| 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. | |