Jupyter Notebooks Skill

This skill provides complete Jupyter notebook interaction capabilities through MCP server integration, enabling notebook-based data science and research workflows.

Capabilities

• Create and manage Jupyter notebooks (.ipynb files)
• Execute cells and entire notebooks
• Read and write cell content (code and markdown)
• Access cell outputs and execution results
• Manipulate notebook structure (add, delete, move cells)
• Cell-level operations with execution state tracking
• Support for JupyterLab and Jupyter Notebook interfaces
• Integration with Python data science stack (NumPy, Pandas, PyTorch, etc.)

When to Use This Skill

Use this skill when you need to:

• Create interactive computational notebooks
• Run data analysis workflows
• Execute machine learning experiments
• Generate reproducible research documents
• Visualize data with matplotlib/seaborn
• Prototype code interactively
• Create tutorial or educational notebooks
• Document analysis procedures with code + narrative

Prerequisites

• Jupyter notebooks installed (jupyter and jupyterlab available in /opt/venv)
• MCP server running on stdio
• Python virtual environment at /opt/venv with data science packages

Available Operations

Notebook Management

• create_notebook - Create new notebook with optional cells
• list_notebooks - List all notebooks in directory
• get_notebook_info - Get metadata and structure info
• delete_notebook - Remove notebook file

Cell Operations

• add_cell - Add code or markdown cell at position
• delete_cell - Remove cell by index
• move_cell - Reorder cells
• get_cell - Read cell content and metadata
• update_cell - Modify cell content

Execution

• execute_cell - Run specific cell and capture output
• execute_notebook - Run entire notebook sequentially
• clear_outputs - Clear all cell outputs
• restart_kernel - Restart notebook kernel

Content Access

• get_all_cells - Read all cells in notebook
• get_output - Access cell execution results
• export_notebook - Convert to HTML, PDF, or Python script

Instructions

Creating a New Notebook

To create a notebook for data analysis:

1. Use create_notebook with file path
2. Optionally provide initial cells (imports, setup)
3. Notebook created with nbformat 4.x schema

Example cells structure:

[
  {
    "cell_type": "code",
    "source": "import numpy as np\nimport pandas as pd\nimport matplotlib.pyplot as plt"
  },
  {
    "cell_type": "markdown",
    "source": "# Data Analysis\n\nThis notebook analyzes..."
  }
]

Executing Notebooks

For data processing pipelines:

1. Use execute_notebook for full run
2. Or execute_cell for incremental execution
3. Outputs captured with display data, errors, and execution counts

PyTorch/ML Workflow

Typical machine learning notebook structure:

1. Setup cell: Import torch, torchvision, datasets
2. Data cell: Load and preprocess data
3. Model cell: Define neural network architecture
4. Training cell: Training loop with loss tracking
5. Evaluation cell: Test metrics and visualizations
6. Export cell: Save model weights

Integration with CUDA

For GPU-accelerated computing:

import torch
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
model = MyModel().to(device)

The skill automatically detects CUDA availability and uses GPU when present.

Environment Variables

• JUPYTER_CONFIG_DIR - Jupyter configuration directory
• JUPYTER_DATA_DIR - Data files location
• JUPYTER_RUNTIME_DIR - Runtime files (kernels, etc.)

Output Formats

Notebooks can be exported to:

• HTML - Static web page with outputs
• PDF - Via LaTeX (requires texlive installation)
• Python - Pure Python script (.py file)
• Markdown - Documentation format
• Slides - Reveal.js presentation

Best Practices

1. Cell Organization: Keep cells focused on single tasks
2. Markdown Documentation: Use markdown cells for explanations
3. Restart & Run All: Test full execution before sharing
4. Version Control: Use nbdime for notebook diffs
5. Clear Outputs: Clear sensitive data before committing
6. Kernel Management: Restart kernel when imports change

Example Workflows

Data Science Pipeline

1. Create notebook with data exploration cells
2. Execute EDA (exploratory data analysis)
3. Add visualization cells
4. Run statistical analysis
5. Export results to HTML report

Machine Learning Experiment

1. Set up experiment notebook
2. Load training data
3. Define model architecture
4. Train with progress tracking
5. Evaluate on test set
6. Save model and metrics

Research Documentation

1. Create markdown cells for methodology
2. Add code cells for implementations
3. Include result visualizations
4. Export to PDF for publication

Error Handling

The skill provides detailed error messages for:

• Kernel execution failures
• Cell syntax errors
• Missing dependencies
• File I/O errors
• nbformat validation issues

Performance Considerations

• Notebooks execute in isolated kernels
• CUDA operations utilize GPU when available
• Large datasets may require memory management
• Long-running cells can be interrupted
• Output size limits may apply

Related Skills

• pytorch-ml - Deep learning workflows
• latex-documents - Scientific paper generation
• data-visualization - Advanced plotting
• cuda-development - GPU programming

Technical Details

• Protocol: Model Context Protocol (MCP) over stdio
• Server: Node.js-based MCP server
• Format: nbformat 4.x JSON schema
• Kernel: IPython kernel with Python 3.x
• Extensions: JupyterLab extensions supported

Troubleshooting

Kernel Not Starting

• Check /opt/venv/bin/python exists
• Verify ipykernel installed
• Check kernel specifications: jupyter kernelspec list

Import Errors

• Activate virtual environment: source /opt/venv/bin/activate
• Install missing packages: pip install <package>
• Verify CUDA installation for GPU packages

Cell Execution Hangs

• Interrupt kernel execution
• Restart kernel
• Check for infinite loops or blocking operations

Configuration

MCP server configuration in ~/.claude/settings.json:

{
  "mcpServers": {
    "jupyter-notebooks": {
      "command": "node",
      "args": ["/home/devuser/.claude/skills/jupyter-notebooks/server.js"],
      "cwd": "/home/devuser/.claude/skills/jupyter-notebooks"
    }
  }
}

Notes

• Compatible with Claude Code and other MCP clients
• Supports both JupyterLab and classic Notebook interfaces
• Full compatibility with existing .ipynb files
• Execution state preserved across sessions
• Output includes rich media (images, HTML, LaTeX)