clio-kit 2.5.23__tar.gz → 2.6.2__tar.gz

{clio_kit-2.5.23 → clio_kit-2.6.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: clio-kit
-Version: 2.5.23
+Version: 2.6.2
 Summary: CLIO Kit - MCP Servers, Clients, and Tools for AI Agents
 Project-URL: Homepage, https://github.com/iowarp/clio-kit
 Project-URL: Repository, https://github.com/iowarp/clio-kit
@@ -275,7 +275,7 @@ distinct `not_installed` semantic, while real Spack failures remain errors.
 | **`geo`** | 2.2.3 | Geospatial | Render GeoJSON vector layers with basemaps | `clio-kit mcp-server geo` |
 | **`geojson`** | 2.2.3 | Geospatial | Inspect, validate, and summarize GeoJSON | `clio-kit mcp-server geojson` |
 | **`hdf5`** | 2.2.3 | Data I/O | HPC-optimized scientific data with 27 tools, AI insights, caching, streaming | `clio-kit mcp-server hdf5` |
-| **`jarvis`** | 3.5.4 | Workflow | Durable pipeline, bounded package discovery, progress, artifact, and service-runtime management | `clio-kit mcp-server jarvis` |
+| **`jarvis`** | 3.6.0 | Workflow | Durable pipeline, bounded package discovery, progress, artifact, and service-runtime management | `clio-kit mcp-server jarvis` |
 | **`lmod`** | 2.2.3 | Environment | Environment module management | `clio-kit mcp-server lmod` |
 | **`ndp`** | 2.2.3 | Data Protocol | Search and discover datasets across CKAN instances | `clio-kit mcp-server ndp` |
 | **`node-hardware`** | 2.2.3 | System | System hardware information | `clio-kit mcp-server node-hardware` |

{clio_kit-2.5.23 → clio_kit-2.6.2}/README.md

@@ -249,7 +249,7 @@ distinct `not_installed` semantic, while real Spack failures remain errors.
 | **`geo`** | 2.2.3 | Geospatial | Render GeoJSON vector layers with basemaps | `clio-kit mcp-server geo` |
 | **`geojson`** | 2.2.3 | Geospatial | Inspect, validate, and summarize GeoJSON | `clio-kit mcp-server geojson` |
 | **`hdf5`** | 2.2.3 | Data I/O | HPC-optimized scientific data with 27 tools, AI insights, caching, streaming | `clio-kit mcp-server hdf5` |
-| **`jarvis`** | 3.5.4 | Workflow | Durable pipeline, bounded package discovery, progress, artifact, and service-runtime management | `clio-kit mcp-server jarvis` |
+| **`jarvis`** | 3.6.0 | Workflow | Durable pipeline, bounded package discovery, progress, artifact, and service-runtime management | `clio-kit mcp-server jarvis` |
 | **`lmod`** | 2.2.3 | Environment | Environment module management | `clio-kit mcp-server lmod` |
 | **`ndp`** | 2.2.3 | Data Protocol | Search and discover datasets across CKAN instances | `clio-kit mcp-server ndp` |
 | **`node-hardware`** | 2.2.3 | System | System hardware information | `clio-kit mcp-server node-hardware` |

{clio_kit-2.5.23 → clio_kit-2.6.2}/clio-kit-mcp-servers/adios/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.5.23",
+      "version": "2.6.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.5.23 → clio_kit-2.6.2}/clio-kit-mcp-servers/arxiv/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.5.23",
+      "version": "2.6.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.5.23 → clio_kit-2.6.2}/clio-kit-mcp-servers/chronolog/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.5.23",
+      "version": "2.6.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.5.23 → clio_kit-2.6.2}/clio-kit-mcp-servers/compression/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.5.23",
+      "version": "2.6.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.5.23 → clio_kit-2.6.2}/clio-kit-mcp-servers/darshan/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.5.23",
+      "version": "2.6.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.5.23 → clio_kit-2.6.2}/clio-kit-mcp-servers/geo/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.5.23",
+      "version": "2.6.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.5.23 → clio_kit-2.6.2}/clio-kit-mcp-servers/geojson/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.5.23",
+      "version": "2.6.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.5.23 → clio_kit-2.6.2}/clio-kit-mcp-servers/hdf5/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.5.23",
+      "version": "2.6.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.5.23 → clio_kit-2.6.2}/clio-kit-mcp-servers/jarvis/.claude-plugin/plugin.json

