requirements.txt

#
# This file is autogenerated by pip-compile with Python 3.9
# by the following command:
#
#    pip-compile requirements.in
#
absl-py==2.0.0
    # via
    #   chex
    #   ml-collections
    #   optax
    #   orbax-checkpoint
anndata==0.7.6
    # via
    #   -r requirements.in
    #   scanpy
anyio==3.7.1
    # via jupyter-server
argon2-cffi==23.1.0
    # via
    #   jupyter-server
    #   nbclassic
argon2-cffi-bindings==21.2.0
    # via argon2-cffi
attrs==23.1.0
    # via
    #   jsonschema
    #   referencing
babel==2.13.1
    # via jupyterlab-server
backcall==0.2.0
    # via ipython
beautifulsoup4==4.12.2
    # via nbconvert
bleach==6.1.0
    # via nbconvert
certifi==2023.7.22
    # via requests
cffi==1.16.0
    # via argon2-cffi-bindings
charset-normalizer==3.3.1
    # via requests
chex==0.1.7
    # via optax
cmake==3.27.7
    # via triton
contextlib2==21.6.0
    # via ml-collections
contourpy==1.1.1
    # via matplotlib
cycler==0.12.1
    # via matplotlib
decorator==5.1.1
    # via ipython
defusedxml==0.7.1
    # via nbconvert
dm-tree==0.1.8
    # via chex
equinox==0.11.1
    # via lineax
etils[epath,epy]==1.5.2
    # via orbax-checkpoint
exceptiongroup==1.1.3
    # via anyio
fastjsonschema==2.18.1
    # via nbformat
filelock==3.13.0
    # via
    #   torch
    #   triton
flax==0.7.4
    # via ott-jax
fonttools==4.43.1
    # via matplotlib
fsspec==2023.10.0
    # via etils
h5py==3.10.0
    # via
    #   anndata
    #   scanpy
idna==3.4
    # via
    #   anyio
    #   requests
importlib-metadata==6.8.0
    # via
    #   jax
    #   jupyter-client
    #   jupyterlab-server
    #   nbconvert
importlib-resources==6.1.0
    # via
    #   etils
    #   matplotlib
ipykernel==5.5.6
    # via nbclassic
ipython==7.18.1
    # via
    #   -r requirements.in
    #   ipykernel
    #   jupyterlab
ipython-genutils==0.2.0
    # via
    #   ipykernel
    #   nbclassic
jax==0.4.13
    # via
    #   -r requirements.in
    #   chex
    #   equinox
    #   flax
    #   jaxopt
    #   lineax
    #   optax
    #   orbax-checkpoint
    #   ott-jax
jaxlib==0.4.13
    # via
    #   -r requirements.in
    #   chex
    #   jaxopt
    #   optax
    #   orbax-checkpoint
    #   ott-jax
jaxopt==0.8.1
    # via ott-jax
jaxtyping==0.2.23
    # via
    #   equinox
    #   lineax
jedi==0.19.1
    # via ipython
jinja2==3.1.2
    # via
    #   jupyter-server
    #   jupyterlab
    #   jupyterlab-server
    #   nbclassic
    #   nbconvert
    #   torch
joblib==1.3.2
    # via
    #   pynndescent
    #   scanpy
    #   scikit-learn
json5==0.9.14
    # via jupyterlab-server
jsonschema==4.19.1
    # via
    #   jupyterlab-server
    #   nbformat
jsonschema-specifications==2023.7.1
    # via jsonschema
jupyter-client==8.5.0
    # via
    #   ipykernel
    #   jupyter-server
    #   nbclassic
    #   nbclient
jupyter-core==5.4.0
    # via
    #   jupyter-client
    #   jupyter-server
    #   jupyterlab
    #   nbclassic
    #   nbclient
    #   nbconvert
    #   nbformat
jupyter-server==1.24.0
    # via
    #   jupyterlab
    #   jupyterlab-server
    #   nbclassic
    #   notebook-shim
jupyterlab==3.0.16
    # via -r requirements.in
jupyterlab-pygments==0.2.2
    # via nbconvert
jupyterlab-server==2.25.0
    # via jupyterlab
kiwisolver==1.4.5
    # via matplotlib
lineax==0.0.3
    # via ott-jax
lit==17.0.3
    # via triton
llvmlite==0.41.1
    # via
    #   numba
    #   pynndescent
markdown-it-py==3.0.0
    # via rich
markupsafe==2.1.3
    # via
    #   jinja2
    #   nbconvert
matplotlib==3.7.2
    # via
    #   -r requirements.in
    #   scanpy
    #   seaborn
mdurl==0.1.2
    # via markdown-it-py
mistune==3.0.2
    # via nbconvert
ml-collections==0.1.0
    # via -r requirements.in
ml-dtypes==0.3.1
    # via
    #   jax
    #   jaxlib
    #   tensorstore
mpmath==1.3.0
    # via sympy
msgpack==1.0.7
    # via
    #   flax
    #   orbax-checkpoint
natsort==8.4.0
    # via
    #   anndata
    #   scanpy
nbclassic==0.5.6
    # via jupyterlab
nbclient==0.8.0
    # via nbconvert
nbconvert==7.9.2
    # via
    #   jupyter-server
    #   nbclassic
nbformat==5.9.2
    # via
    #   jupyter-server
    #   nbclassic
    #   nbclient
    #   nbconvert
nest-asyncio==1.5.8
    # via
    #   nbclassic
    #   orbax-checkpoint
networkx==3.2
    # via
    #   scanpy
    #   torch
notebook-shim==0.2.3
    # via nbclassic
numba==0.58.1
    # via
    #   pynndescent
    #   scanpy
    #   umap-learn
numpy==1.24.4
    # via
    #   -r requirements.in
    #   anndata
    #   chex
