# This file was autogenerated by uv via the following command:
#    uv pip compile pyproject.toml -o requirements.txt
--index-url https://xget.xi-xu.me/pypi/simple/
--trusted-host xget.xi-xu.me
anndata==0.10.9
    # via
    #   scmagnify (pyproject.toml)
    #   cellrank
    #   mudata
    #   palantir
    #   scanpy
    #   scvelo
    #   seacells
array-api-compat==1.11.2
    # via anndata
biopython==1.85
    # via pycirclize
cellrank==2.0.7
    # via scmagnify (pyproject.toml)
click==8.1.8
    # via loompy
cmake==4.0.3
    # via triton
contourpy==1.3.0
    # via matplotlib
cycler==0.12.1
    # via matplotlib
docrep==0.3.2
    # via
    #   cellrank
    #   pygpcca
exceptiongroup==1.3.0
    # via anndata
filelock==3.18.0
    # via
    #   torch
    #   triton
fonttools==4.59.0
    # via matplotlib
get-annotations==0.1.2
    # via scanpy
h5py==3.14.0
    # via
    #   anndata
    #   loompy
    #   mudata
    #   scanpy
igraph==0.11.9
    # via palantir
importlib-metadata==8.7.0
    # via jax
importlib-resources==6.5.2
    # via matplotlib
jax==0.4.30
    # via
    #   jaxopt
    #   mellon
jaxlib==0.4.30
    # via
    #   jax
    #   jaxopt
jaxopt==0.8.5
    # via mellon
jinja2==3.0.3
    # via
    #   pygpcca
    #   torch
joblib==1.5.1
    # via
    #   cellrank
    #   palantir
    #   pynndescent
    #   scanpy
    #   scikit-learn
kiwisolver==1.4.7
    # via matplotlib
legacy-api-wrap==1.4.1
    # via scanpy
lit==18.1.8
    # via triton
llvmlite==0.43.0
    # via
    #   numba
    #   pynndescent
loompy==3.0.8
    # via scvelo
markdown-it-py==3.0.0
    # via rich
markupsafe==3.0.2
    # via jinja2
matplotlib==3.9.4
    # via
    #   cellrank
    #   palantir
    #   pycirclize
    #   pycomplexheatmap
    #   scanpy
    #   scvelo
    #   seaborn
mdurl==0.1.2
    # via markdown-it-py
mellon==1.6.1
    # via palantir
ml-dtypes==0.5.3
    # via
    #   jax
    #   jaxlib
    #   palantir
moods-python==1.9.4.1
    # via scmagnify (pyproject.toml)
mpmath==1.3.0
    # via sympy
mudata==0.2.4
    # via scmagnify (pyproject.toml)
natsort==8.4.0
    # via
    #   anndata
    #   pyranges
    #   scanpy
ncls==0.0.70
    # via pyranges
networkx==3.2.1
    # via
    #   cellrank
    #   palantir
    #   scanpy
    #   torch
numba==0.60.0
    # via
    #   cellrank
    #   loompy
    #   pynndescent
    #   scanpy
    #   scvelo
    #   seacells
    #   umap-learn
numpy==2.0.2
    # via
    #   anndata
    #   biopython
    #   cellrank
    #   contourpy
    #   h5py
    #   jax
    #   jaxlib
    #   jaxopt
    #   loompy
    #   matplotlib
    #   ml-dtypes
    #   mudata
    #   ncls
    #   numba
    #   numpy-groupies
    #   palantir
    #   pandas
    #   patsy
    #   pycirclize
    #   pycomplexheatmap
    #   pygam
    #   pygpcca
    #   scanpy
    #   scikit-learn
    #   scipy
    #   scvelo
    #   seaborn
    #   seacells
    #   sorted-nearest
    #   statsmodels
    #   tensorly
    #   umap-learn
numpy-groupies==0.11.3
    # via loompy
nvidia-cublas-cu11==11.10.3.66
    # via
    #   nvidia-cudnn-cu11
    #   nvidia-cusolver-cu11
    #   torch
nvidia-cuda-cupti-cu11==11.7.101
    # via torch
nvidia-cuda-nvrtc-cu11==11.7.99
    # via torch
nvidia-cuda-runtime-cu11==11.7.99
    # via torch
nvidia-cudnn-cu11==8.5.0.96
    # via torch
nvidia-cufft-cu11==10.9.0.58
    # via torch
nvidia-curand-cu11==10.2.10.91
    # via torch
nvidia-cusolver-cu11==11.4.0.1
    # via torch
