Metadata-Version: 2.4
Name: clio-kit
Version: 2.11.0
Summary: CLIO Kit - A meta-marketplace for scientific MCP servers, skills, plugins, agents, and community contributions
Project-URL: Homepage, https://github.com/iowarp/clio-kit
Project-URL: Repository, https://github.com/iowarp/clio-kit
Project-URL: Issues, https://github.com/iowarp/clio-kit/issues
Author-email: IoWarp Team - Gnosis Research Center <grc@illinoistech.edu>
License: BSD-3-Clause
License-File: LICENSE
Keywords: ai-agents,hdf5,hpc,llm-tools,mcp,model-context-protocol,parquet,research-tools,scientific-computing,slurm
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=3.10
Requires-Dist: click>=8.3.3
Requires-Dist: pyyaml>=6.0.2
Requires-Dist: tomli-w>=1.2
Requires-Dist: tomli>=2; python_version < '3.11'
Provides-Extra: verification
Requires-Dist: jsonschema>=4; extra == 'verification'
Requires-Dist: mcp<3,>=2.2; extra == 'verification'
Description-Content-Type: text/markdown

# CLIO Kit

<!-- mcp-name: io.github.iowarp/adios-mcp -->
<!-- mcp-name: io.github.iowarp/arxiv-mcp -->
<!-- mcp-name: io.github.iowarp/chronolog-mcp -->
<!-- mcp-name: io.github.iowarp/compression-mcp -->
<!-- mcp-name: io.github.iowarp/darshan-mcp -->
<!-- mcp-name: io.github.iowarp/geo-mcp -->
<!-- mcp-name: io.github.iowarp/hdf5-mcp -->
<!-- mcp-name: io.github.iowarp/jarvis-mcp -->
<!-- mcp-name: io.github.iowarp/lmod-mcp -->
<!-- mcp-name: io.github.iowarp/ndp-mcp -->
<!-- mcp-name: io.github.iowarp/node-hardware-mcp -->
<!-- mcp-name: io.github.iowarp/pandas-mcp -->
<!-- mcp-name: io.github.iowarp/parallel-sort-mcp -->
<!-- mcp-name: io.github.iowarp/paraview-mcp -->
<!-- mcp-name: io.github.iowarp/parquet-mcp -->
<!-- mcp-name: io.github.iowarp/plot-mcp -->
<!-- mcp-name: io.github.iowarp/seismology-mcp -->
<!-- mcp-name: io.github.iowarp/scientific-catalog-mcp -->
<!-- mcp-name: io.github.iowarp/slurm-mcp -->
<!-- mcp-name: io.github.iowarp/spack-mcp -->
<!-- mcp-name: io.github.iowarp/terrain-mcp -->
<!-- mcp-name: io.github.iowarp/web-mcp -->

[![License: BSD-3-Clause](https://img.shields.io/badge/License-BSD--3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
[![PyPI version](https://img.shields.io/pypi/v/clio-kit.svg)](https://pypi.org/project/clio-kit/)
[![Python](https://img.shields.io/badge/Python-3.10%2B-blue)](https://www.python.org/)
[![FastMCP](https://img.shields.io/badge/FastMCP-4.0-purple)](https://github.com/jlowin/fastmcp)
[![CI](https://github.com/iowarp/clio-kit/actions/workflows/quality_control.yml/badge.svg)](https://github.com/iowarp/clio-kit/actions/workflows/quality_control.yml)
[![Coverage](https://codecov.io/gh/iowarp/clio-kit/branch/main/graph/badge.svg)](https://codecov.io/gh/iowarp/clio-kit)

[![MCP Servers](https://img.shields.io/badge/MCP%20Servers-22-green)](https://github.com/iowarp/clio-kit/tree/main/mcp-servers)
[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
[![Type Checked](https://img.shields.io/badge/mypy-type%20checked-blue)](http://mypy-lang.org/)
[![Package Manager](https://img.shields.io/badge/uv-package%20manager-orange)](https://github.com/astral-sh/uv)
[![Security Audit](https://img.shields.io/badge/pip--audit-security%20scanned-green)](https://github.com/pypa/pip-audit)

**CLIO Kit** is the IoWarp meta-marketplace for scientific computing. It brings together MCP servers, workflow skills, plugins, agent definitions, and community contributions—including plugins from external marketplaces—and enables AI agents to interact with HPC resources, scientific data formats, and research datasets.

