absl-py==2.0.0
    # via
    #   chex
    #   ml-collections
    #   optax
    #   orbax-checkpoint
aiobotocore==2.7.0
    # via s3fs
aiohttp==3.8.6
    # via
    #   aiobotocore
    #   fsspec
    #   gcsfs
    #   s3fs
aioitertools==0.11.0
    # via aiobotocore
aiosignal==1.3.1
    # via aiohttp
anndata==0.10.2
    # via
    #   mudata
    #   scanpy
    #   scvi-tools
annotated-types==0.6.0
    # via pydantic
anyio==3.7.1
    # via
    #   fastapi
    #   jupyter-server
    #   starlette
appnope==0.1.3
    # via
    #   ipykernel
    #   ipython
argon2-cffi==23.1.0
    # via jupyter-server
argon2-cffi-bindings==21.2.0
    # via argon2-cffi
array-api-compat==1.4
    # via anndata
arrow==1.3.0
    # via
    #   isoduration
    #   lightning
asttokens==2.4.0
    # via stack-data
async-lru==2.0.4
    # via jupyterlab
async-timeout==4.0.3
    # via aiohttp
attrs==23.1.0
    # via
    #   aiohttp
    #   jsonschema
    #   referencing
babel==2.13.0
    # via jupyterlab-server
backcall==0.2.0
    # via ipython
backoff==2.2.1
    # via lightning
bandit[toml]==1.7.5
    # via efaar-benchmarking (pyproject.toml)
beautifulsoup4==4.12.2
    # via
    #   lightning
    #   nbconvert
black==23.10.1
    # via efaar-benchmarking (pyproject.toml)
bleach==6.1.0
    # via nbconvert
blessed==1.20.0
    # via inquirer
boto3==1.28.64
    # via lightning-cloud
botocore==1.31.64
    # via
    #   aiobotocore
    #   boto3
    #   s3transfer
cachetools==5.3.1
    # via
    #   google-auth
    #   tox
certifi==2023.7.22
    # via requests
cffi==1.16.0
    # via argon2-cffi-bindings
cfgv==3.4.0
    # via pre-commit
chardet==5.2.0
    # via tox
charset-normalizer==3.3.1
    # via
    #   aiohttp
    #   requests
chex==0.1.8
    # via
    #   optax
    #   scvi-tools
click==8.1.7
    # via
    #   black
    #   docstr-coverage
    #   lightning
    #   lightning-cloud
    #   uvicorn
colorama==0.4.6
    # via
    #   radon
    #   tox
comm==0.1.4
    # via ipykernel
contextlib2==21.6.0
    # via ml-collections
contourpy==1.1.1
    # via matplotlib
coverage[toml]==7.3.2
    # via
    #   efaar-benchmarking (pyproject.toml)
    #   pytest-cov
croniter==1.4.1
    # via lightning
cycler==0.12.1
    # via matplotlib
dateutils==0.6.12
    # via lightning
debugpy==1.8.0
    # via ipykernel
decorator==5.1.1
    # via
    #   gcsfs
    #   ipython
deepdiff==6.6.1
    # via lightning
defusedxml==0.7.1
    # via nbconvert
distlib==0.3.7
    # via virtualenv
dm-tree==0.1.8
    # via chex
docrep==0.3.2
    # via scvi-tools
docstr-coverage==2.3.0
    # via efaar-benchmarking (pyproject.toml)
etils[epath,epy]==1.5.1
    # via orbax-checkpoint
exceptiongroup==1.1.3
    # via
    #   anndata
    #   anyio
    #   ipython
    #   pytest
executing==2.0.0
    # via stack-data
fastapi==0.104.0
    # via
    #   lightning
    #   lightning-cloud
fastjsonschema==2.18.1
    # via
    #   nbformat
    #   validate-pyproject
filelock==3.12.4
    # via
    #   torch
    #   tox
    #   virtualenv
flake8==6.1.0
    # via efaar-benchmarking (pyproject.toml)
flax==0.7.4
    # via scvi-tools
fonttools==4.43.1
    # via matplotlib
fqdn==1.5.1
    # via jsonschema
frozenlist==1.4.0
    # via
    #   aiohttp
    #   aiosignal
fsspec[http]==2023.10.0
    # via
    #   efaar-benchmarking (pyproject.toml)
    #   etils
    #   gcsfs
    #   lightning
    #   pytorch-lightning
    #   s3fs
    #   torch
gcsfs==2023.10.0
