activeinferenceinstitute/gnn-environment-setup
src/setup/SKILL.md
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.
$ install --global
skillsauthnpx skillsauth add activeinferenceinstitute/generalizednotationnotation gnn-environment-setupInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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SKILL.md
- 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 (includes Step 12 Python backends: jax, numpyro, torch, discopy)
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 | jax, jaxlib, flax, optax | JAX stack (pymdp is a core dep) |
| execution-frameworks | jax, numpyro, torch, discopy | Same pins as core Step 12 stack (explicit uv sync --extra) |
| 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_existsfind_project_gnn_filesget_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
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