**Choose individual MCPs, skills, agents and hooks—or a plugin that bundles what your workflow needs.** A plugin can include any of these components; it does not need all four.

[**Website**](https://toolkit.iowarp.ai/) | [**IOWarp**](https://iowarp.ai)

[**Documentation**](docs/README.md) · **For agents:** [read here](AGENTS.md).

Chat with us on [**Zulip**](https://iowarp.zulipchat.com/#narrow/channel/543872-Agent-Toolkit) or [**join us**](https://iowarp.zulipchat.com/join/e4wh24du356e4y2iw6x6jeay/)

Developed by <img src="https://grc.iit.edu/img/logo.png" alt="GRC Logo" width="18" height="18"> [**Gnosis Research Center**](https://grc.iit.edu/)

---

## ❌ Without CLIO Kit

Working with scientific data and HPC resources requires manual scripting and tool-specific knowledge:

- ❌ Write custom scripts for every HDF5/Parquet file exploration
- ❌ Manually craft Slurm job submission scripts
- ❌ Switch between multiple tools for data analysis
- ❌ No AI assistance for scientific workflows
- ❌ Repetitive coding for common research tasks

## ✅ With CLIO Kit

Install workflow bundles, use skills to guide your agent, and discover community tools:

- ✅ **"Analyze the temperature dataset in this HDF5 file"** - HDF5 MCP does it
- ✅ **"Submit this simulation to Slurm with 32 cores"** - Slurm MCP handles it
- ✅ **"Find papers on neural networks from ArXiv"** - ArXiv MCP searches
- ✅ **"Plot the results from this CSV file"** - Plot MCP visualizes
- ✅ **"Optimize memory usage for this pandas DataFrame"** - Pandas MCP optimizes
- ✅ **Workflow guidance** - Skills explain tool sequences; optional agents help plan and review results
- ✅ **Community contributions** - Discover external plugins and marketplace collections

**MCP servers · Skills · Plugins · Agents · Hooks · Community marketplaces**

CLIO Kit is part of the IoWarp platform's tooling ecosystem for AI agents. Its meta-marketplace brings tools and reusable workflows together for scientific computing—from exploring HDF5 datasets and managing Slurm jobs to analyzing results and finding research papers. Built by researchers, for researchers, at Illinois Institute of Technology with NSF support.

> **Part of IoWarp Platform:** CLIO Kit is the platform's meta-marketplace and tooling layer, bringing together MCP servers, skills, workflow plugins, agent definitions, and community marketplace collections.

> **One launcher for MCP servers. Individual components or workflow bundles.** BSD-3-Clause licensed, with automated checks and real installation, MCP, and HPC workflow tests. See the [validation guide](docs/marketplace.md#scientific-acceptance-boundaries) for tested coverage and environment requirements.

## 🚀 Quick Installation

```bash
git clone https://github.com/iowarp/clio-kit.git
cd clio-kit
```

**Recommended:** Ask your agent:

```text
Read setup.md and set up CLIO Kit for me.
```

**Manual setup:** Install this checkout's launcher, then choose an option below.
For the no-clone release route (2.11.0 or newer), see [selective installation](docs/installation.md).

```bash
uv tool install --force --reinstall --editable ".[verification]"
```

### Claude Code

Install a workflow plugin (bundle) with its MCP servers and skills:

```bash
claude plugin marketplace add "$PWD"
claude plugin install clio-hpc@clio-kit
claude mcp list
```

Restart Claude Code after installation and confirm the servers connect.
First launches download dependencies; see [startup recovery](setup.md#update-and-troubleshoot)
if a server exceeds the client's connection timeout.