    # via efaar-benchmarking (pyproject.toml)
gitdb==4.0.11
    # via gitpython
gitpython==3.1.40
    # via bandit
google-api-core==2.12.0
    # via
    #   google-cloud-core
    #   google-cloud-storage
google-auth==2.23.3
    # via
    #   gcsfs
    #   google-api-core
    #   google-auth-oauthlib
    #   google-cloud-core
    #   google-cloud-storage
google-auth-oauthlib==1.1.0
    # via gcsfs
google-cloud-core==2.3.3
    # via google-cloud-storage
google-cloud-storage==2.12.0
    # via gcsfs
google-crc32c==1.5.0
    # via
    #   google-cloud-storage
    #   google-resumable-media
google-resumable-media==2.6.0
    # via google-cloud-storage
googleapis-common-protos==1.61.0
    # via google-api-core
h11==0.14.0
    # via uvicorn
h5py==3.10.0
    # via
    #   anndata
    #   mudata
    #   scanpy
    #   scvi-tools
identify==2.5.30
    # via pre-commit
idna==3.4
    # via
    #   anyio
    #   jsonschema
    #   requests
    #   yarl
imageio==2.31.6
    # via scikit-image
importlib-resources==6.1.0
    # via etils
iniconfig==2.0.0
    # via pytest
inquirer==3.1.3
    # via lightning
ipykernel==6.25.2
    # via jupyterlab
ipython==8.16.1
    # via ipykernel
isoduration==20.11.0
    # via jsonschema
isort==5.12.0
    # via efaar-benchmarking (pyproject.toml)
itsdangerous==2.1.2
    # via starsessions
jax==0.4.19
    # via
    #   chex
    #   flax
    #   numpyro
    #   optax
    #   orbax-checkpoint
    #   scvi-tools
jaxlib==0.4.19
    # via
    #   chex
    #   numpyro
    #   optax
    #   orbax-checkpoint
    #   scvi-tools
jedi==0.19.1
    # via ipython
jinja2==3.1.2
    # via
    #   jupyter-server
    #   jupyterlab
    #   jupyterlab-server
    #   lightning
    #   nbconvert
    #   torch
jmespath==1.0.1
    # via
    #   boto3
    #   botocore
joblib==1.3.2
    # via
    #   pynndescent
    #   scanpy
    #   scikit-learn
json5==0.9.14
    # via jupyterlab-server
jsonpointer==2.4
    # via jsonschema
jsonschema[format-nongpl]==4.19.1
    # via
    #   jupyter-events
    #   jupyterlab-server
    #   nbformat
jsonschema-specifications==2023.7.1
    # via jsonschema
jupyter-client==8.4.0
    # via
    #   ipykernel
    #   jupyter-server
    #   nbclient
jupyter-core==5.4.0
    # via
    #   ipykernel
    #   jupyter-client
    #   jupyter-server
    #   jupyterlab
    #   nbclient
    #   nbconvert
    #   nbformat
jupyter-events==0.8.0
    # via jupyter-server
jupyter-lsp==2.2.0
    # via jupyterlab
jupyter-server==2.8.0
    # via
    #   jupyter-lsp
    #   jupyterlab
    #   jupyterlab-server
    #   notebook-shim
jupyter-server-terminals==0.4.4
    # via jupyter-server
jupyterlab==4.0.7
    # via efaar-benchmarking (pyproject.toml)
jupyterlab-pygments==0.2.2
    # via nbconvert
jupyterlab-server==2.25.0
    # via jupyterlab
kiwisolver==1.4.5
    # via matplotlib
lazy-loader==0.3
    # via scikit-image
lightning==2.0.9.post0
    # via scvi-tools
lightning-cloud==0.5.43
    # via lightning
lightning-utilities==0.9.0
    # via
    #   lightning
    #   pytorch-lightning
    #   torchmetrics
llvmlite==0.41.1
    # via
    #   numba
    #   pynndescent
mando==0.7.1
    # via radon
markdown-it-py==3.0.0
    # via rich
markupsafe==2.1.3
    # via
    #   jinja2
    #   nbconvert
matplotlib==3.8.0
    # via
    #   efaar-benchmarking (pyproject.toml)
    #   scanpy
    #   seaborn
matplotlib-inline==0.1.6
    # via
    #   ipykernel
    #   ipython
mccabe==0.7.0
