accelerate>=1.4.0
addict>=2.4.0
altair[all]>=5.5.0
bitsandbytes>=0.43.0
captum>=0.7.0
colorama>=0.4.6
datasets<=5.1.0
einops>=0.7.0
evaluate>=0.4.3
huggingface-hub>=0.29.0
ipykernel>=6.29.5
ipywidgets>=8
aiohttp>=3.9.0
jax>=0.5.2
loguru>=0.7.0
mambapy>=1.2.0
mcp<2,>=1.3.0
modelscope[framework]>=1.23.2
oss2>=2.18.0
nbstripout>=0.8.1
ninja>1
numba>0.56.2
numpy>=2.0.0
optuna>=3.6.0
openpyxl>=3.1.5
pandas>=2.2.3
peft>=0.14.0
pydantic>=2.10.6
python-dotenv>=1.0.0
pyyaml>=6.0
rich>=13.7.0
scikit-allel<2,>=1.3.13
scikit-learn>=1.4.0
scipy>=1.15.2
sentencepiece>=0.2.0
seqeval>=1.2.2
starlette<1.8.0,>=0.40.0
tensorboardx>=2.6.2.2
tokenizers>=0.21.0
torch<2.12,>=2.4.0
tqdm>=4.67.1
transformers<6,>=4.49.0
umap-learn>=0.5.7
uvicorn>=0.24.0
wandb>=0.19.8
websockets>=12.0
wheel>=0.45.0

[all]
dnallm[base,dev,docs,fla,mcp,notebook,test,ui]

[base]
dnallm[dev,mcp,notebook,test]
isort>=6.0.1
types-transformers>=0.1.0

[cpu]
torch<2.12,>=2.4.0

[cuda121]
torch<2.12,>=2.2.0

[cuda124]
torch<2.12,>=2.4.0

[cuda126]
torch<2.12,>=2.6.0

[cuda128]
torch<2.12,>=2.6.0

[cuda130]
torch<2.12,>=2.9.0

[dev]
dnallm[notebook,test]
ruff==0.16.10
pre-commit>=3.6.0
mypy>=1.15.0
pandas-stubs>=2.3.0
logomaker>=0.8.2
pyfastx>=2.2.0
seaborn>=0.13.0

[dev:platform_system != "Windows"]
pybedtools>=0.11.0

[docs]
mkdocs-jupyter>=0.24.0
mkdocs-material>=9.6.1
mkdocstrings-python>=1.16.10
click<8.5.1

[fla]
flash-linear-attention<0.6,>=0.5.2

[mamba]
causal_conv1d==1.7.0
mamba-ssm==2.3.2.post1
torch<2.12,>=2.6.0

[mcp]
mcp<2,>=1.0.0
langchain>=1.3.6
langchain_mcp_adapters>=0.2.1
langchain-ollama>=1.1.0
nest-asyncio>=1.5.9
pydantic-ai<2,>=1.107.0

[notebook]
jupyter>=1.1.1
marimo>=0.16.3
nbclient>=0.10
ipython<9,>=8.31

[notebook:platform_system != "Windows"]
pygenometracks>=3.9

[rocm]
torch<2.12,>=2.5.0

[test]
pytest>=8.4
pytest-asyncio>=1.0
pytest-cov>=7.0
pytest-progress>=0.1.0
pytest-timeout<2.5,>=2.3.1
coverage[toml]>=7.10.6
nbclient>=0.10

[ui]
gradio>=4.0.0
