 inference.[/green]")
     else:
         console.print("[bold red]Local Ollama backend is reachable, but the requested model is missing.[/bold red]")
+    if status.get("version_ok") is False:
+        console.print("[bold red]Ollama is too old for the open Ministral 3 runtime.[/bold red]")
+
+
+@app.command("models")
+def models() -> None:
+    console = Console()
+    table = Table(title="IINTS AI Local Mistral Model Guide")
+    table.add_column("Model Tag", style="cyan", no_wrap=True)
+    table.add_column("Best For", style="green")
+    table.add_column("Approx Download")
+    table.add_column("System RAM")
+    table.add_column("GPU VRAM")
+    table.add_column("Notes", overflow="fold")
+
+    for profile in list_local_mistral_models():
+        vram = f"{profile.recommended_vram_gb}+ GB" if profile.recommended_vram_gb is not None else "CPU-only"
+        table.add_row(
+            profile.tag,
+            profile.fit,
+            f"{profile.approx_download_gb:.1f} GB",
+            f"{profile.recommended_system_ram_gb}+ GB",
+            vram,
+            profile.notes,
+        )
+
+    console.print(table)
+    console.print(
+        "[dim]Tip:[/dim] start with "
+        f"`{DEFAULT_MINISTRAL_MODEL}` unless you know your hardware can comfortably run a larger local model."
+    )
+
+
+@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(
@@ -135,8 +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",
@@ -148,13 +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,
@@ -169,8 +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",
@@ -182,13 +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,
@@ -203,8 +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",
@@ -216,13 +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,
@@ -237,8 +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",
@@ -250,13 +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,