requirements.txt

# ESM3Di Requirements
# Compatible with ESM++ (Synthyra) models and PEFT LoRA training
#
# For GPU support with bitsandbytes, install with:
#   pip install -r requirements.txt bitsandbytes triton

# Core ML dependencies
torch>=2.5.0
transformers>=4.45.0,<4.49.0      # Compatible with peft 0.12.x and ESM++ (Synthyra)
peft>=0.12.0,<0.14.0              # LoRA adapters
accelerate>=1.0.0                  # Required by peft and transformers
safetensors>=0.4.0                 # Fast model loading

# Tokenizer dependencies
sentencepiece>=0.2.0
tokenizers>=0.20.0
protobuf>=4.0.0

# Scientific computing
numpy>=1.24.0
scipy>=1.10.0
pandas>=2.0.0
scikit-learn>=1.3.0

# Bioinformatics
biopython>=1.80

# Utilities
tqdm>=4.65.0
huggingface-hub>=0.20.0
einops>=0.7.0
tensorboard>=2.14.0
pyyaml>=6.0
requests>=2.28.0
fsspec>=2023.1.0

# Optional: GPU optimization (uncomment if needed)
# bitsandbytes>=0.42.0    # 8-bit optimization
# triton>=2.1.0           # Flash attention kernels