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Installation

Requirements

Quick Setup

Platform note: The commands below are for macOS. For Linux or Windows, see SETUP.md.

# Install just (macOS)
brew install just

# Install uv
curl -LsSf https://astral.sh/uv/install.sh | sh

# Clone and set up the project
git clone https://github.com/zircote/farm-notebook-examples.git
cd farm-notebook-examples
just setup

just setup installs all Python dependencies and the NSIP CLI binary.

NSIP version freshness: The setup pins a specific NSIP CLI version. Check the latest release to see if a newer version is available.

Individual Steps

just install          # Install all Python deps (data + dev extras)
just install-nsip     # Download and install the NSIP CLI
just install-mcp      # Pull the NSIP MCP Docker image (optional)

Running Notebooks

just lab              # Start JupyterLab
just notebook         # Start classic Jupyter Notebook

Verifying Your Setup

just check            # Run all checks (validate notebooks, lint, NSIP)
just versions         # Show installed tool versions

All Available Commands

Run just with no arguments to see every available recipe.

Recipe Description
just setup Full setup: install all deps + NSIP CLI
just install Install all Python dependencies (data + dev extras)
just install-minimal Install only the minimal dependencies (Jupyter + kernel)
just install-data Install data science extras (pandas, numpy, matplotlib, tabulate)
just install-dev Install dev tools (nbqa, ruff)
just install-nsip Download and install the NSIP CLI binary
just install-mcp Pull the NSIP MCP Docker image
just lab Start JupyterLab
just notebook Start classic Jupyter Notebook
just lint Lint all notebooks with ruff (via nbqa)
just fix Auto-fix lint issues in all notebooks
just lint-one <name> Lint a specific notebook by name
just validate Validate all notebooks are well-formed JSON
just check-nsip Verify NSIP CLI is working
just check Run all checks (validate, lint, NSIP)
just info Show notebook inventory (cell counts, sizes)
just versions Show installed tool versions

Cloud Alternatives (No Install Required)

Don't want to install anything? Run the notebooks in the cloud:

  • Google Colab: Open any notebook directly from GitHub at https://colab.research.google.com/ (just add !pip install tabulate in the first cell). Note: the NSIP CLI is not available in Colab, so genetics notebooks that call nsip commands will not work without manual setup.
  • GitHub Codespaces: Click the green "Code" button on the repo page, then "Create codespace on main" for a full VS Code environment in your browser

See SETUP.md for detailed instructions.

Detailed Instructions

  • New to all of this? See SETUP.md for step-by-step instructions covering every tool from scratch.
  • Windows users: See the Complete Windows Walkthrough for both WSL and native PowerShell approaches.
  • Prefer the cloud? See Cloud Alternatives for Google Colab and GitHub Codespaces guides.