@@ -1,5 +1,5 @@
 {
   "name": "clio-jarvis",
   "description": "JARVIS-CD MCP with a compact user pipeline contract and explicit admin compatibility profiles",
-  "version": "3.5.4"
+  "version": "3.6.0"
 }

{clio_kit-2.5.23 → clio_kit-2.6.2}/clio-kit-mcp-servers/jarvis/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "jarvis-mcp"
-version = "3.5.4"
+version = "3.6.0"
 description = "JARVIS-CD MCP with a compact user pipeline contract and explicit admin compatibility profiles"
 readme = "README.md"
 requires-python = ">=3.11"
@@ -15,7 +15,7 @@ dependencies = [
   "fastmcp>=3.2.0",
   "fastapi",
   "python-dotenv>=1.2.2",
-  "jarvis-cd @ https://github.com/grc-iit/jarvis-cd/releases/download/v1.4.8/jarvis_cd-1.4.8-py3-none-any.whl#sha256=ebf5e5f375b921f20c79075d461926431a5a017ca8b45e598878a89b229b3935",
+  "jarvis-cd @ https://github.com/grc-iit/jarvis-cd/releases/download/v1.6.0/jarvis_cd-1.6.0-py3-none-any.whl#sha256=c4853138f3263715e806fcd794233d89f4aa58161e3c5fbab59e7f96d24f0e98",
   "starlette>=1.3.1",
   "authlib>=1.6.12",
   "cryptography>=48.0.1",

{clio_kit-2.5.23 → clio_kit-2.6.2}/clio-kit-mcp-servers/jarvis/scripts/live_ares_semantic_mcp_probe.py

@@ -18,13 +18,13 @@ from urllib.parse import urlsplit
 
 
 Json = dict[str, Any]
-EXPECTED_JARVIS_VERSION = "1.4.8"
+EXPECTED_JARVIS_VERSION = "1.6.0"
 EXPECTED_JARVIS_URL = (
-    "https://github.com/grc-iit/jarvis-cd/releases/download/v1.4.8/"
-    "jarvis_cd-1.4.8-py3-none-any.whl"
+    "https://github.com/grc-iit/jarvis-cd/releases/download/v1.6.0/"
+    "jarvis_cd-1.6.0-py3-none-any.whl"
 )
 EXPECTED_JARVIS_SHA256 = (
-    "ebf5e5f375b921f20c79075d461926431a5a017ca8b45e598878a89b229b3935"
+    "c4853138f3263715e806fcd794233d89f4aa58161e3c5fbab59e7f96d24f0e98"
 )
 
 

