GitHub Skill

gnn-environment-setup

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.

ActiveInferenceInstitute☆ 23 Repository stars2 Repository forks

View source ↗Installation

Installation

Follow the repository instructions for this skill and your agent. Review the files and dependencies before adding it to your workflow.

View source ↗Guides

Skill instructions

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:

Group	Key Packages	Purpose
`active-inference`	pymdp, jax, jaxlib, flax, optax	Active Inference simulation
`visualization`	plotly, altair, seaborn, bokeh, holoviews	Visualization
`llm`	openai, anthropic, cohere, ollama	LLM integration
`audio`	librosa, soundfile, pedalboard, pydub	Audio generation
`gui`	gradio, streamlit	GUI interface
`ml-ai`	torch, transformers, datasets	Machine learning
`graphs`	igraph, graphviz, discopy	Graph libraries
`dev`	pytest-*, mypy, ruff	Development tools
`database`	sqlalchemy, alembic	Database integration
`research`	jupyterlab, sympy, numba, cython	Research tools
`scaling`	dask, distributed, joblib	Parallel processing
`all`	Everything above	Full installation

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

Issue	Solution
`uv: command not found`	`curl -LsSf https://astral.sh/uv/install.sh \| sh`
PyMDP import fails	`uv sync --extra active-inference`
matplotlib missing	`uv sync --extra visualization`
CUDA not detected	Check `torch.cuda.is_available()` after `uv sync --extra ml-ai`

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

Examples

Read the usage examples in the source repository.

View source ↗

Source history

Indexed on: 2026-03-11
Index updated: 2026-03-11
Branch: main

Index and sync dates describe this directory. View the source repository for code history.

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