clio-kit 2.3.1__tar.gz → 2.3.2__tar.gz

{clio_kit-2.3.1 → clio_kit-2.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: clio-kit
-Version: 2.3.1
+Version: 2.3.2
 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
@@ -107,7 +107,7 @@ CLIO Kit is part of the IoWarp platform's comprehensive tooling ecosystem for AI
 
 ```bash
 # Install the released CLI into its own persistent tool environment
-uv tool install 'clio-kit==2.3.0'
+uv tool install 'clio-kit==2.3.2'
 # If uv reports that its executable directory is not on PATH:
 uv tool update-shell
 
@@ -129,7 +129,7 @@ clio-kit prompt code-coverage-prompt # Use a prompt
 ```
 
 `uv tool install` keeps CLIO Kit in a persistent, isolated tool environment.
-Use `uvx --from 'clio-kit==2.3.0' clio-kit ...` only for a temporary, one-shot
+Use `uvx --from 'clio-kit==2.3.2' clio-kit ...` only for a temporary, one-shot
 invocation.
 
 Released `clio-kit` wheels execute each embedded MCP server from that server's
@@ -250,9 +250,14 @@ See [Claude Desktop MCP docs](https://modelcontextprotocol.io/quickstart/user) f
 
 The version below is each MCP server's agent-facing contract version, not the
 containing `clio-kit` wheel version. JARVIS and SLURM are 3.0 because their
-contracts were redesigned for agent use. Spack starts at 2.0, while the other
+contracts were redesigned for agent use. Spack is at 2.0, while the other
 contracts retain their existing 2.x identities until a focused upgrade.
 
+The Spack install contract makes concretization explicit: `reuse=true` passes
+`spack install --reuse`, while `reuse=false` passes `spack install --fresh`.
+Agents should discover first, install only when needed, then pass the exact
+`spack_locate` result to JARVIS for runtime loading.
+
 <div align="center">
 
 | 📦 **Package** | 📌 **Ver** | 🔧 **System** | 📋 **Description** | ⚡ **Install Command** |
@@ -277,7 +282,7 @@ contracts retain their existing 2.x identities until a focused upgrade.
 | **`sac`** | 2.2.3 | Seismology | Analyze SAC waveforms and archives | `clio-kit mcp-server sac` |
 | **`seismic`** | 2.2.3 | Seismology | Analyze earthquake catalogs and sequences | `clio-kit mcp-server seismic` |
 | **`slurm`** | 3.0.0 | HPC | Job submission and management | `clio-kit mcp-server slurm` |
-| **`spack`** | 2.0.0 | Package Management | Structured package discovery, installation, and location | `clio-kit mcp-server spack` |
+| **`spack`** | 2.0.1 | Package Management | Structured package discovery, installation, and location | `clio-kit mcp-server spack` |
 | **`terrain`** | 2.2.3 | Geospatial | Analyze DEMs and terrain point clouds | `clio-kit mcp-server terrain` |
 
 </div>
@@ -405,7 +410,7 @@ pip install uv
 Then install CLIO Kit persistently and expose uv's tool directory:
 
 ```bash
-uv tool install 'clio-kit==2.3.0'
+uv tool install 'clio-kit==2.3.2'
 uv tool update-shell
 ```
 

{clio_kit-2.3.1 → clio_kit-2.3.2}/README.md

@@ -81,7 +81,7 @@ CLIO Kit is part of the IoWarp platform's comprehensive tooling ecosystem for AI
 
 ```bash
 # Install the released CLI into its own persistent tool environment
-uv tool install 'clio-kit==2.3.0'
+uv tool install 'clio-kit==2.3.2'
 # If uv reports that its executable directory is not on PATH:
 uv tool update-shell
 
@@ -103,7 +103,7 @@ clio-kit prompt code-coverage-prompt # Use a prompt
 ```
 
 `uv tool install` keeps CLIO Kit in a persistent, isolated tool environment.
-Use `uvx --from 'clio-kit==2.3.0' clio-kit ...` only for a temporary, one-shot
+Use `uvx --from 'clio-kit==2.3.2' clio-kit ...` only for a temporary, one-shot
 invocation.
 