{clio_kit-2.5.23 → clio_kit-2.6.2}/clio-kit-mcp-servers/jarvis/server.json

@@ -3,7 +3,7 @@
   "name": "io.github.iowarp/jarvis-mcp",
   "title": "CLIO Jarvis",
   "description": "JARVIS-CD MCP with a compact user pipeline contract and explicit admin compatibility profiles",
-  "version": "3.5.4",
+  "version": "3.6.0",
   "repository": {
     "url": "https://github.com/iowarp/clio-kit",
     "source": "github"
@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.5.23",
+      "version": "2.6.2",
       "transport": {
         "type": "stdio"
       },
@@ -35,11 +35,11 @@
     },
     {
       "name": "jarvis_describe",
-      "description": "Describe JARVIS packages, one package, a pipeline, or one pipeline step. For a named application, first use target='package' with its unique short name or fully qualified package name. Use target='package_search' for bounded discovery, then describe the selected canonical name. target='packages' is an exhaustive legacy inventory with every package's settings and can be large; use it only when the complete installed catalog is explicitly required."
+      "description": "Describe JARVIS packages, one package, a pipeline, or one pipeline step. For a named application, first use target='package' with its unique short name or fully qualified package name. Use target='package_search' for bounded discovery, then describe the selected canonical name. A package description returns package-owned configuration metadata and, when supported, a versioned deployment contract covering execution profiles, runtime requirements, readiness, and configuration rules. Package settings include only semantic parameters explicitly marked agent-visible. A setting may include a versioned input_binding descriptor for a declared local input that must be staged; callers must not infer file semantics from setting names or prose. Installer, scheduler, and other implementation controls remain owned by their dedicated contracts. target='packages' is an exhaustive legacy inventory with every agent-visible package setting and can be large; use it only when the complete installed catalog is explicitly required."
     },
     {
       "name": "jarvis_add_step",
-      "description": "Add and configure a package-backed step in a JARVIS pipeline. First use jarvis_describe(target='package') for the selected package; config keys must use its canonical setting names exactly, except for aliases explicitly listed there. User-level step configuration is always validated and cannot be bypassed."
+      "description": "Add and configure a package-backed step in a JARVIS pipeline. First use jarvis_describe(target='package') for the selected package; config keys must use its canonical setting names exactly, except for aliases explicitly listed there. Explicit null is accepted only when that setting reports nullable=true; omit a setting to use its declared default. Only settings marked agent-visible by the package are accepted here. User-level step configuration is always validated and cannot be bypassed."
     },
     {
       "name": "jarvis_edit_step",
@@ -47,11 +47,11 @@
     },
     {
       "name": "jarvis_run",
-      "description": "Start a configured JARVIS pipeline and return its durable execution handle without waiting for workload completion. Optional execution intent selects local, cluster, or hostfile mode without exposing scheduler internals. Optional spack_specs are resolved into a filtered environment that JARVIS persists before direct or scheduler execution. Use jarvis_get_execution with the returned pipeline_id and execution_id to query lifecycle, progress, artifacts, and execution-owned service runtimes."
+      "description": "Start a configured JARVIS pipeline and return its durable execution handle without waiting for workload completion. Optional execution intent selects local, cluster, or hostfile mode without exposing scheduler internals. For each runtime resolved with Spack, copy spack_locate.output.load_spec unchanged into one element of jarvis_run.input.spack_specs; do not derive an executable path from the Spack prefix. JARVIS resolves those specs into a filtered environment and persists it before direct or scheduler execution. Use jarvis_get_execution with the returned pipeline_id and execution_id to query lifecycle, progress, artifacts, and execution-owned service runtimes."
     },
     {
       "name": "jarvis_get_execution",
-      "description": "Query one JARVIS execution handle, durable lifecycle record, and runtime metadata. Progress is included by default and can be omitted. Set include_service_runtimes=true to include execution-owned network services such as an interactive ParaView runtime; authenticated services expose only a non-secret bearer token SHA-256 fingerprint. Set artifacts to {} or filters to include one bounded artifact page; omit artifacts to avoid querying the artifact manifest."
+      "description": "Query one JARVIS execution handle, durable lifecycle record, and runtime metadata. Progress is included by default and can be omitted. Set include_service_runtimes=true to include execution-owned network services; authenticated services expose only a non-secret bearer token SHA-256 fingerprint. Set artifacts to {} or filters to include one bounded artifact page; omit artifacts to avoid querying the artifact manifest."
     }
   ],
   "resources": [

{clio_kit-2.5.23 → clio_kit-2.6.2}/clio-kit-mcp-servers/jarvis/src/jarvis_mcp/admin_server.py

@@ -6,8 +6,10 @@ import argparse
 import os
 
 from .server import (
+    add_jarvis_root_argument,
     add_spack_command_argument,
     apply_tool_profile,
+    configure_jarvis_root,
     configure_spack_command,
     mcp,
 )
@@ -21,8 +23,10 @@ def main() -> None:
     parser.add_argument("--transport", choices=["stdio", "http"], default=None)
     parser.add_argument("--host", default="0.0.0.0")
     parser.add_argument("--port", type=int, default=8000)
+    add_jarvis_root_argument(parser)
     add_spack_command_argument(parser)
     args = parser.parse_args()
+    configure_jarvis_root(args.jarvis_root)
     configure_spack_command(args.spack_command)
     transport = args.transport or os.getenv("MCP_TRANSPORT", "stdio")
     if transport == "http":

{clio_kit-2.5.23 → clio_kit-2.6.2}/clio-kit-mcp-servers/jarvis/src/jarvis_mcp/capabilities/__init__.py

@@ -3,12 +3,12 @@ Jarvis MCP Server
 
 Jarvis-CD MCP - Pipeline Management for High-Performance Computing with comprehensive workflow operations
 
-Version: 3.5.4
+Version: 3.6.0
 Author: IoWarp Team - Gnosis Research Center
 License: BSD-3-Clause
 """
 
-__version__ = "3.5.4"
+__version__ = "3.6.0"
 __author__ = "IoWarp Team - Gnosis Research Center"
 __email__ = "grc@illinoistech.edu"
 __license__ = "BSD-3-Clause"

{clio_kit-2.5.23 → clio_kit-2.6.2}/clio-kit-mcp-servers/jarvis/src/jarvis_mcp/capabilities/jarvis_handler.py

