Metadata-Version: 2.4
Name: root-mcp
Version: 0.1.5
Summary: Production-grade MCP server for CERN ROOT file analysis
Author: Mohamed Elashri
Maintainer: Mohamed Elashri
License: MIT License
        
        Copyright (c) 2025 Mohamed Elashri
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
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Project-URL: Homepage, https://github.com/MohamedElashri/root-mcp
Project-URL: Repository, https://github.com/MohamedElashri/root-mcp
Project-URL: Issues, https://github.com/MohamedElashri/root-mcp/issues
Project-URL: Documentation, https://github.com/MohamedElashri/root-mcp/tree/main/docs
Project-URL: Changelog, https://github.com/MohamedElashri/root-mcp/blob/main/CHANGELOG.md
Keywords: ROOT,CERN,HEP,MCP,particle physics
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
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: Programming Language :: Python :: 3.14
Classifier: Topic :: Scientific/Engineering :: Physics
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: uproot<6.0.0,>=5.0.0
Requires-Dist: awkward<3.0.0,>=2.0.0
Requires-Dist: numpy<2.0.0,>=1.24.0
Requires-Dist: pandas<3.0.0,>=2.0.0
Requires-Dist: mcp>=0.9.0
Requires-Dist: pydantic<3.0.0,>=2.0.0
Requires-Dist: pydantic-settings>=2.0.0
Requires-Dist: aiofiles>=23.0.0
Requires-Dist: fsspec>=2023.0.0
Requires-Dist: pyarrow>=14.0.0
Requires-Dist: pyyaml>=6.0
Requires-Dist: xxhash>=3.0.0
Requires-Dist: scipy>=1.10.0
Requires-Dist: matplotlib>=3.7.0
Provides-Extra: dev
Requires-Dist: pytest>=7.0.0; extra == "dev"
Requires-Dist: pytest-asyncio>=0.21.0; extra == "dev"
Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
Requires-Dist: black>=23.0.0; extra == "dev"
Requires-Dist: ruff>=0.1.0; extra == "dev"
Requires-Dist: ty>=0.0.2; extra == "dev"
Requires-Dist: types-PyYAML>=6.0.0.0; extra == "dev"
Requires-Dist: pre-commit>=3.0.0; extra == "dev"
Requires-Dist: build>=1.0.0; extra == "dev"
Requires-Dist: twine>=4.0.0; extra == "dev"
Provides-Extra: xrootd
Requires-Dist: XRootD>=5.5.0; extra == "xrootd"
Provides-Extra: root
Dynamic: license-file

# ROOT-MCP: LLM Powered HEP Analysis

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[![License](https://img.shields.io/pypi/l/root-mcp.svg)](LICENSE)
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**ROOT-MCP** empowers Large Language Models (LLMs) to natively understand and analyze CERN ROOT files.

By exposing a set of specialized tools via the [Model Context Protocol (MCP)](https://modelcontextprotocol.io/), it turns Claude (and other MCP-compliant agents) into capable physics research assistants that can:
- **Inspect** ROOT file structures (Trees, Branches, Histograms)
- **Analyze** data distributions (Compute Histograms, Statistics)
- **Compute** kinematic quantities (Invariant Mass)
- **Visualize** results (Plot 1D/2D histograms directly)
- **Filter** data using physics cuts ("selections")

> **Why this matters**: Instead of asking an LLM to "write a script" that you have to debug and run, you can ask the LLM to *"Check the muon pT distribution in this file"* and it will **just do it**.

---

## Architecture

ROOT-MCP features a **dual-mode architecture**:

- **Core Mode**: File I/O, data reading, and basic statistics
- **Extended Mode**: Full analysis capabilities including fitting, kinematics, and correlations

The mode is controlled via configuration, and the server automatically loads only the components you need. Runtime mode switching is also available.

