configargparse>=1.7
joblib>=1.4.2
packaging>=25.0
pydantic>=2.11.4
pydantic-settings>=2.9.1
pyyaml>=6.0.2
requests>=2.32.3
rich>=13.9.1
tqdm>=4.66.5

[all]
biopython>=1.84
boto3>=1.35.31
colorcet>=3.2.1
dcor>=0.6
dropbox>=12.0.2
fastapi>=0.115.0
fsspec>=2024.10.0
gmpy2>=2.1.5
google-cloud-storage>=2.18.2
graphviz>=0.20.3
h5py>=3.11.0
httpx>=0.28.1
imageio>=2.35.1
ipython>=8.28.0
lightgbm>=4.6.0
lime>=0.2.0.1
llvmlite>=0.43.0
matplotlib>=3.9.2
mcp<2.0.0,>=1.28.0
mpmath>=1.3.0
networkx>=3.3
numba>=0.60.0
numpy>=1.26.4
openbabel-wheel>=3.1.0
optuna>=3.6.1
optuna-dashboard>=0.16.2
optuna-integration>=4.0.0
pandas>=2.2.3
pdb2pqr>=3.7.1
pillow>=10.4.0
pingouin>=0.5.5
psycopg>=3.2.0
pymysql>=1.1.1
rdkit!=2026.3.3,>=2024.09.1
rustworkx>=0.15.1
scikit-image>=0.24.0
scikit-learn>=1.5.2
scipy>=1.14.1
seaborn>=0.13.2
shap>=0.44.0
six>=1.17.0
snakemake>=7.32.4
snakemake-logger-plugin-snkmt>=0.1.6
spyrmsd>=0.8.0
sqlalchemy>=2.0.35
sqlalchemy-utils>=0.41.2
starlette>=1.3.1
statsmodels>=0.14.3
sympy>=1.13.3
tifffile>=2024.9.20
torch>=2.4.1
torchaudio>=2.4.1
torchsummary
torchviz
torchvision>=0.19.1
uvicorn>=0.32.0
visualtorch>=0.2.3
xgboost>=2.1.1

[all:sys_platform != "darwin"]
cupy-cuda11x>=13.0.0

[analysis]
colorcet>=3.2.1
dcor>=0.6
fsspec>=2024.10.0
gmpy2>=2.1.5
graphviz>=0.20.3
h5py>=3.11.0
imageio>=2.35.1
ipython>=8.28.0
lime>=0.2.0.1
llvmlite>=0.43.0
matplotlib>=3.9.2
mpmath>=1.3.0
networkx>=3.3
numba>=0.60.0
numpy>=1.26.4
pandas>=2.2.3
pillow>=10.4.0
pingouin>=0.5.5
rustworkx>=0.15.1
scikit-image>=0.24.0
scipy>=1.14.1
seaborn>=0.13.2
shap>=0.44.0
statsmodels>=0.14.3
sympy>=1.13.3
tifffile>=2024.9.20

[api]
fastapi>=0.115.0
starlette>=1.3.1
uvicorn>=0.32.0

[build]
build>=1.2.2.post1
setuptools>=80.8.0
twine>=6.1.0
wheel>=0.47.0

[cloud]
boto3>=1.35.31
dropbox>=12.0.2
google-cloud-storage>=2.18.2

[db]
psycopg>=3.2.0
pymysql>=1.1.1
sqlalchemy>=2.0.35
sqlalchemy-utils>=0.41.2

[dev]
coverage>=7.8.1
detect-secrets>=1.5.0
mypy>=1.0.0
pre-commit>=4.0.1
py-mini-racer>=0.6.0
pytest>=8.3.3
pytest-cov>=6.1.1
pytest-order>=1.3.0
ruff>=0.8.0

[docking]
biopython>=1.84
numpy>=1.26.4
openbabel-wheel>=3.1.0
pandas>=2.2.3
pdb2pqr>=3.7.1
rdkit!=2026.3.3,>=2024.09.1
scikit-learn>=1.5.2
scipy>=1.14.1
six>=1.17.0
spyrmsd>=0.8.0

[docs]
furo
myst-parser>=4.0.1
sphinx>=8.2.3
sphinx-argparse>=0.5.2
sphinx-rtd-theme>=3.0.2

[full]
biopython>=1.84
boto3>=1.35.31
colorcet>=3.2.1
dcor>=0.6
dropbox>=12.0.2
fastapi>=0.115.0
fsspec>=2024.10.0
furo
gmpy2>=2.1.5
google-cloud-storage>=2.18.2
graphviz>=0.20.3
h5py>=3.11.0
httpx>=0.28.1
imageio>=2.35.1
ipython>=8.28.0
lightgbm>=4.6.0
lime>=0.2.0.1
llvmlite>=0.43.0
matplotlib>=3.9.2
mcp<2.0.0,>=1.28.0
mpmath>=1.3.0
myst-parser>=4.0.1
networkx>=3.3
numba>=0.60.0
numpy>=1.26.4
openbabel-wheel>=3.1.0
optuna>=3.6.1
optuna-dashboard>=0.16.2
optuna-integration>=4.0.0
pandas>=2.2.3
pillow>=10.4.0
pingouin>=0.5.5
psycopg>=3.2.0
pymysql>=1.1.1
rdkit!=2026.3.3,>=2024.09.1
rustworkx>=0.15.1
scikit-image>=0.24.0
scikit-learn>=1.5.2
scipy>=1.14.1
seaborn>=0.13.2
shap>=0.44.0
six>=1.17.0
snakemake>=7.32.4
snakemake-logger-plugin-snkmt>=0.1.6
spyrmsd>=0.8.0
sphinx>=8.2.3
sphinx-argparse>=0.5.2
sphinx-rtd-theme>=3.0.2
sqlalchemy>=2.0.35
sqlalchemy-utils>=0.41.2
starlette>=1.3.1
statsmodels>=0.14.3
sympy>=1.13.3
tifffile>=2024.9.20
torch>=2.4.1
torchaudio>=2.4.1
torchsummary
torchviz
torchvision>=0.19.1
uvicorn>=0.32.0
visualtorch>=0.2.3
xgboost>=2.1.1

[full:sys_platform != "darwin"]
cupy-cuda11x>=13.0.0

[gpu]

[gpu:sys_platform != "darwin"]
cupy-cuda11x>=13.0.0

[mcp]
httpx>=0.28.1
mcp<2.0.0,>=1.28.0

[ml]
lightgbm>=4.6.0
numpy>=1.26.4
optuna>=3.6.1
optuna-dashboard>=0.16.2
optuna-integration>=4.0.0
pandas>=2.2.3
scikit-learn>=1.5.2
scipy>=1.14.1
torch>=2.4.1
torchaudio>=2.4.1
torchsummary
torchviz
torchvision>=0.19.1
visualtorch>=0.2.3
xgboost>=2.1.1

[workflow]
snakemake>=7.32.4
snakemake-logger-plugin-snkmt>=0.1.6
