name: gnn-environment-setup description: GNN environment setup and dependency management. Use when configuring the development environment, installing dependencies, managing virtual environments, or troubleshooting dependency issues for the GNN pipeline.

GNN Environment Setup (Step 1)

Purpose

Manages environment configuration, virtual environment creation, and dependency installation for the GNN pipeline. Supports both core and optional dependency groups via uv or pip.

Key Commands

# Run setup step
python src/1_setup.py --target-dir input/gnn_files --output-dir output --verbose

# As part of pipeline
python src/main.py --only-steps 1 --verbose

# Using uv (recommended)
uv sync                    # Core dependencies
uv sync --extra dev        # Development tools
uv sync --all-extras       # Everything

Optional Dependency Groups

These groups match [project.optional-dependencies] in pyproject.toml:

Environment Requirements

• Python: 3.11+ (recommended 3.12.x or 3.13.x)
• Package manager: uv (recommended) or pip
• Core deps: numpy, networkx, pyyaml, jsonschema

Troubleshooting

MCP Tools

This module registers tools with the GNN MCP server (see mcp.py):

• ensure_directory_exists
• find_project_gnn_files
• get_standard_output_paths

References

• AGENTS.md — Module documentation
• README.md — Usage guide
• SPEC.md — Module specification
• ../../SETUP_GUIDE.md — Full setup guide
• ../../pyproject.toml — Dependency definitions

Documentation

• README: Module Overview
• AGENTS: Agentic Workflows
• SPEC: Architectural Specification
• SKILL: Capability API