nvidia-cusparse-cu11==11.7.4.91
    # via torch
nvidia-nccl-cu11==2.14.3
    # via torch
nvidia-nvtx-cu11==11.7.91
    # via torch
opt-einsum==3.4.0
    # via jax
packaging==25.0
    # via
    #   anndata
    #   matplotlib
    #   scanpy
    #   statsmodels
palantir==1.4.1
    # via seacells
palettable==3.3.3
    # via pycomplexheatmap
pandas==2.3.1
    # via
    #   anndata
    #   cellrank
    #   mudata
    #   palantir
    #   pycirclize
    #   pycomplexheatmap
    #   pyranges
    #   scanpy
    #   scvelo
    #   seaborn
    #   seacells
    #   statsmodels
patsy==1.0.1
    # via
    #   scanpy
    #   statsmodels
pillow==11.3.0
    # via matplotlib
progressbar2==4.5.0
    # via pygam
pycirclize==1.9.1
    # via scmagnify (pyproject.toml)
pycomplexheatmap==1.8.2
    # via scmagnify (pyproject.toml)
pygam==0.10.1
    # via
    #   scmagnify (pyproject.toml)
    #   cellrank
pygments==2.19.2
    # via rich
pygpcca==1.0.4
    # via cellrank
pynndescent==0.5.13
    # via
    #   mellon
    #   scanpy
    #   umap-learn
pyparsing==3.2.3
    # via matplotlib
pyranges==0.1.4
    # via
    #   scmagnify (pyproject.toml)
    #   seacells
python-dateutil==2.9.0.post0
    # via
    #   matplotlib
    #   pandas
python-utils==3.9.1
    # via progressbar2
pytz==2025.2
    # via pandas
rich==14.1.0
    # via scmagnify (pyproject.toml)
scanpy==1.10.3
    # via
    #   scmagnify (pyproject.toml)
    #   cellrank
    #   palantir
    #   scvelo
    #   seacells
scikit-learn==1.6.1
    # via
    #   cellrank
    #   mellon
    #   palantir
    #   pynndescent
    #   scanpy
    #   scvelo
    #   umap-learn
scipy==1.13.1
    # via
    #   anndata
    #   cellrank
    #   jax
    #   jaxlib
    #   jaxopt
    #   loompy
    #   palantir
    #   pycomplexheatmap
    #   pygam
    #   pygpcca
    #   pynndescent
    #   scanpy
    #   scikit-learn
    #   scvelo
    #   seacells
    #   statsmodels
    #   tensorly
    #   umap-learn
scvelo==0.3.3
    # via cellrank
seaborn==0.13.2
    # via
    #   cellrank
    #   scanpy
seacells==0.3.3
    # via scmagnify (pyproject.toml)
session-info==1.0.1
    # via
    #   scmagnify (pyproject.toml)
    #   scanpy
setuptools==80.9.0
    # via
    #   loompy
    #   nvidia-cublas-cu11
    #   nvidia-cuda-cupti-cu11
    #   nvidia-cuda-runtime-cu11
    #   nvidia-curand-cu11
    #   nvidia-cusparse-cu11
    #   nvidia-nvtx-cu11
six==1.17.0
    # via
    #   docrep
    #   python-dateutil
sorted-nearest==0.0.39
    # via pyranges
statsmodels==0.14.5
    # via scanpy
stdlib-list==0.11.1
    # via session-info
sympy==1.13.1
    # via torch
tabulate==0.9.0
    # via pyranges
tensorly==0.9.0
    # via scmagnify (pyproject.toml)
texttable==1.7.0
    # via igraph
threadpoolctl==3.6.0
    # via scikit-learn
torch==2.0.0
    # via
    #   scmagnify (pyproject.toml)
    #   triton
tqdm==4.67.1
    # via
    #   scanpy
    #   umap-learn
triton==2.0.0
    # via torch
typing-extensions==4.14.1
    # via
    #   exceptiongroup
    #   python-utils
    #   torch
tzdata==2025.2
    # via pandas
umap-learn==0.5.9.post2
    # via
    #   scanpy
    #   scvelo
wheel==0.45.1
    # via
    #   nvidia-cublas-cu11
    #   nvidia-cuda-cupti-cu11
    #   nvidia-cuda-runtime-cu11
    #   nvidia-curand-cu11
    #   nvidia-cusparse-cu11
    #   nvidia-nvtx-cu11
wrapt==1.17.2
    # via cellrank
zipp==3.23.0
    # via
    #   importlib-metadata
    #   importlib-resources
