numpy

[baserender]
pydantic<3,>=2.12.5
pyyaml
typer
pyarrow>=23.0.1
matplotlib
pillow>=13.0.0
psutil>=7.2.1

[cluster]
dnadesign-tools[seqledger]
scanpy==1.10.3
igraph
leidenalg
scikit-learn<2,>=1.8
scipy>=1.17.0
seaborn
matplotlib
umap-learn>=0.5.11
python-levenshtein
click>=8.3.3

[construct]
dnadesign-tools[folding,seqledger]
vl-convert-python>=1.9.0

[cruncher]
dnadesign-tools[baserender]
biopython>=1.87
python-levenshtein
arviz>=0.23.0
certifi>=2026.10.19
click>=8.3.3
logomaker
numba
pandas
pysam>=0.23.3
rich
tqdm

[cruncher-notebook]
dnadesign-tools[cruncher]
marimo>=0.23.16

[folding]
pydantic<3,>=2.12.5
pyyaml
typer
psutil>=7.2.1
viennarna>=2.7.2

[full]
dnadesign-tools[baserender,cluster,construct,cruncher-notebook,folding,infer,junction,latentdna-notebook,notify,opal-notebook,ops,permuter,seqledger]
anyio>=4.14.2
markdown-it-py<5,>=4.0.0
pygments>=2.20.0
xlrd
netcdf4>=1.7.3
fastparquet>=2025.12.0
filelock<5,>=4.2.4
zstd!=1.5.7.3,>=1.5.7.2
py3dmol==2.5.5

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

[infer]
dnadesign-tools[seqledger]
tqdm

[infer-evo2]
dnadesign-tools[infer]

[infer-evo2:sys_platform == "linux" and platform_machine == "x86_64"]
torch<2.14,>=2.13
pip>=26.1.2
setuptools>=84.1.0
wheel>=0.48.0
packaging
ninja
cmake>=3.18
flash-attn<3,>=2.8.3.post2
transformer-engine[pytorch]<3,>=2.0
evo2>=0.5.3
onnx>=1.22.0
transformers

[junction]
pydantic<3,>=2.12.5
pyyaml
typer
matplotlib
psutil>=7.2.1

[latentdna]
dnadesign-tools[seqledger]
anndata
igraph
leidenalg
pynndescent
scipy>=1.17.0
scikit-learn<2,>=1.8
matplotlib
umap-learn>=0.5.11

[latentdna-notebook]
dnadesign-tools[latentdna]
marimo>=0.23.16

[notify]
typer
click>=8.3.3
keyring>=25.6.0
certifi>=2026.10.19

[opal]
pandas
pyarrow>=23.0.1
polars>=1.36.1
scikit-learn<2,>=1.8
scipy>=1.17.0
joblib
pydantic<3,>=2.12.5
pyyaml
rich
typer
typing-extensions
matplotlib
openpyxl

[opal-notebook]
dnadesign-tools[opal]
marimo>=0.23.16
altair>=6.0.0
plotly>=6.9.0
vegafusion>=2.0.3
vl-convert-python>=1.9.0
pillow>=13.0.0

[ops]
pydantic<3,>=2.12.5
pyyaml
typer
pyarrow>=23.0.1
click>=8.3.3

[permuter]
pandas
pyarrow>=23.0.1
pydantic<3,>=2.12.5
pyyaml
rich
typer
matplotlib
seaborn
psutil>=7.2.1

[seqledger]
biopython>=1.87
duckdb<2,>=1.5.5
pandas
pyarrow>=23.0.1
pydantic<3,>=2.12.5
pyyaml
rich
typer
psutil>=7.2.1