Or install an individual MCP or a skill collection:

```bash
claude plugin install clio-hdf5@clio-kit                  # HDF5 server
claude plugin install clio-scientific-io-skills@clio-kit  # Scientific I/O skills
```

Claude Code uses `plugin install` for component packages too. CLIO Kit lists
those separately from workflow plugins; see [components and plugins](docs/plugins.md).

### Codex and Other Agents

Install a workflow's skills and MCP configuration together:

```bash
clio-kit plugin install clio-scientific-io --client codex --project /path/to/project
```

Also supports `opencode`, `cursor`, `antigravity`, `vscode` and `claude-code`.
This sets up project components; native agents and hooks need client-specific
adapters. See [client installation and limits](docs/intro.md#install-a-workflow-for-your-client).

Install a bundle or one skill into your project:

```bash
# Bundle
clio-kit skill install --bundle clio-scientific-io --target /path/to/project/.agents/skills
# Individual skill
clio-kit skill install dataset-explore --target /path/to/project/.agents/skills
```

Configure the required MCP servers using [setup.md](setup.md). Use your agent’s supported skill directory.

### Install Skills with npm

Requires Node.js 22.20.0+. From your working project:

```bash
# All skills
npx skills@1.5.25 add /path/to/clio-kit --skill '*' --agent codex --copy
# Individual skill
npx skills@1.5.25 add /path/to/clio-kit --skill dataset-explore --agent codex --copy
```

Replace `codex` with `claude-code` or `antigravity`. MCP servers require separate configuration.

Choose either the Python or npm installer for each skill. See the [skills CLI guide](docs/marketplace.md#optional-skills-cli) for selecting skills, updates and removal.

### One Command for Any Server

```bash
# From the CLIO Kit checkout, install the CLI in a persistent tool environment
uv tool install --force --reinstall --editable .
# If uv's executable directory is not on PATH:
uv tool update-shell

# List all 22 available MCP servers
clio-kit mcp-servers

# Run an individual server
clio-kit mcp-server hdf5
clio-kit mcp-server pandas
clio-kit mcp-server slurm
```

Once 2.11.0 is published, install it with `uv tool install 'clio-kit>=2.11.0'`
(2.11.0 or newer; earlier releases lack the `skill`, `plugin` and `doctor` commands).
`uv tool install` creates a persistent, isolated environment; use
`uvx --from 'clio-kit>=2.11.0' clio-kit ...` for a temporary, one-shot invocation.

The release separates the small launcher from component downloads: one MCP
fetches only that server, one skill fetches only its files, and a workflow selects
its components. Server dependencies stay isolated and locked. See
[selective installation](docs/installation.md) for release, checkout and native plugin routes.
The `--branch` option is for development, not an immutable release installation.

The wheel also includes machine-readable tool contracts for JARVIS, Slurm, Spack
and Scientific Catalog, with SHA-256 digests for downstream verification:

```bash
clio-kit mcp-contracts
clio-kit mcp-contract clio-kit-jarvis-user-v3.7.2
clio-kit mcp-contract clio-kit-slurm-user-v3
clio-kit mcp-contract clio-kit-spack-user-v2.3
clio-kit mcp-contract clio-kit-scientific-catalog-user-v1.1
```

### Workflow Bundles

These are broad workflow plugins. Each combines its MCP servers and skills.

| Bundle | Purpose | MCP servers |
|---|---|---|
| `clio-hpc` | Build software and run cluster jobs | spack, lmod, jarvis, slurm, node-hardware |
| `clio-performance` | Diagnose slow jobs and inspect logs | darshan, chronolog, parallel-sort |
| `clio-scientific-io` | Explore scientific data files | hdf5, adios, parquet, compression |
| `clio-analysis` | Analyze results and create figures | pandas, plot, paraview |
| `clio-geoscience` | Work with maps, terrain and waveforms | geo, terrain, seismology |
| `clio-research` | Find papers and datasets | arxiv, ndp, scientific-catalog, web |

Some servers require additional system software. See [setup and prerequisites](setup.md#native-backend-setup).
See [plugin composition](docs/plugins.md) for primary bundles and task plugins that combine components across them.

