numpy

[full]
anyio>=4.14.2
arviz>=0.23.0
biopython>=1.87
click>=8.3.3
html5lib<2,>=1.1
igraph
leidenalg
logomaker
markdown-it-py<5,>=4.0.0
matplotlib
openpyxl
ortools<9.10,>=9.9
pandas
pillow>=12.3.0
pyarrow>=23.0.1
pydantic
pygments>=2.20.0
pymc
python-levenshtein
pyyaml
rich
scanpy==1.10.3
scikit-learn<2,>=1.8
scipy>=1.17.0
seaborn
tqdm
typer
umap-learn>=0.5.11
upa-url<2,>=1.1.0
duckdb<2,>=1.5.5
xlrd
dense-arrays==0.2.0
polars>=1.36.1
altair>=6.0.0
vegafusion>=2.0.3
vl-convert-python>=1.9.0
pysam>=0.23.3
netcdf4>=1.7.3
certifi>=2025.11.12
keyring>=25.6.0
fastparquet>=2025.12.0
filelock<4,>=3.20.3
marimo>=0.23.16
openai>=2.14.0
viennarna>=2.7.2
zstd!=1.5.7.3,>=1.5.7.2
py3dmol==2.5.5
plotly>=6.9.0
psutil>=7.2.1

[full:(sys_platform == "darwin" and platform_machine == "arm64") or (sys_platform == "linux" and platform_machine == "x86_64")]
torch<2.14,>=2.13

[infer-evo2]

[infer-evo2:sys_platform == "linux" and platform_machine == "x86_64"]
torch<2.14,>=2.13
pip>=26.1.2
setuptools>=84.0.0
wheel>=0.48.0
packaging
ninja
cmake>=3.18
flash-attn<3,>=2.8.0.post2
transformer-engine[pytorch]<3,>=2.0
evo2>=0.5.3
onnx>=1.22.0
transformers
