absl-py==2.0.0
    # via
    #   chex
    #   ml-collections
    #   optax
    #   orbax-checkpoint
aiobotocore==2.13.1
    # via s3fs
aiohttp==3.9.2
    # via
    #   aiobotocore
    #   fsspec
    #   s3fs
aioitertools==0.11.0
    # via aiobotocore
aiosignal==1.3.1
    # via aiohttp
anndata==0.10.3
    # via
    #   mudata
    #   scvi-tools
anyio==4.2.0
    # via jupyter-server
appnope==0.1.3
    # via ipykernel
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
asttokens==2.4.1
    # via stack-data
async-lru==2.0.4
    # via jupyterlab
attrs==23.1.0
    # via
    #   aiohttp
    #   jsonschema
    #   referencing
babel==2.14.0
    # via jupyterlab-server
bandit[toml]==1.7.6
    # via efaar_benchmarking (pyproject.toml)
beautifulsoup4==4.12.2
    # via nbconvert
black==23.12.1
    # via efaar_benchmarking (pyproject.toml)
bleach==6.1.0
    # via nbconvert
botocore==1.34.131
    # via aiobotocore
cachetools==5.3.2
    # via tox
certifi==2023.11.17
    # 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==3.3.2
    # via requests
chex==0.1.8
    # via optax
click==8.1.7
    # via
    #   black
    #   docstr-coverage
colorama==0.4.6
    # via
    #   radon
    #   tox
comm==0.2.0
    # via ipykernel
contextlib2==21.6.0
    # via ml-collections
contourpy==1.2.0
    # via matplotlib
coverage[toml]==7.4.0
    # via
    #   efaar_benchmarking (pyproject.toml)
    #   pytest-cov
cycler==0.12.1
    # via matplotlib
debugpy==1.8.0
    # via ipykernel
decorator==5.1.1
    # via ipython
defusedxml==0.7.1
    # via nbconvert
distlib==0.3.8
    # 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]==1.6.0
    # via orbax-checkpoint
executing==2.0.1
    # via stack-data
fastjsonschema==2.19.1
    # via
    #   nbformat
    #   validate-pyproject
filelock==3.13.1
    # via
    #   torch
    #   tox
    #   virtualenv
flake8==6.1.0
    # via efaar_benchmarking (pyproject.toml)
flax==0.7.5
    # via scvi-tools
fonttools==4.47.0
    # via matplotlib
fqdn==1.5.1
    # via jsonschema
frozenlist==1.4.1
    # via
    #   aiohttp
    #   aiosignal
fsspec[http]==2023.12.2
    # via
    #   etils
    #   lightning
    #   pytorch-lightning
    #   s3fs
    #   torch
geomloss==0.2.6
    # via efaar_benchmarking (pyproject.toml)
gitdb==4.0.11
    # via gitpython
gitpython==3.1.41
    # via bandit
h5py==3.10.0
    # via
    #   anndata
    #   mudata
    #   scvi-tools
identify==2.5.33
    # via pre-commit
idna==3.6
    # via
    #   anyio
    #   jsonschema
    #   requests
    #   yarl
importlib-resources==6.1.1
    # via etils
iniconfig==2.0.0
    # via pytest
ipykernel==6.28.0
    # via jupyterlab
ipython==8.19.0
    # via ipykernel
isoduration==20.11.0
    # via jsonschema
isort==5.13.2
    # via efaar_benchmarking (pyproject.toml)
jax==0.4.23
    # via
    #   chex
    #   flax
    #   numpyro
    #   optax
    #   orbax-checkpoint
    #   scvi-tools
jaxlib==0.4.23
    # via
    #   chex
    #   numpyro
    #   optax
    #   orbax-checkpoint
    #   scvi-tools
jedi==0.19.1
    # via ipython
jinja2==3.1.3
    # via
    #   jupyter-server
    #   jupyterlab
    #   jupyterlab-server
    #   nbconvert
    #   torch
jmespath==1.0.1
    # via botocore
joblib==1.3.2
    # via
    #   efaar_benchmarking (pyproject.toml)
    #   scikit-learn
json5==0.9.14
    # via jupyterlab-server
jsonpointer==2.4
    # via jsonschema
jsonschema[format-nongpl]==4.20.0
    # via
    #   jupyter-events
    #   jupyterlab-server
    #   nbformat
jsonschema-specifications==2023.12.1
    # via jsonschema
jupyter-client==8.6.0
    # via
    #   ipykernel
    #   jupyter-server
    #   nbclient
jupyter-core==5.6.0
    # via
    #   ipykernel
    #   jupyter-client
    #   jupyter-server
    #   jupyterlab
    #   nbclient
    #   nbconvert
    #   nbformat
jupyter-events==0.9.0
    # via jupyter-server
jupyter-lsp==2.2.2