For a complete dataset-report workflow—HDF5, Pandas, Plot, a skill, evidence review and a verification hook:

```bash
claude plugin install clio-dataset-report@clio-kit
```

See [dataset reports](docs/plugins.md#scientific-dataset-report) for inputs and verification limits.

### Skills and Agents

Skills provide workflow instructions and guidance for interpreting results. Claude Code users can install skills or agent definitions separately:

```bash
claude plugin install clio-skills@clio-kit
claude plugin install clio-agents@clio-kit
```

The shared installer supports Codex, Claude Code, OpenCode, Cursor, Antigravity and VS Code. Codex, Claude Code and OpenCode also have adapters for the scientific agents and Dataset Report hooks. See [client support](docs/clients.md#component-support).

Add the optional Clio Coder coding and research skills, including Materio procedures:

```bash
clio-kit skill install --bundle clio-coder --target .agents/skills
# Or through Claude Code:
claude plugin install clio-coder-skills@clio-kit
```

Individual skills also work: `clio-kit skill install clio-kit-scientific-debugging --target .agents/skills`.
Adapted Clio Coder skills use the `clio-kit-` prefix to distinguish them from upstream originals.
See [Clio Coder integration](docs/marketplace.md#clio-coder-integration) for upstream packages and native plugin support.

### Contribute Servers, Skills or Plugins

Contribute a package folder under `plugins/`, `skills/`, `agents/` or `hooks/`;
website builds and CI update the catalogues automatically. See the [folder contribution guide](docs/authoring.md#add-a-component-folder-to-clio-kit).

Add skills here, or list a plugin maintained in your own repository:

```bash
clio-kit plugin init my-plugin
clio-kit plugin validate my-plugin
clio-kit plugin submit my-plugin --repo owner/name
```

`submit` generates a community entry for a pull request. External servers can use any language; servers hosted inside CLIO currently support Python, Node.js and Go.

Add an optional Claude Code hook with `clio-kit plugin init my-plugin --hook`. See the [hook guide](community/README.md#hooks).

See the [contribution guide](CONTRIBUTING.md) and [community guide](community/README.md) for requirements and submission details.

<a id="agent-integrations"></a>

<details>
<summary><b>Install in Cursor</b></summary>

Add to `.cursor/mcp.json` in your project, or `~/.cursor/mcp.json`:

```json
{
  "mcpServers": {
    "clio-hdf5": { "command": "clio-kit", "args": ["mcp-server", "hdf5"] },
    "clio-adios": { "command": "clio-kit", "args": ["mcp-server", "adios"] },
    "clio-parquet": { "command": "clio-kit", "args": ["mcp-server", "parquet"] },
    "clio-compression": { "command": "clio-kit", "args": ["mcp-server", "compression"] }
  }
}
```

Install the workflow skills from your project:

```bash
clio-kit skill install --bundle clio-scientific-io --target .cursor/skills
```

See [Cursor MCP docs](https://cursor.com/docs/mcp) and
[skills docs](https://cursor.com/docs/skills).

</details>

<details>
<summary><b>Install in Claude Code</b></summary>

From the CLIO Kit checkout, install the workflow plugin with its MCPs and skills:

```bash
claude plugin marketplace add "$PWD"
claude plugin install clio-scientific-io@clio-kit
claude mcp list
```

Skills-only and agent plugins:

```bash
claude plugin install clio-skills@clio-kit    # scientific workflow skills, no MCP servers
claude plugin install clio-agents@clio-kit    # workflow planner and evidence reviewer
```

See [setup.md](setup.md#claude-code-native-marketplace) for details.