    # via flake8
mdurl==0.1.2
    # via markdown-it-py
mistune==3.0.2
    # via nbconvert
ml-collections==0.1.1
    # via scvi-tools
ml-dtypes==0.3.1
    # via
    #   jax
    #   jaxlib
    #   tensorstore
mpmath==1.3.0
    # via sympy
msgpack==1.0.7
    # via
    #   flax
    #   orbax-checkpoint
mudata==0.2.3
    # via scvi-tools
multidict==6.0.4
    # via
    #   aiohttp
    #   yarl
multipledispatch==1.0.0
    # via numpyro
mypy==1.6.1
    # via efaar-benchmarking (pyproject.toml)
mypy-extensions==1.0.0
    # via
    #   black
    #   mypy
natsort==8.4.0
    # via
    #   anndata
    #   scanpy
nbclient==0.8.0
    # via nbconvert
nbconvert==7.9.2
    # via jupyter-server
nbformat==5.9.2
    # via
    #   jupyter-server
    #   nbclient
    #   nbconvert
nest-asyncio==1.5.8
    # via
    #   ipykernel
    #   orbax-checkpoint
networkx==3.2
    # via
    #   scanpy
    #   scikit-image
    #   torch
nodeenv==1.8.0
    # via pre-commit
notebook-shim==0.2.3
    # via jupyterlab
numba==0.58.1
    # via
    #   pynndescent
    #   scanpy
    #   sparse
    #   umap-learn
numpy==1.26.1
    # via
    #   anndata
    #   chex
    #   contourpy
    #   flax
    #   h5py
    #   imageio
    #   jax
    #   jaxlib
    #   lightning
    #   matplotlib
    #   ml-dtypes
    #   mudata
    #   numba
    #   numpyro
    #   opt-einsum
    #   optax
    #   orbax-checkpoint
    #   pandas
    #   patsy
    #   pyarrow
    #   pyro-ppl
    #   pytorch-lightning
    #   scanpy
    #   scikit-image
    #   scikit-learn
    #   scipy
    #   scvi-tools
    #   seaborn
    #   sparse
    #   statsmodels
    #   tensorstore
    #   tifffile
    #   torchmetrics
    #   umap-learn
    #   xarray
numpyro==0.13.2
    # via scvi-tools
oauthlib==3.2.2
    # via requests-oauthlib
opt-einsum==3.3.0
    # via
    #   jax
    #   pyro-ppl
optax==0.1.7
    # via
    #   flax
    #   scvi-tools
orbax-checkpoint==0.4.1
    # via flax
ordered-set==4.1.0
    # via deepdiff
overrides==7.4.0
    # via jupyter-server
packaging==23.2
    # via
    #   anndata
    #   black
    #   ipykernel
    #   jupyter-server
    #   jupyterlab
    #   jupyterlab-server
    #   lightning
    #   lightning-utilities
    #   matplotlib
    #   nbconvert
    #   pyproject-api
    #   pytest
    #   pytorch-lightning
    #   scanpy
    #   scikit-image
    #   statsmodels
    #   tox
    #   validate-pyproject
    #   xarray
pandas==2.1.1
    # via
    #   anndata
    #   efaar-benchmarking (pyproject.toml)
    #   mudata
    #   scanpy
    #   scvi-tools
    #   seaborn
    #   statsmodels
    #   xarray
pandocfilters==1.5.0
    # via nbconvert
parso==0.8.3
    # via jedi
pathspec==0.11.2
    # via black
patsy==0.5.3
    # via
    #   scanpy
    #   statsmodels
pbr==5.11.1
    # via stevedore
pexpect==4.8.0
    # via ipython
pickleshare==0.7.5
    # via ipython
pillow==10.0.1
    # via
    #   imageio
    #   matplotlib
    #   scikit-image
platformdirs==3.11.0
    # via
    #   black
    #   jupyter-core
    #   tox
    #   virtualenv
pluggy==1.3.0
    # via
    #   pytest
    #   tox
pre-commit==3.5.0
    # via efaar-benchmarking (pyproject.toml)
prometheus-client==0.17.1
    # via jupyter-server
prompt-toolkit==3.0.39
    # via ipython
protobuf==4.24.4
    # via
    #   google-api-core
    #   googleapis-common-protos
    #   orbax-checkpoint
psutil==5.9.6
    # via
    #   ipykernel
    #   lightning
ptyprocess==0.7.0