    # via jupyterlab
jupyter-server==2.12.1
    # via
    #   jupyter-lsp
    #   jupyterlab
    #   jupyterlab-server
    #   notebook-shim
jupyter-server-terminals==0.5.1
    # via jupyter-server
jupyterlab==4.0.11
    # via efaar_benchmarking (pyproject.toml)
jupyterlab-pygments==0.3.0
    # via nbconvert
jupyterlab-server==2.25.2
    # via jupyterlab
kiwisolver==1.4.5
    # via matplotlib
lightning==2.1.3
    # via scvi-tools
lightning-utilities==0.10.0
    # via
    #   lightning
    #   pytorch-lightning
    #   torchmetrics
mando==0.7.1
    # via radon
markdown-it-py==3.0.0
    # via rich
markupsafe==2.1.3
    # via
    #   jinja2
    #   nbconvert
matplotlib==3.8.2
    # via
    #   efaar_benchmarking (pyproject.toml)
    #   matplotlib-venn
    #   seaborn
matplotlib-inline==0.1.6
    # via
    #   ipykernel
    #   ipython
matplotlib-venn==0.11.10
    # via efaar_benchmarking (pyproject.toml)
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==1.8.0
    # via efaar_benchmarking (pyproject.toml)
mypy-extensions==1.0.0
    # via
    #   black
    #   mypy
natsort==8.4.0
    # via anndata
nbclient==0.9.0
    # via nbconvert
nbconvert==7.13.1
    # via jupyter-server
nbformat==5.9.2
    # via
    #   jupyter-server
    #   nbclient
    #   nbconvert
nest-asyncio==1.5.8
    # via
    #   ipykernel
    #   orbax-checkpoint
networkx==3.2.1
    # via torch
nodeenv==1.8.0
    # via pre-commit
notebook-shim==0.2.3
    # via jupyterlab
numpy==1.26.2
    # via
    #   anndata
    #   chex
    #   contourpy
    #   efaar_benchmarking (pyproject.toml)
    #   flax
    #   geomloss
    #   h5py
    #   jax
    #   jaxlib
    #   lightning
    #   matplotlib
    #   matplotlib-venn
    #   ml-dtypes
    #   mudata
    #   numpyro
    #   opt-einsum
    #   optax
    #   orbax-checkpoint
    #   pandas
    #   pyro-ppl
    #   pytorch-lightning
    #   scikit-learn
    #   scipy
    #   scvi-tools
    #   seaborn
    #   tensorstore
    #   torchmetrics
numpyro==0.13.2
    # via scvi-tools
opt-einsum==3.3.0
    # via
    #   jax
    #   pyro-ppl
optax==0.1.7
    # via
    #   flax
    #   scvi-tools
orbax-checkpoint==0.4.8
    # via flax
overrides==7.4.0
    # via jupyter-server
packaging==23.2
    # via
    #   anndata
    #   black
    #   ipykernel
    #   jupyter-server
    #   jupyterlab
    #   jupyterlab-server
    #   lightning
    #   lightning-utilities
    #   matplotlib
    #   nbconvert
    #   plotly
    #   pyproject-api
    #   pytest
    #   pytorch-lightning
    #   torchmetrics
    #   tox
    #   validate-pyproject
pandas==2.1.4
    # via
    #   anndata
    #   efaar_benchmarking (pyproject.toml)
    #   mudata
    #   scvi-tools
    #   seaborn
pandocfilters==1.5.0
    # via nbconvert
parso==0.8.3
    # via jedi
pathspec==0.12.1
    # via black
pbr==6.0.0
    # via stevedore
pexpect==4.9.0
    # via ipython
pillow==10.3.0
    # via matplotlib
platformdirs==4.1.0
    # via
    #   black
    #   jupyter-core
    #   tox
    #   virtualenv
plotly==5.22.0
    # via upsetplotly
pluggy==1.3.0
    # via
    #   pytest
    #   tox
pre-commit==3.6.0
    # via efaar_benchmarking (pyproject.toml)
prometheus-client==0.19.0
    # via jupyter-server
prompt-toolkit==3.0.43
    # via ipython
protobuf==4.25.1
    # via orbax-checkpoint
psutil==5.9.7
    # via ipykernel
ptyprocess==0.7.0
    # via
    #   pexpect
    #   terminado
pure-eval==0.2.2
    # via stack-data
pycodestyle==2.11.1
    # via flake8
pycparser==2.21
    # via cffi
pyflakes==3.1.0
    # via flake8
pygments==2.17.2
    # via
    #   ipython
    #   nbconvert
    #   rich
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==7.4.3
    # 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
    #   jupyter-client
    #   matplotlib
    #   pandas
python-json-logger==2.0.7
    # via jupyter-events
pytorch-lightning==2.1.3
