BioFoundation

An ecosystem for biological foundation models.

Installation

Create and activate a virtual environment:

uv venv
source .venv/bin/activate

Pre-requisites:

• Pytorch (e.g. uv pip install torch)

Install the package:

uv pip install -e .

Additional Dependencies

# PlantCaduceus
uv pip install -e .[mamba]
# GPN
uv pip install -e .[gpn]
# GLM-Experiments
uv pip install -e .[glm-experiments]
# Then manually install glm-experiments to avoid circular dependency:
uv pip install git+https://github.com/Open-Athena/glm-experiments

Docker Installation (For Evo2)

For evo2 support, Docker is recommended as it handles all complex CUDA/cuDNN dependencies automatically.

See docker/evo2/README.md for detailed instructions.

Quick start:

cd docker/evo2
./run.sh local  # or ./run.sh github

Usage

Run the example scripts:

source .venv/bin/activate
# light job
python examples/marin_evolutionary_constraint.py
# heavier job, split across 8 GPUs with 8 CPU threads per GPU
OMP_NUM_THREADS=8 torchrun --nproc_per_node=8 examples/plantcad_llr.py

Development Setup

To set up the development environment with linting, formatting, type checking, and testing:

# Install development dependencies
uv pip install --group dev
# Install pre-commit hooks
pre-commit install

Development Tools

Running Quality Checks

# Run all pre-commit hooks (linting, formatting, type checking)
pre-commit run

Running Tests

# Run all tests
pytest