 Released `clio-kit` wheels execute each embedded MCP server from that server's
@@ -224,9 +224,14 @@ See [Claude Desktop MCP docs](https://modelcontextprotocol.io/quickstart/user) f
 
 The version below is each MCP server's agent-facing contract version, not the
 containing `clio-kit` wheel version. JARVIS and SLURM are 3.0 because their
-contracts were redesigned for agent use. Spack starts at 2.0, while the other
+contracts were redesigned for agent use. Spack is at 2.0, while the other
 contracts retain their existing 2.x identities until a focused upgrade.
 
+The Spack install contract makes concretization explicit: `reuse=true` passes
+`spack install --reuse`, while `reuse=false` passes `spack install --fresh`.
+Agents should discover first, install only when needed, then pass the exact
+`spack_locate` result to JARVIS for runtime loading.
+
 <div align="center">
 
 | 📦 **Package** | 📌 **Ver** | 🔧 **System** | 📋 **Description** | ⚡ **Install Command** |
@@ -251,7 +256,7 @@ contracts retain their existing 2.x identities until a focused upgrade.
 | **`sac`** | 2.2.3 | Seismology | Analyze SAC waveforms and archives | `clio-kit mcp-server sac` |
 | **`seismic`** | 2.2.3 | Seismology | Analyze earthquake catalogs and sequences | `clio-kit mcp-server seismic` |
 | **`slurm`** | 3.0.0 | HPC | Job submission and management | `clio-kit mcp-server slurm` |
-| **`spack`** | 2.0.0 | Package Management | Structured package discovery, installation, and location | `clio-kit mcp-server spack` |
+| **`spack`** | 2.0.1 | Package Management | Structured package discovery, installation, and location | `clio-kit mcp-server spack` |
 | **`terrain`** | 2.2.3 | Geospatial | Analyze DEMs and terrain point clouds | `clio-kit mcp-server terrain` |
 
 </div>
@@ -379,7 +384,7 @@ pip install uv
 Then install CLIO Kit persistently and expose uv's tool directory:
 
 ```bash
-uv tool install 'clio-kit==2.3.0'
+uv tool install 'clio-kit==2.3.2'
 uv tool update-shell
 ```
 

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/adios/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.3.1",
+      "version": "2.3.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/arxiv/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.3.1",
+      "version": "2.3.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/chronolog/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.3.1",
+      "version": "2.3.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/compression/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.3.1",
+      "version": "2.3.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/darshan/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.3.1",
+      "version": "2.3.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/geo/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.3.1",
+      "version": "2.3.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/geojson/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.3.1",
+      "version": "2.3.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/hdf5/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.3.1",
+      "version": "2.3.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/jarvis/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.3.1",
+      "version": "2.3.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/lmod/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.3.1",
+      "version": "2.3.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/ndp/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.3.1",
+      "version": "2.3.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/node-hardware/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.3.1",
+      "version": "2.3.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/pandas/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.3.1",
+      "version": "2.3.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/parallel-sort/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.3.1",
+      "version": "2.3.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/paraview/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.3.1",
+      "version": "2.3.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/parquet/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.3.1",
+      "version": "2.3.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/plot/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.3.1",
+      "version": "2.3.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/sac/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.3.1",
+      "version": "2.3.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/seismic/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.3.1",
+      "version": "2.3.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/slurm/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.3.1",
+      "version": "2.3.2",
       "transport": {
         "type": "stdio"
       },

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/spack/.claude-plugin/plugin.json

@@ -1,5 +1,5 @@
 {
   "name": "clio-spack",
   "description": "Structured Spack discovery and installation tools for scientific agents",
-  "version": "2.0.0"
+  "version": "2.0.1"
 }

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/spack/README.md

@@ -17,10 +17,24 @@ persists it in the pipeline, and reloads it inside direct or scheduled execution
 value to `jarvis_run` so a later install cannot make the runtime selection
 ambiguous.
 