    # via
    #   pexpect
    #   terminado
pure-eval==0.2.2
    # via stack-data
pyarrow==13.0.0
    # via efaar-benchmarking (pyproject.toml)
pyasn1==0.5.0
    # via
    #   pyasn1-modules
    #   rsa
pyasn1-modules==0.3.0
    # via google-auth
pycodestyle==2.11.1
    # via flake8
pycparser==2.21
    # via cffi
pydantic==2.1.1
    # via
    #   fastapi
    #   lightning
pydantic-core==2.4.0
    # via pydantic
pyflakes==3.1.0
    # via flake8
pygments==2.16.1
    # via
    #   ipython
    #   nbconvert
    #   rich
pyjwt==2.8.0
    # via lightning-cloud
pynndescent==0.5.10
    # via umap-learn
pyparsing==3.1.1
    # via matplotlib
pyproject-api==1.6.1
    # via tox
pyro-api==0.1.2
    # via pyro-ppl
pyro-ppl==1.8.6
    # via scvi-tools
pytest==7.4.2
    # via
    #   efaar-benchmarking (pyproject.toml)
    #   pytest-cov
pytest-cov==4.1.0
    # via efaar-benchmarking (pyproject.toml)
python-dateutil==2.8.2
    # via
    #   arrow
    #   botocore
    #   croniter
    #   dateutils
    #   jupyter-client
    #   matplotlib
    #   pandas
python-editor==1.0.4
    # via inquirer
python-json-logger==2.0.7
    # via jupyter-events
python-multipart==0.0.6
    # via
    #   lightning
    #   lightning-cloud
pytorch-lightning==2.1.0
    # via lightning
pytz==2023.3.post1
    # via
    #   dateutils
    #   pandas
pyupgrade==3.15.0
    # via efaar-benchmarking (pyproject.toml)
pyyaml==6.0.1
    # via
    #   bandit
    #   docstr-coverage
    #   flax
    #   jupyter-events
    #   lightning
    #   ml-collections
    #   orbax-checkpoint
    #   pre-commit
    #   pytorch-lightning
pyzmq==25.1.1
    # via
    #   ipykernel
    #   jupyter-client
    #   jupyter-server
radon==6.0.1
    # via efaar-benchmarking (pyproject.toml)
readchar==4.0.5
    # via inquirer
referencing==0.30.2
    # via
    #   jsonschema
    #   jsonschema-specifications
    #   jupyter-events
requests==2.31.0
    # via
    #   fsspec
    #   gcsfs
    #   google-api-core
    #   google-cloud-storage
    #   jupyterlab-server
    #   lightning
    #   lightning-cloud
    #   requests-oauthlib
requests-oauthlib==1.3.1
    # via google-auth-oauthlib
rfc3339-validator==0.1.4
    # via
    #   jsonschema
    #   jupyter-events
rfc3986-validator==0.1.1
    # via
    #   jsonschema
    #   jupyter-events
rich==13.6.0
    # via
    #   bandit
    #   flax
    #   lightning
    #   lightning-cloud
    #   scvi-tools
rpds-py==0.10.6
    # via
    #   jsonschema
    #   referencing
rsa==4.9
    # via google-auth
s3fs==2023.10.0
    # via efaar-benchmarking (pyproject.toml)
s3transfer==0.7.0
    # via boto3
scanpy==1.9.5
    # via efaar-benchmarking (pyproject.toml)
scikit-image==0.22.0
    # via efaar-benchmarking (pyproject.toml)
scikit-learn==1.3.2
    # via
    #   efaar-benchmarking (pyproject.toml)
    #   pynndescent
    #   scanpy
    #   scvi-tools
    #   umap-learn
scipy==1.11.3
    # via
    #   anndata
    #   jax
    #   jaxlib
    #   pynndescent
    #   scanpy
    #   scikit-image
    #   scikit-learn
    #   scvi-tools
    #   sparse
    #   statsmodels
    #   umap-learn
scvi-tools==1.0.4
    # via efaar-benchmarking (pyproject.toml)
seaborn==0.13.0
    # via
    #   efaar-benchmarking (pyproject.toml)
    #   scanpy
send2trash==1.8.2
    # via jupyter-server
session-info==1.0.0
    # via scanpy
six==1.16.0
    # via
    #   asttokens
    #   bleach
    #   blessed
    #   docrep
    #   lightning-cloud