</details>

<details>
<summary><b>Install in VS Code</b></summary>

Add to `.vscode/mcp.json` for GitHub Copilot:

```json
{
  "servers": {
    "clio-hdf5": { "type": "stdio", "command": "clio-kit", "args": ["mcp-server", "hdf5"] },
    "clio-adios": { "type": "stdio", "command": "clio-kit", "args": ["mcp-server", "adios"] },
    "clio-parquet": { "type": "stdio", "command": "clio-kit", "args": ["mcp-server", "parquet"] },
    "clio-compression": { "type": "stdio", "command": "clio-kit", "args": ["mcp-server", "compression"] }
  }
}
```

Install the workflow skills from your project:

```bash
clio-kit skill install --bundle clio-scientific-io --target .github/skills
```

Start the servers with **MCP: List Servers**. The Codex extension uses the
Codex configuration below. See [VS Code MCP docs](https://code.visualstudio.com/docs/agent-customization/mcp-servers)
and [skills docs](https://code.visualstudio.com/docs/agent-customization/agent-skills).

</details>

<details>
<summary><b>Install in Claude Desktop</b></summary>

Edit `claude_desktop_config.json` through **Settings → Developer → Edit Config**:

```json
{
  "mcpServers": {
    "clio-hdf5": { "command": "clio-kit", "args": ["mcp-server", "hdf5"] },
    "clio-adios": { "command": "clio-kit", "args": ["mcp-server", "adios"] },
    "clio-parquet": { "command": "clio-kit", "args": ["mcp-server", "parquet"] },
    "clio-compression": { "command": "clio-kit", "args": ["mcp-server", "compression"] }
  }
}
```

Restart Claude Desktop. This config adds MCP servers only; CLIO's native
skill and agent plugins target Claude Code.
See [Claude Desktop MCP docs](https://modelcontextprotocol.io/docs/develop/connect-local-servers).

</details>

<details>
<summary><b>Install in Codex</b></summary>

Add the MCP servers for Codex CLI or its IDE extension:

```bash
codex mcp add clio-hdf5 -- clio-kit mcp-server hdf5
codex mcp add clio-adios -- clio-kit mcp-server adios
codex mcp add clio-parquet -- clio-kit mcp-server parquet
codex mcp add clio-compression -- clio-kit mcp-server compression
codex mcp list
```

Install the workflow skills from your project:

```bash
clio-kit skill install --bundle clio-scientific-io --target .agents/skills
```

Check `/mcp` and `/skills` in Codex. To install a complete supported workflow, use
`clio-kit plugin install clio-dataset-report --client codex --project .`; review
its hooks with `/hooks` before running it.
See [Codex MCP docs](https://developers.openai.com/codex/mcp) and
[skills docs](https://developers.openai.com/codex/skills).

</details>

<details>
<summary><b>Install in Antigravity</b></summary>

Open **MCP Servers → Manage MCP Servers → View raw config** and add:

```json
{
  "mcpServers": {
    "clio-hdf5": { "command": "clio-kit", "args": ["mcp-server", "hdf5"] },
    "clio-adios": { "command": "clio-kit", "args": ["mcp-server", "adios"] },
    "clio-parquet": { "command": "clio-kit", "args": ["mcp-server", "parquet"] },
    "clio-compression": { "command": "clio-kit", "args": ["mcp-server", "compression"] }
  }
}
```

Install the workflow skills from your project:

```bash
clio-kit skill install --bundle clio-scientific-io --target .agents/skills
```

Reload the MCP configuration. For Antigravity CLI, start the first session from
this project with `agy --new-project` so its local skills and MCP configuration
are loaded. Reopen it with `agy --project <project-name-or-id>`.
Reuse `.agents/skills` if already installed for Codex.
CLIO does not yet ship a native Antigravity plugin.
See [Antigravity MCP docs](https://antigravity.google/docs/mcp) and
[skills docs](https://antigravity.google/docs/skills/).

