---
title: OpenEnv Pathway Analysis Environment
emoji: 🧬
colorFrom: blue
colorTo: green
sdk: docker
app_port: 8000
tags:
  - openenv
  - bioinformatics
  - ai-agents
---

# OpenEnv Pathway Analysis Environment

This repository packages `pathway_analysis_env` for Hugging Face Hub publication.

## Contents
- `envs/pathway_analysis_env/` environment code
- reproducible GEO benchmark inputs for 3 tasks
- task expansion scripts:
  - `create_geo_task.py`
  - `append_task_to_manifest.py`

## Run locally
```bash
uv sync --all-extras
PYTHONPATH=src:envs uv run python envs/pathway_analysis_env/scripts/run_agent_eval_suite.py   --manifest envs/pathway_analysis_env/data/eval_manifest_geo3.json
```

## Note on Spaces
Publishing as a Docker Space from a free user namespace may require Hugging Face PRO.
This repo is ready for maintainers to deploy under an entitled namespace.