    #   mando
    #   ml-collections
    #   patsy
    #   python-dateutil
    #   rfc3339-validator
smmap==5.0.1
    # via gitdb
sniffio==1.3.0
    # via anyio
soupsieve==2.5
    # via beautifulsoup4
sparse==0.14.0
    # via scvi-tools
stack-data==0.6.3
    # via ipython
starlette==0.27.0
    # via
    #   fastapi
    #   lightning
    #   starsessions
starsessions==1.3.0
    # via lightning
statsmodels==0.14.0
    # via scanpy
stdlib-list==0.9.0
    # via session-info
stevedore==5.1.0
    # via bandit
sympy==1.12
    # via torch
tensorstore==0.1.46
    # via
    #   flax
    #   orbax-checkpoint
terminado==0.17.1
    # via
    #   jupyter-server
    #   jupyter-server-terminals
threadpoolctl==3.2.0
    # via scikit-learn
tifffile==2023.9.26
    # via scikit-image
tinycss2==1.2.1
    # via nbconvert
tokenize-rt==5.2.0
    # via pyupgrade
tomli==2.0.1
    # via
    #   bandit
    #   black
    #   coverage
    #   jupyterlab
    #   mypy
    #   pyproject-api
    #   pytest
    #   tox
    #   validate-pyproject
toolz==0.12.0
    # via chex
torch==2.1.0
    # via
    #   lightning
    #   pyro-ppl
    #   pytorch-lightning
    #   scvi-tools
    #   torchmetrics
torchmetrics==1.2.0
    # via
    #   lightning
    #   pytorch-lightning
    #   scvi-tools
tornado==6.3.3
    # via
    #   ipykernel
    #   jupyter-client
    #   jupyter-server
    #   jupyterlab
    #   terminado
tox==4.11.3
    # via efaar-benchmarking (pyproject.toml)
tqdm==4.63.1
    # via
    #   docstr-coverage
    #   lightning
    #   numpyro
    #   pyro-ppl
    #   pytorch-lightning
    #   scanpy
    #   scvi-tools
    #   umap-learn
traitlets==5.11.2
    # via
    #   comm
    #   ipykernel
    #   ipython
    #   jupyter-client
    #   jupyter-core
    #   jupyter-events
    #   jupyter-server
    #   jupyterlab
    #   lightning
    #   matplotlib-inline
    #   nbclient
    #   nbconvert
    #   nbformat
trove-classifiers==2023.10.18
    # via validate-pyproject
types-pkg-resources==0.1.3
    # via efaar-benchmarking (pyproject.toml)
types-python-dateutil==2.8.19.14
    # via arrow
types-setuptools==68.2.0.0
    # via efaar-benchmarking (pyproject.toml)
typing-extensions==4.8.0
    # via
    #   async-lru
    #   black
    #   chex
    #   etils
    #   fastapi
    #   flax
    #   lightning
    #   lightning-utilities
    #   mypy
    #   orbax-checkpoint
    #   pydantic
    #   pydantic-core
    #   pytorch-lightning
    #   torch
    #   uvicorn
tzdata==2023.3
    # via pandas
umap-learn==0.5.4
    # via scanpy
uri-template==1.3.0
    # via jsonschema
urllib3==2.0.7
    # via
    #   botocore
    #   lightning
    #   lightning-cloud
    #   requests
uvicorn==0.23.2
    # via
    #   lightning
    #   lightning-cloud
validate-pyproject[all]==0.15
    # via efaar-benchmarking (pyproject.toml)
virtualenv==20.24.6
    # via
    #   pre-commit
    #   tox
wcwidth==0.2.8
    # via
    #   blessed
    #   prompt-toolkit
webcolors==1.13
    # via jsonschema
webencodings==0.5.1
    # via
    #   bleach
    #   tinycss2
websocket-client==1.6.4
    # via
    #   jupyter-server
    #   lightning
    #   lightning-cloud
websockets==12.0
    # via lightning
wget==3.2
    # via efaar-benchmarking (pyproject.toml)
wrapt==1.15.0
    # via aiobotocore
xarray==2023.10.1
    # via scvi-tools
yarl==1.9.2
    # via aiohttp
zipp==3.17.0
    # via etils

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