</details>

## Available Packages

The version below identifies each MCP server's contract and runtime release,
independently of the containing `clio-kit` wheel version. JARVIS 3.7 and SLURM 3.0 have contracts
redesigned for agent use. Spack is at 2.3, 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. A find with no installed
match is normal typed data (`count=0`, `packages=[]`); locate reports the
distinct `not_installed` semantic, while real Spack failures remain errors.

<div align="center">

| 📦 **Package** | 📌 **Ver** | 🔧 **System** | 📋 **Description** | ⚡ **Install Command** |
|:---|:---:|:---:|:---|:---|
| **`adios`** | 2.2.5 | Data I/O | Read data using ADIOS2 engine | `clio-kit mcp-server adios` |
| **`arxiv`** | 2.2.5 | Research | Fetch research papers from ArXiv | `clio-kit mcp-server arxiv` |
| **`chronolog`** | 2.0.3 | Logging | Log and retrieve data from ChronoLog | `clio-kit mcp-server chronolog` |
| **`compression`** | 2.2.5 | Utilities | File compression with gzip | `clio-kit mcp-server compression` |
| **`darshan`** | 2.2.5 | Performance | I/O performance trace analysis | `clio-kit mcp-server darshan` |
| **`geo`** | 2.3.1 | Geospatial | Render GeoJSON vector layers with basemaps | `clio-kit mcp-server geo` |
| **`hdf5`** | 2.2.6 | Data I/O | HPC-optimized scientific data with 27 tools, AI insights, caching, streaming | `clio-kit mcp-server hdf5` |
| **`jarvis`** | 3.7.4 | Workflow | Durable pipeline, bounded package discovery, progress, artifact, and service-runtime management | `clio-kit mcp-server jarvis` |
| **`lmod`** | 3.0.1 | Environment | Environment module management | `clio-kit mcp-server lmod` |
| **`ndp`** | 2.2.5 | Data Protocol | Search and discover datasets across CKAN instances | `clio-kit mcp-server ndp` |
| **`node-hardware`** | 2.3.0 | System | System hardware information | `clio-kit mcp-server node-hardware` |
| **`pandas`** | 2.3.0 | Data Analysis | CSV data loading and filtering | `clio-kit mcp-server pandas` |
| **`parallel-sort`** | 2.3.0 | Computing | Large file sorting | `clio-kit mcp-server parallel-sort` |
| **`paraview`** | 2.2.5 | Visualization | Scientific 3D visualization and analysis | `clio-kit mcp-server paraview` |
| **`parquet`** | 2.2.5 | Data I/O | Read Parquet file columns | `clio-kit mcp-server parquet` |
| **`plot`** | 2.2.5 | Visualization | Generate plots from CSV data | `clio-kit mcp-server plot` |
| **`seismology`** | 2.3.1 | Seismology | Analyze SAC waveforms and archives | `clio-kit mcp-server seismology` |
| **`scientific-catalog`** | 1.1.4 | Discovery | Operator-owned scientific dataset discovery | `clio-kit mcp-server scientific-catalog` |
| **`slurm`** | 3.0.2 | HPC | Job submission and management | `clio-kit mcp-server slurm` |
| **`spack`** | 2.3.1 | Package Management | Structured package discovery, installation, and location | `clio-kit mcp-server spack` |
| **`terrain`** | 2.2.5 | Geospatial | Analyze DEMs and terrain point clouds | `clio-kit mcp-server terrain` |
| **`web`** | 2.1.3 | Web | Web search and URL fetch, with queryable, cancellable fetch tasks; DOI and document conversion need a remote service | `clio-kit mcp-server web` |

</div>

---

## 📖 Usage Examples

### HDF5: Scientific Data Analysis

```
"What datasets are in climate_simulation.h5? Show me the temperature field structure and read the first 100 timesteps."
```

**Tools used:** `open_file`, `analyze_dataset_structure`, `read_partial_dataset`, `list_attributes`

### Slurm: HPC Job Management

```
"Submit simulation.py to Slurm with 32 cores, 64GB memory, 24-hour runtime. Monitor progress and retrieve output when complete."
```