@@ -482,6 +482,7 @@ async def append_pkg(
     pkg_type: str,
     pkg_id: Optional[str] = None,
     do_configure: bool = True,
+    agent_visible_only: bool = False,
     **kwargs: Any,
 ) -> dict:
     try:
@@ -489,6 +490,8 @@ async def append_pkg(
         config_flag = do_configure
         if "do_configure" in raw_kwargs:
             config_flag = raw_kwargs.pop("do_configure")
+        if agent_visible_only:
+            _reject_non_agent_visible_package_settings(pkg_type, raw_kwargs)
 
         with _protocol_stdout_to_stderr():
             pipeline = _load_pipeline(pipeline_id)
@@ -506,13 +509,19 @@ async def append_pkg(
                 pipeline.append(pkg_type, package_alias=pkg_id, config_args=config_args)
                 try:
                     expected = _normalize_package_config_request(
-                        pipeline, resolved_pkg_id, raw_kwargs
+                        pipeline,
+                        resolved_pkg_id,
+                        raw_kwargs,
+                        agent_visible_only=agent_visible_only,
                     )
                     persisted_config = _package_config(
                         _get_package(pipeline, resolved_pkg_id)
                     )
                     _require_persisted_package_config(
-                        resolved_pkg_id, expected, persisted_config
+                        resolved_pkg_id,
+                        expected,
+                        persisted_config,
+                        pipeline=pipeline,
                     )
                     if config_flag:
                         pipeline.configure_package(resolved_pkg_id, config_args)
@@ -521,7 +530,10 @@ async def append_pkg(
                             _get_package(persisted, resolved_pkg_id)
                         )
                         _require_persisted_package_config(
-                            resolved_pkg_id, expected, persisted_config
+                            resolved_pkg_id,
+                            expected,
+                            persisted_config,
+                            pipeline=persisted,
                         )
                 except BaseException as exc:
                     try:
@@ -581,20 +593,43 @@ async def update_pipeline(pipeline_id: str) -> dict:
 
 
 @_locked_pipeline_operation
-async def configure_pkg(pipeline_id: str, pkg_id: str, **kwargs: Any) -> dict:
+async def configure_pkg(
+    pipeline_id: str,
+    pkg_id: str,
+    *,
+    agent_visible_only: bool = False,
+    **kwargs: Any,
+) -> dict:
     try:
         with _protocol_stdout_to_stderr():
             pipeline = _load_pipeline(pipeline_id)
             if _is_legacy_pipeline(pipeline):
+                if agent_visible_only:
+                    _normalize_package_config_request(
+                        pipeline,
+                        pkg_id,
+                        kwargs,
+                        agent_visible_only=True,
+                    )
                 pipeline.configure(pkg_id, **kwargs)
                 _save_pipeline(pipeline)
                 persisted_config = _package_config(_get_package(pipeline, pkg_id))
             else:
-                expected = _normalize_package_config_request(pipeline, pkg_id, kwargs)
+                expected = _normalize_package_config_request(
+                    pipeline,
+                    pkg_id,
+                    kwargs,
+                    agent_visible_only=agent_visible_only,
+                )
                 pipeline.configure_package(pkg_id, _kwargs_to_config_args(kwargs))
                 persisted = _load_pipeline(pipeline_id)
                 persisted_config = _package_config(_get_package(persisted, pkg_id))
-                _require_persisted_package_config(pkg_id, expected, persisted_config)
+                _require_persisted_package_config(
+                    pkg_id,
+                    expected,
+                    persisted_config,
+                    pipeline=persisted,
+                )
         return {
             "pipeline_id": pipeline_id,
             "configured": pkg_id,
@@ -3242,7 +3277,11 @@ def _package_config(pkg: Any) -> Any:
 
 
 def _normalize_package_config_request(
-    pipeline: Any, pkg_id: str, kwargs: dict[str, Any]
+    pipeline: Any,
+    pkg_id: str,
+    kwargs: dict[str, Any],
+    *,
+    agent_visible_only: bool = False,
 ) -> dict[str, Any]:
     """Validate and normalize structured settings with the package-owned parser."""
     pkg = _get_package(pipeline, pkg_id)
@@ -3261,6 +3300,7 @@ def _normalize_package_config_request(
     if not isinstance(menu, list):
         raise RuntimeError(f"Package '{pkg_id}' returned an invalid configuration menu")
     canonical_names: dict[str, str] = {}
+    nullable_names: set[str] = set()
     for spec in menu:
         if not isinstance(spec, dict):
             raise RuntimeError(
@@ -3271,7 +3311,11 @@ def _normalize_package_config_request(
             raise RuntimeError(
                 f"Package '{pkg_id}' returned an invalid configuration option name"
             )
+        if agent_visible_only and spec.get("agent_visible", True) is False:
+            continue
         canonical_names[name] = name
+        if "default" in spec and spec["default"] is None:
+            nullable_names.add(name)
         aliases = spec.get("aliases", [])
         if not isinstance(aliases, list) or not all(
             isinstance(alias, str) and alias for alias in aliases
@@ -3286,11 +3330,15 @@ def _normalize_package_config_request(
         raise ValueError(
             f"Package '{pkg_id}' does not support settings: {', '.join(unknown)}"
         )
-    null_names = sorted(name for name, value in kwargs.items() if value is None)
+    null_names = sorted(
+        name
+        for name, value in kwargs.items()
+        if value is None and canonical_names[name] not in nullable_names
+    )
     if null_names:
         raise ValueError(
-            "Package settings cannot be null; provide a concrete value for: "
-            + ", ".join(null_names)
+            "Package settings cannot be null unless their package description reports "
+            "nullable=true; provide a concrete value for: " + ", ".join(null_names)
         )
 
