accelerate==1.7.0
bio==1.8.0
biopython==1.85
biotite==1.2.0
biotraj==1.2.2
Brotli==1.1.0
datasets
decorator==5.2.1
dotenv==0.9.9
einops==0.8.1
fair-esm==2.0.0
fbpca==1.0
filelock==3.18.0
fsspec==2025.3.2
gprofiler-official==1.0.0
h5py==3.13.0
huggingface-hub==0.32.3
hydra-core==1.3.2
hydra-optuna-sweeper==1.2.0
idna==3.10
ipykernel>=7.0.1
ipython==8.36.0
loguru>=0.7.3
memory-profiler==0.61.0
mygene==3.2.2
networkx==3.4.2
numpy==2.2.5
omegaconf==2.3.0
optuna==2.10.1
pandas==2.2.2
peft==0.15.2
python-dateutil
python-dotenv==1.1.0
PyYAML==6.0.2
ruff==0.14.0
safetensors==0.5.3
scikit-learn==1.6.1
scipy==1.15.3
tokenizers==0.21.1
torch==2.7.0
torchtext==0.18.0
torchvision==0.22.0
tqdm==4.67.1
transformers==4.48.1
typing_extensions==4.13.2
urllib3==2.4.0

[:sys_platform == "linux"]
nvidia-cublas-cu12==12.6.4.1
nvidia-cuda-cupti-cu12==12.6.80
nvidia-cuda-nvrtc-cu12==12.6.77
nvidia-cuda-runtime-cu12==12.6.77
nvidia-cudnn-cu12==9.5.1.17
nvidia-cufft-cu12==11.3.0.4
nvidia-cufile-cu12==1.11.1.6
nvidia-curand-cu12==10.3.7.77
nvidia-cusolver-cu12==11.7.1.2
nvidia-cusparse-cu12==12.5.4.2
nvidia-cusparselt-cu12==0.6.3
nvidia-nccl-cu12==2.26.2
nvidia-nvjitlink-cu12==12.6.85
nvidia-nvtx-cu12==12.6.77

[dev]
ruff
pytest
pre-commit