**Tools used:** `slurm_submit`, `slurm_list`, `slurm_describe`

### ArXiv: Research Discovery

```
"Find the latest papers on diffusion models from ArXiv, get details on the top 3, and export citations to BibTeX."
```

**Tools used:** `search_arxiv`, `get_paper_details`, `export_to_bibtex`, `download_paper_pdf`

### Pandas: Data Processing

```
"Load sales_data.csv, clean missing values, compute statistics by region, and save as Parquet."
```

**Tools used:** `load_data`, `handle_missing_data`, `groupby_operations`, `save_data`

### Plot: Data Visualization

```
"Create a line plot showing temperature trends over time from weather.csv with proper axis labels."
```

**Tools used:** `line_plot`, `data_info`

---

## 🚨 Troubleshooting

<details>
<summary><b>Server Not Found Error</b></summary>

If `clio-kit mcp-server <server-name>` fails:

```bash
# Verify server name is correct
clio-kit mcp-servers

# Common names: hdf5, pandas, slurm, arxiv (not hdf5-mcp, pandas-mcp)
```

</details>

<details>
<summary><b>Import Errors or Missing Dependencies</b></summary>

For development or local testing:

```bash
cd mcp-servers/hdf5
uv sync --all-extras --dev
uv run hdf5-mcp
```

</details>


<details>
<summary><b>uv or clio-kit Command Not Found</b></summary>

Install uv package manager:

```bash
# Linux/macOS
curl -LsSf https://astral.sh/uv/install.sh | sh

# Windows
powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"

# Or via pip
pip install uv
```

Then install CLIO Kit persistently and expose uv's tool directory:

```bash
uv tool install --force --reinstall --editable .
uv tool update-shell
```

Open a new shell after `update-shell`, then check it resolved:

```bash
clio-kit mcp-servers
```

</details>

---

## Team 

- **[Gnosis Research Center (GRC)](https://grc.iit.edu/)** - [Illinois Institute of Technology](https://www.iit.edu/) | Lead 
- **[HDF Group](https://www.hdfgroup.org/)** - Data format and library developers | Industry Partner    
- **[University of Utah](https://www.utah.edu/)** - Research collaboration | Domain Science Partner

## Sponsored By

<img src="https://www.nsf.gov/themes/custom/nsf_theme/components/molecules/logo/logo-desktop.png" alt="NSF Logo" width="24" height="24"> **[NSF (National Science Foundation)](https://www.nsf.gov/)** - Supporting scientific computing research and AI integration initiatives

 > we welcome more sponsorships. please contact the [Principal Investigator](mailto:grc@illinoistech.edu)

## Ways to Contribute

- **Submit Issues**: Report bugs or request features via [GitHub Issues](https://github.com/iowarp/clio-kit/issues)
- **Build MCP Servers**: Contribute Python, Node.js or Go servers ([guide](CONTRIBUTING.md#contributing-a-server-in-another-language))
- **Write Skills**: Share reusable scientific workflows ([guide](CONTRIBUTING.md#contributing-a-skill))
- **Share Plugins or Marketplaces**: List tools maintained in your own repository ([guide](community/README.md))
- **Improve Documentation**: Help make guides clearer
- **Share Use Cases**: Tell us how you're using CLIO Kit in your research

**Full Guide**: [CONTRIBUTING.md](CONTRIBUTING.md) 

### Community & Support

- **Chat**: [Zulip Community](https://iowarp.zulipchat.com/#narrow/channel/543872-Agent-Toolkit)
- **Join**: [Invitation Link](https://iowarp.zulipchat.com/join/e4wh24du356e4y2iw6x6jeay/)
- **Issues**: [GitHub Issues](https://github.com/iowarp/clio-kit/issues)
- **Website**: [https://toolkit.iowarp.ai/](https://toolkit.iowarp.ai/)
- **Project**: [IOWarp Project](https://iowarp.ai)

---