    #   contourpy
    #   flax
    #   h5py
    #   jax
    #   jaxlib
    #   jaxopt
    #   jaxtyping
    #   matplotlib
    #   ml-dtypes
    #   numba
    #   opt-einsum
    #   optax
    #   orbax-checkpoint
    #   ott-jax
    #   pandas
    #   patsy
    #   scanpy
    #   scikit-learn
    #   scipy
    #   seaborn
    #   statsmodels
    #   tensorstore
    #   umap-learn
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==3.3.0
    # via jax
optax==0.1.7
    # via
    #   flax
    #   ott-jax
orbax-checkpoint==0.4.1
    # via flax
ott-jax==0.4.2
    # via -r requirements.in
packaging==23.2
    # via
    #   anndata
    #   jupyter-server
    #   jupyterlab
    #   jupyterlab-server
    #   matplotlib
    #   nbconvert
    #   scanpy
    #   statsmodels
pandas==2.0.3
    # via
    #   -r requirements.in
    #   anndata
    #   scanpy
    #   seaborn
    #   statsmodels
pandocfilters==1.5.0
    # via nbconvert
parso==0.8.3
    # via jedi
patsy==0.5.3
    # via
    #   scanpy
    #   statsmodels
pexpect==4.8.0
    # via ipython
pickleshare==0.7.5
    # via ipython
pillow==10.1.0
    # via matplotlib
platformdirs==3.11.0
    # via jupyter-core
prometheus-client==0.17.1
    # via
    #   jupyter-server
    #   nbclassic
prompt-toolkit==3.0.39
    # via ipython
protobuf==4.24.4
    # via orbax-checkpoint
ptyprocess==0.7.0
    # via
    #   pexpect
    #   terminado
pycparser==2.21
    # via cffi
pygments==2.16.1
    # via
    #   ipython
    #   nbconvert
    #   rich
pynndescent==0.5.10
    # via umap-learn
pyparsing==3.0.9
    # via matplotlib
python-dateutil==2.8.2
    # via
    #   jupyter-client
    #   matplotlib
    #   pandas
pytz==2023.3.post1
    # via pandas
pyyaml==6.0.1
    # via
    #   flax
    #   ml-collections
    #   orbax-checkpoint
pyzmq==25.1.1
    # via
    #   jupyter-client
    #   jupyter-server
    #   nbclassic
referencing==0.30.2
    # via
    #   jsonschema
    #   jsonschema-specifications
requests==2.31.0
    # via jupyterlab-server
rich==13.6.0
    # via flax
rpds-py==0.10.6
    # via
    #   jsonschema
    #   referencing
scanpy==1.9.3
    # via -r requirements.in
scikit-learn==1.3.0
    # via
    #   -r requirements.in
    #   pynndescent
    #   scanpy
    #   umap-learn
scipy==1.11.1
    # via
    #   -r requirements.in
    #   anndata
    #   jax
    #   jaxlib
    #   jaxopt
    #   pynndescent
    #   scanpy
    #   scikit-learn
    #   statsmodels
    #   umap-learn
seaborn==0.12.2
    # via
    #   -r requirements.in
    #   scanpy
send2trash==1.8.2
    # via
    #   jupyter-server
    #   nbclassic
session-info==1.0.0
    # via scanpy
six==1.16.0
    # via
    #   bleach
    #   ml-collections
    #   patsy
    #   python-dateutil
sniffio==1.3.0
    # via anyio
soupsieve==2.5
    # via beautifulsoup4
statsmodels==0.14.0
    # via scanpy
stdlib-list==0.9.0
    # via session-info
sympy==1.12
    # via torch
tbb==2021.10.0
    # via umap-learn
tensorstore==0.1.46
    # via
    #   flax
    #   orbax-checkpoint
terminado==0.17.1
    # via
    #   jupyter-server
    #   nbclassic
threadpoolctl==3.2.0
    # via scikit-learn
tinycss2==1.2.1
    # via nbconvert
toolz==0.12.0
    # via chex
torch==2.0.1
    # via
    #   -r requirements.in
    #   triton
tornado==6.3.3
    # via
    #   ipykernel
    #   jupyter-client
    #   jupyter-server
    #   jupyterlab
    #   nbclassic
    #   terminado
tqdm==4.66.1
    # via
    #   scanpy
    #   umap-learn
traitlets==5.12.0
    # via
    #   ipykernel
    #   ipython
    #   jupyter-client
    #   jupyter-core
    #   jupyter-server
    #   nbclassic
    #   nbclient
    #   nbconvert
    #   nbformat
triton==2.0.0
    # via torch
typeguard==2.13.3
    # via jaxtyping
typing-extensions==4.8.0
    # via
    #   chex
    #   equinox
    #   etils
    #   flax
    #   jaxtyping
    #   lineax
    #   orbax-checkpoint
    #   torch
tzdata==2023.3
    # via pandas
umap-learn==0.5.4
    # via scanpy
urllib3==2.0.7
    # via requests
wcwidth==0.2.8
    # via prompt-toolkit
webencodings==0.5.1
    # via
    #   bleach
    #   tinycss2
websocket-client==1.6.4
    # via jupyter-server
wheel==0.41.2
    # via
    #   nvidia-cublas-cu11
    #   nvidia-cuda-cupti-cu11
    #   nvidia-cuda-runtime-cu11
    #   nvidia-curand-cu11
    #   nvidia-cusparse-cu11
    #   nvidia-nvtx-cu11
xlrd==1.2.0
    # via anndata
zipp==3.17.0
    # via
    #   etils
    #   importlib-metadata
    #   importlib-resources

# The following packages are considered to be unsafe in a requirements file:
# setuptools