environment.yml

# BioDesignBench - Complete Environment (Python 3.11)
# Install: conda env create -f environment.yml
# Update: conda env update -f environment.yml --prune
# Activate: conda activate biodesignbench

name: biodesignbench
channels:
  - conda-forge
  - bioconda
  - pytorch
  - defaults

dependencies:
  # Core Python
  - python=3.11
  - pip

  # Data Science
  - numpy>=1.24
  - pandas>=2.0
  - scipy>=1.10
  - scikit-learn>=1.3

  # Bio Libraries (conda)
  - biopython>=1.81

  # PyTorch (CPU - change to pytorch-cuda=11.8 for GPU)
  - pytorch>=2.0
  - torchvision

  # Testing & Quality
  - pytest>=9.0
  - pytest-cov>=4.0
  - pytest-asyncio>=0.21
  - black>=23.0
  - isort>=5.12
  - mypy>=1.0
  - ruff>=0.1

  # Utilities
  - pyyaml>=6.0
  - requests>=2.28
  - tqdm>=4.65
  - rich>=13.0
  - click>=8.1

  # Jupyter (for analysis)
  - jupyterlab>=4.0
  - matplotlib>=3.7
  - seaborn>=0.12

  # Pip-only packages
  - pip:
    # === Project Core ===
    - pydantic>=2.0
    - jsonschema>=4.17
    - python-dotenv>=1.0
    - docker>=7.0
    - aiohttp>=3.8
    - aiofiles>=23.0

    # === Bio Tools ===
    - biotite>=0.37
    - prody>=2.4
    - tmtools>=0.1

    # === LLM API Clients (for general-purpose agents) ===
    - anthropic>=0.75
    - openai>=1.12
    - google-generativeai>=0.8

    # === Bio-Specific Agent Packages ===
    # Biomni - Stanford's bio-specific agent (requires Python 3.11+)
    - biomni @ git+https://github.com/snap-stanford/Biomni.git@main
    # AIDE (BioML) - ML-focused tree-search agent
    # NOTE: aideml>=0.2 pins pytest<8. We override with pytest>=9 via conda above.
    - aideml>=0.2
    # NOTE: open-interpreter pins anthropic<0.38, conflicting with >=0.75.
    # Install separately if needed: pip install open-interpreter --no-deps

    # === LangChain (required by biomni) ===
    - langchain-openai
    - langchain-anthropic
    - langchain-google-genai
    - langchain-community

    # === Install BioDesignBench itself (editable) ===
    - -e .