     parser = cast(Any, get_argparse())
@@ -3314,10 +3362,65 @@ def _normalize_package_config_request(
     return normalized
 
 
+def _reject_non_agent_visible_package_settings(
+    package_name: str,
+    kwargs: dict[str, Any],
+) -> None:
+    """Reject implementation settings before a user append can mutate a pipeline."""
+
+    if not kwargs:
+        return
+    try:
+        from jarvis_cd.core.pkg import Pkg  # type: ignore[import-untyped]
+
+        instance = Pkg.load_standalone(package_name)
+        menu = instance.configure_menu()
+    except Exception as exc:
+        raise RuntimeError(
+            f"Package '{package_name}' does not expose agent configuration metadata"
+        ) from exc
+    if not isinstance(menu, list):
+        raise RuntimeError(
+            f"Package '{package_name}' returned an invalid configuration menu"
+        )
+    hidden_names: set[str] = set()
+    for spec in menu:
+        if not isinstance(spec, dict):
+            raise RuntimeError(
+                f"Package '{package_name}' returned an invalid configuration option"
+            )
+        if spec.get("agent_visible", True) is not False:
+            continue
+        name = spec.get("name")
+        if not isinstance(name, str) or not name:
+            raise RuntimeError(
+                f"Package '{package_name}' returned an invalid configuration option name"
+            )
+        hidden_names.add(name)
+        aliases = spec.get("aliases", [])
+        if not isinstance(aliases, list) or not all(
+            isinstance(alias, str) and alias for alias in aliases
+        ):
+            raise RuntimeError(
+                f"Package '{package_name}' returned invalid aliases for '{name}'"
+            )
+        hidden_names.update(aliases)
+    requested = sorted(set(kwargs) & hidden_names)
+    if requested:
+        raise ValueError(
+            "Package settings are implementation-owned and not agent-visible: "
+            + ", ".join(requested)
+        )
+
+
 def _require_persisted_package_config(
-    pkg_id: str, expected: dict[str, Any], persisted: Any
+    pkg_id: str,
+    expected: dict[str, Any],
+    persisted: Any,
+    *,
+    pipeline: Any | None = None,
 ) -> None:
-    """Fail unless every normalized setting survived a durable pipeline reload."""
+    """Require exact persistence or a verified package-owned input rewrite."""
     if not isinstance(persisted, dict):
         raise RuntimeError(f"Package '{pkg_id}' persisted an invalid configuration")
     mismatches = [
@@ -3325,6 +3428,31 @@ def _require_persisted_package_config(
         for name, value in expected.items()
         if name not in persisted or _jsonable(persisted[name]) != _jsonable(value)
     ]
+    if mismatches and pipeline is not None:
+        package = _get_package(pipeline, pkg_id)
+        loader = getattr(pipeline, "_load_package_instance", None)
+        instance = (
+            loader(package, getattr(pipeline, "env", {}))
+            if package is not None and callable(loader)
+            else package
+        )
+        verifier = getattr(
+            instance,
+            "configuration_input_materialization_matches",
+            None,
+        )
+        if callable(verifier):
+            verified: set[str] = set()
+            for name in mismatches:
+                if name not in persisted:
+                    continue
+                try:
+                    matches = verifier(name, expected[name], persisted[name])
+                except Exception:
+                    matches = False
+                if matches is True:
+                    verified.add(name)
+            mismatches = [name for name in mismatches if name not in verified]
     if mismatches:
         raise ValueError(
             f"Package '{pkg_id}' did not persist settings: {', '.join(mismatches)}"