+## Install concretization
+
+`spack_install` always selects the Spack concretization policy explicitly:
+
+- `spack_install(spec, reuse=true)` runs `spack install --reuse <spec>` and may
+  reuse compatible installed packages or buildcaches while concretizing.
+- `spack_install(spec, reuse=false)` runs `spack install --fresh <spec>` and
+  excludes installed packages and buildcaches while concretizing.
+
+Fresh concretization does not mean "blindly reinstall an existing concrete
+hash." Agents should first call `spack_find`, install only when the required
+software is absent, then call `spack_locate` and pass its canonical `load_spec`
+to `jarvis_run`.
+
 Run the default server with:
 
 ```bash
-uv tool install 'clio-kit==2.3.0'
+uv tool install 'clio-kit==2.3.2'
 clio-kit mcp-server spack
 ```
 

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/spack/server.json

@@ -3,7 +3,7 @@
   "name": "io.github.iowarp/spack-mcp",
   "title": "CLIO Spack",
   "description": "Structured Spack discovery and installation tools for scientific agents",
-  "version": "2.0.0",
+  "version": "2.0.1",
   "repository": {
     "url": "https://github.com/iowarp/clio-kit",
     "source": "github"
@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.3.1",
+      "version": "2.3.2",
       "transport": {
         "type": "stdio"
       },
@@ -39,7 +39,7 @@
     },
     {
       "name": "spack_install",
-      "description": "Install one Spack spec and verify that a matching install is observable."
+      "description": "Install one Spack spec with explicit reusable or fresh concretization and verify that a matching install is observable."
     }
   ],
   "resources": [

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/spack/src/spack_mcp/backend.py

@@ -325,7 +325,7 @@ def install_spec(
     reuse: bool = True,
     timeout_seconds: int = 14_400,
 ) -> SpackInstallResult:
-    """Install one Spack spec without invoking a shell."""
+    """Install one Spack spec with explicit reuse semantics and no shell."""
     normalized = _validated_spec(spec)
     if timeout_seconds < 1 or timeout_seconds > _MAX_INSTALL_TIMEOUT_SECONDS:
         raise SpackBackendError(
@@ -333,10 +333,7 @@ def install_spec(
             f"timeout_seconds must be between 1 and {_MAX_INSTALL_TIMEOUT_SECONDS}",
             operation="install",
         )
-    args = ["install"]
-    if reuse:
-        args.append("--reuse")
-    args.append(normalized)
+    args = ["install", "--reuse" if reuse else "--fresh", normalized]
     result = _run_spack(args, operation="install", timeout_seconds=timeout_seconds)
     found = find_installed(normalized)
     if not found.packages:

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/spack/src/spack_mcp/server.py

@@ -7,11 +7,12 @@ import asyncio
 import os
 from collections.abc import Callable
 from pathlib import Path
-from typing import TypeVar
+from typing import Annotated, TypeVar
 
 from fastmcp import FastMCP
 from fastmcp.exceptions import ToolError
 from fastmcp.prompts import Message
+from pydantic import Field
 
 from spack_mcp.backend import (
     SpackBackendError,
@@ -75,7 +76,10 @@ async def spack_locate_tool(spec: str) -> SpackLocateResult:
 
 @mcp.tool(
     name="spack_install",
-    description="Install one Spack spec and verify that a matching install is observable.",
+    description=(
+        "Install one Spack spec with explicit reusable or fresh concretization and "
+        "verify that a matching install is observable."
+    ),
     annotations={
         "readOnlyHint": False,
         "destructiveHint": False,
@@ -86,10 +90,19 @@ async def spack_locate_tool(spec: str) -> SpackLocateResult:
 )
 async def spack_install_tool(
     spec: str,
-    reuse: bool = True,
+    reuse: Annotated[
+        bool,
+        Field(
+            description=(
+                "Choose Spack concretization explicitly: true passes --reuse and may "
+                "reuse compatible installed packages or buildcaches; false passes "
+                "--fresh and excludes them while concretizing."
+            )
+        ),
+    ] = True,
     timeout_seconds: int = 14_400,
 ) -> SpackInstallResult:
-    """Install one spec with bounded output, timeout, and child cleanup."""
+    """Install one spec with explicit concretization, timeout, and child cleanup."""
     return await _call_backend(
         install_spec,
         spec,

{clio_kit-2.3.1 → clio_kit-2.3.2}/clio-kit-mcp-servers/terrain/server.json

@@ -12,7 +12,7 @@
     {
       "registryType": "pypi",
       "identifier": "clio-kit",
-      "version": "2.3.1",
+      "version": "2.3.2",
       "transport": {
         "type": "stdio"
       },