requirements.txt

dask>=2023.3.2
bokeh==2.4.3
imageio==2.31.1
numpy==1.23.5
matplotlib==3.7.1
pandas>=1.5.3
scipy==1.10.1
seaborn==0.12.2
h5py>=3.7.0
gefpy>=1.1.20
setuptools==69.5.1
#todo python3.8/site-packages/umap/distances.py:1053: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator.
#The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0.
#See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
numba==0.56.4
statsmodels>=0.14.0
leidenalg>=0.10.1
umap-learn==0.5.1
KDEpy==1.1.0
shapely>=2.0.0
# pyviz-comms==2.2.1
packaging>=23.1
panel==0.14.4
holoviews==1.17.1
param==1.13.0
hvplot>=0.9.0
colorcet>=3.1.0
datashader>=0.15.2
anndata>=0.7.5
phenograph==1.5.7
requests>=2.31.0
urllib3==2.1.0
typing-extensions>=4.7.1
natsort~=7.1.1
joblib>=1.3.2
patsy~=0.5.1
louvain>=0.8.0
# igraph==0.9.11
arboreto==0.1.6
squidpy==1.2.2
xarray==0.20.1

slideio>=1.0.0
tqdm>=4.60.0
scikit-learn>=1.3.0
pillow>=10.1.0
scikit-image>=0.21.0
tifffile>=2023.2.3
opencv-python>=4.8.0.76
hotspotsc==1.1.1
# hotspotsc @ git+https://github.com/YosefLab/Hotspot.git@v1.1.2
distributed>=2023.3.2.1
pyarrow>=10.0.1
spatialpandas>=0.4.4
loompy==3.0.6
gtfparse==1.2.1
harmonypy==0.0.6
SQLAlchemy==1.3.24
fbpca>=1.0
geosketch>=1.2
pyscenic>=0.12.1
# onnxruntime==1.15.1
POT==0.9.1
distinctipy>=1.2.2
lxml>=4.8.0
fastcluster>=1.2.6
pycirclize>=0.5.0
plotly>=5.15.0
# cusingler
cell-bin==1.3.4.1

# pysal<=2.6.0
# pygam>=0.8.0