torch<3,>=2.1.0
transformers<6,>=4.41.0
numpy<3,>=1.23
biopython<2,>=1.80
pyrodigal<4,>=3.0
huggingface_hub<2,>=0.23.0
safetensors<1,>=0.4.0
matplotlib<4,>=3.7
ViennaRNA<3,>=2.6
plotly<7,>=5.0
datasets<5,>=2.16
accelerate<2,>=0.26
peft<1,>=0.10.0

[dev]
pytest<10,>=7
nbclient<1,>=0.8
ipykernel<8,>=6
ipywidgets<9,>=8

[flash]
flash-attn>=2.5.8

[viz]
bokeh<4,>=3