### Optional Native ROOT Support

ROOT-MCP can optionally integrate with a native [ROOT/PyROOT](https://root.cern/) installation to unlock capabilities beyond what `uproot` provides:

- **`run_root_code`**: Execute arbitrary PyROOT/Python code and get structured results
- **`run_rdataframe`**: Compute histograms using ROOT's RDataFrame (no boilerplate needed)
- **`run_root_macro`**: Execute C++ ROOT macros via `gROOT.ProcessLine`

This feature is **entirely optional** — ROOT-MCP works fully without ROOT installed. When ROOT is available and enabled, these additional tools appear automatically.

**Requirements**: A working ROOT installation (via [conda-forge](https://anaconda.org/conda-forge/root), system package, or binary tarball). ROOT is not pip-installable at this time.

**Enable it** by setting `enable_root: true` in your `config.yaml`:

```yaml
features:
  enable_root: true

# Optional: tune execution settings
root_native:
  execution_timeout: 60
  working_directory: "/tmp/root_mcp_native"
```

Use `get_server_info` to check ROOT availability at runtime:
```json
{
  "root_native_available": true,
  "root_native_enabled": true,
  "root_version": "6.32/02",
  "root_features": {"rdataframe": true, "roofit": true, "tmva": false}
}
```

## Quick Start

### 1. Install

```bash
pip install root-mcp
```

Optional: For remote file access via XRootD protocol:
```bash
pip install "root-mcp[xrootd]"
```

### 2. Configure

**Fastest path — no config file needed:**

```bash
root-mcp --data-path /path/to/your/data
```

Or set an environment variable once:

```bash
export ROOT_MCP_DATA_PATH=/path/to/your/data
```

**Zero-config one-liners:**

```bash
# Core mode (lightweight, no scipy/matplotlib needed)
root-mcp --data-path /data --mode core

# Extended mode with native ROOT, restricted to one directory
root-mcp --data-path /data --enable-root --allowed-root /data

# Remote XRootD resource, no YAML needed
root-mcp --resource cms=root://xrootd.cern.ch//store --allow-remote --mode extended

# Docker / container — fully env-var driven
ROOT_MCP_DATA_PATH=/data ROOT_MCP_MODE=extended ROOT_MCP_EXPORT_PATH=/exports root-mcp

# Quiet server (only warnings+) with a cache increase
root-mcp --data-path /data --log-level WARNING --cache-size 100
```

**Generate a starter config (optional):**

```bash
root-mcp init --permissive   # creates config.yaml pre-filled with current directory
```

**Manual config file** — for persistent settings, remote resources, or native ROOT:

```yaml
server:
  mode: "extended"   # "core" or "extended"

resources:
  - name: "my_analysis"
    uri: "file:///path/to/data"
    allowed_patterns: ["*.root"]

security:
  allowed_roots: []  # empty = any local path is accessible (permissive)
```

**Mode Selection:**
- `mode: "core"` — Lightweight: file operations and basic statistics
- `mode: "extended"` — Full analysis: histograms, fitting, kinematics, correlations

Switch modes at runtime with the `switch_mode` tool — no restart required.

### 3. Run with Claude Desktop

Add to your `claude_desktop_config.json`:

```json
{
  "mcpServers": {
    "root-mcp": {
      "command": "root-mcp",
      "args": ["--data-path", "/path/to/your/data"]
    }
  }
}
```

Or with a persistent config file:

```json
{
  "mcpServers": {
    "root-mcp": {
      "command": "root-mcp",
      "env": {
        "ROOT_MCP_CONFIG": "/path/to/config.yaml"
      }
    }
  }
}
```

## Documentation

- **[Full Documentation](docs/README.md)**: The complete guide.
- **[Tool Reference](docs/api/tools.md)**: Detailed API definition for all tools.
- **[LLM Integration Guide](docs/guides/llm_integration.md)**: How to prompt and work with the agent.

## Citation

If you use ROOT-MCP in your research, please cite:

```bibtex
@software{root_mcp,
  title = {ROOT-MCP: Production-Grade MCP Server for CERN ROOT Files},
  author = {Mohamed Elashri},
  year = {2025},
  url = {https://github.com/MohamedElashri/root-mcp}
}
```
## License

MIT License - see [LICENSE](LICENSE) for details.