    # via lightning
pytz==2023.3.post1
    # via 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==25.1.2
    # via
    #   ipykernel
    #   jupyter-client
    #   jupyter-server
radon==6.0.1
    # via efaar_benchmarking (pyproject.toml)
referencing==0.32.0
    # via
    #   jsonschema
    #   jsonschema-specifications
    #   jupyter-events
requests==2.31.0
    # via
    #   fsspec
    #   jupyterlab-server
rfc3339-validator==0.1.4
    # via
    #   jsonschema
    #   jupyter-events
rfc3986-validator==0.1.1
    # via
    #   jsonschema
    #   jupyter-events
rich==13.7.0
    # via
    #   bandit
    #   flax
    #   scvi-tools
rpds-py==0.16.2
    # via
    #   jsonschema
    #   referencing
s3fs==2023.12.2
    # via efaar_benchmarking (pyproject.toml)
scikit-learn==1.3.2
    # via
    #   efaar_benchmarking (pyproject.toml)
    #   scvi-tools
scipy==1.11.4
    # via
    #   anndata
    #   efaar_benchmarking (pyproject.toml)
    #   jax
    #   jaxlib
    #   matplotlib-venn
    #   scikit-learn
    #   scvi-tools
scvi-tools==1.1.2
    # via efaar_benchmarking (pyproject.toml)
seaborn==0.12.2
    # via efaar_benchmarking (pyproject.toml)
send2trash==1.8.2
    # via jupyter-server
setuptools==70.0.0
    # via
    #   lightning-utilities
    #   nodeenv
six==1.16.0
    # via
    #   asttokens
    #   bleach
    #   docrep
    #   mando
    #   ml-collections
    #   python-dateutil
    #   rfc3339-validator
smmap==5.0.1
    # via gitdb
sniffio==1.3.0
    # via anyio
soupsieve==2.5
    # via beautifulsoup4
stack-data==0.6.3
    # via ipython
stevedore==5.1.0
    # via bandit
sympy==1.12
    # via torch
tenacity==8.3.0
    # via plotly
tensorstore==0.1.51
    # via
    #   flax
    #   orbax-checkpoint
terminado==0.18.0
    # via
    #   jupyter-server
    #   jupyter-server-terminals
threadpoolctl==3.2.0
    # via scikit-learn
tinycss2==1.2.1
    # via nbconvert
tokenize-rt==5.2.0
    # via pyupgrade
toolz==0.12.0
    # via chex
torch==2.1.2
    # via
    #   efaar_benchmarking (pyproject.toml)
    #   geomloss
    #   lightning
    #   pyro-ppl
    #   pytorch-lightning
    #   scvi-tools
    #   torchmetrics
torchmetrics==1.2.1
    # via
    #   lightning
    #   pytorch-lightning
    #   scvi-tools
tornado==6.4
    # via
    #   ipykernel
    #   jupyter-client
    #   jupyter-server
    #   jupyterlab
    #   terminado
tox==4.11.4
    # via efaar_benchmarking (pyproject.toml)
tqdm==4.63.1
    # via
    #   docstr-coverage
    #   lightning
    #   numpyro
    #   pyro-ppl
    #   pytorch-lightning
    #   scvi-tools
    #   upsetplotly
traitlets==5.14.0
    # via
    #   comm
    #   ipykernel
    #   ipython
    #   jupyter-client
    #   jupyter-core
    #   jupyter-events
    #   jupyter-server
    #   jupyterlab
    #   matplotlib-inline
    #   nbclient
    #   nbconvert
    #   nbformat
trove-classifiers==2023.11.29
    # 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==69.0.0.0
    # via efaar_benchmarking (pyproject.toml)
typing-extensions==4.9.0
    # via
    #   chex
    #   etils
    #   flax
    #   lightning
    #   lightning-utilities
    #   mypy
    #   orbax-checkpoint
    #   pytorch-lightning
    #   torch
tzdata==2023.4
    # via pandas
upsetplotly==0.1.7
    # via efaar_benchmarking (pyproject.toml)
uri-template==1.3.0
    # via jsonschema
urllib3==2.0.7
    # via
    #   botocore
    #   requests
validate-pyproject[all]==0.15
    # via efaar_benchmarking (pyproject.toml)
virtualenv==20.25.0
    # via
    #   pre-commit
    #   tox
wcwidth==0.2.12
    # via prompt-toolkit
webcolors==1.13
    # via jsonschema
webencodings==0.5.1
    # via
    #   bleach
    #   tinycss2
websocket-client==1.7.0
    # via jupyter-server
wget==3.2
    # via efaar_benchmarking (pyproject.toml)
wrapt==1.16.0
    # via aiobotocore
yarl==1.9.4
    # via aiohttp
zipp==3.17.0
    # via etils
