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requirements-dev.lock
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# generated by rye
# use `rye lock` or `rye sync` to update this lockfile
#
# last locked with the following flags:
# pre: false
# features: []
# all-features: true
# with-sources: false
# generate-hashes: false
# universal: false
-e file:.
accessible-pygments==0.0.5
# via pydata-sphinx-theme
aiobotocore==2.13.3
# via s3fs
aiofiles==24.1.0
# via vitessce
aiohappyeyeballs==2.4.0
# via aiohttp
aiohttp==3.10.5
# via aiobotocore
# via jupyter-server-proxy
# via ome-zarr
# via s3fs
aioitertools==0.11.0
# via aiobotocore
aiosignal==1.3.1
# via aiohttp
alabaster==1.0.0
# via sphinx
anndata==0.10.8
# via angelolab-vitessce
# via scanpy
# via vitessce
anyio==4.4.0
# via jupyter-server
anywidget==0.9.13
# via vitessce
appnope==0.1.4
# via ipykernel
argon2-cffi==23.1.0
# via jupyter-server
argon2-cffi-bindings==21.2.0
# via argon2-cffi
array-api-compat==1.8
# via anndata
arrow==1.3.0
# via isoduration
asciitree==0.3.3
# via zarr
asttokens==2.4.1
# via stack-data
attrs==24.2.0
# via aiohttp
# via jsonschema
# via jupyter-cache
# via referencing
babel==2.16.0
# via pydata-sphinx-theme
# via sphinx
backports-tarfile==1.2.0
# via jaraco-context
beautifulsoup4==4.12.3
# via nbconvert
# via pydata-sphinx-theme
black==24.8.0
# via vitessce
bleach==6.1.0
# via nbconvert
bokeh==3.5.1
# via dask
botocore==1.34.162
# via aiobotocore
buckaroo==0.6.12
# via angelolab-vitessce
certifi==2024.7.4
# via requests
cffi==1.17.0
# via argon2-cffi-bindings
cfgv==3.4.0
# via pre-commit
charset-normalizer==3.3.2
# via requests
click==8.1.7
# via black
# via dask
# via distributed
# via jupyter-cache
# via uvicorn
cloudpickle==3.0.0
# via dask
# via distributed
comm==0.2.2
# via ipykernel
# via ipywidgets
contourpy==1.2.1
# via bokeh
# via matplotlib
coverage==7.6.1
# via angelolab-vitessce
cycler==0.12.1
# via matplotlib
dask==2024.8.1
# via angelolab-vitessce
# via dask-expr
# via dask-image
# via distributed
# via ome-zarr
dask-expr==1.1.11
# via dask
dask-image==2024.5.3
# via angelolab-vitessce
debugpy==1.8.5
# via ipykernel
decorator==5.1.1
# via ipython
defusedxml==0.7.1
# via nbconvert
distlib==0.3.8
# via virtualenv
distributed==2024.8.1
# via dask
# via ome-zarr
docutils==0.21.2
# via angelolab-vitessce
# via myst-parser
# via pybtex-docutils
# via pydata-sphinx-theme
# via readme-renderer
# via sphinx
# via sphinxcontrib-bibtex
esbuild-py==0.1.5
# via vitessce
executing==2.0.1
# via stack-data
fasteners==0.19
# via zarr
fastjsonschema==2.20.0
# via nbformat
filelock==3.15.4
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fonttools==4.53.1
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fqdn==1.5.1
# via jsonschema
frozenlist==1.4.1
# via aiohttp
# via aiosignal
fsspec==2024.6.1
# via dask
# via ome-zarr
# via s3fs
# via universal-pathlib
generate-tiff-offsets==0.1.7
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graphlib-backport==1.1.0
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h11==0.14.0
# via uvicorn
h5py==3.11.0
# via anndata
# via scanpy
identify==2.6.0
# via pre-commit
idna==3.7
# via anyio
# via jsonschema
# via requests
# via yarl
imageio==2.35.1
# via pims
# via scikit-image
imagesize==1.4.1
# via sphinx
importlib-metadata==8.4.0
# via dask
# via jupyter-cache
# via keyring
# via myst-nb
# via twine
iniconfig==2.0.0
# via pytest
ipykernel==6.29.5
# via angelolab-vitessce
# via myst-nb
ipython==8.26.0
# via angelolab-vitessce
# via ipykernel
# via ipywidgets
# via myst-nb
ipywidgets==8.1.5
# via anywidget
# via buckaroo
isoduration==20.11.0
# via jsonschema
jaraco-classes==3.4.0
# via keyring
jaraco-context==6.0.1
# via keyring
jaraco-functools==4.0.2
# via keyring
jedi==0.19.1
# via ipython
jinja2==3.1.4
# via bokeh
# via dask
# via distributed
# via jupyter-server
# via myst-parser
# via nbconvert
# via sphinx
jmespath==1.0.1
# via botocore
joblib==1.4.2
# via pynndescent
# via scanpy
# via scikit-learn
jsonpointer==3.0.0
# via jsonschema
jsonschema==4.23.0
# via jupyter-events
# via nbformat
# via vitessce
jsonschema-specifications==2023.12.1
# via jsonschema
jupyter-cache==1.0.0
# via myst-nb
jupyter-client==8.6.2
# via ipykernel
# via jupyter-server
# via nbclient
jupyter-core==5.7.2
# via ipykernel
# via jupyter-client
# via jupyter-server
# via nbclient
# via nbconvert
# via nbformat
jupyter-events==0.10.0
# via jupyter-server
jupyter-server==2.14.2
# via jupyter-server-proxy
jupyter-server-proxy==4.3.0
# via vitessce
jupyter-server-terminals==0.5.3
# via jupyter-server
jupyterlab-pygments==0.3.0
# via nbconvert
jupyterlab-widgets==3.0.13
# via ipywidgets
keyring==25.3.0
# via twine
kiwisolver==1.4.5
# via matplotlib
latexcodec==3.0.0
# via pybtex
lazy-loader==0.4
# via scikit-image
legacy-api-wrap==1.4
# via scanpy
llvmlite==0.43.0
# via numba
# via pynndescent
locket==1.0.0
# via distributed
# via partd
lz4==4.3.3
# via dask
markdown-it-py==3.0.0
# via mdit-py-plugins
# via myst-parser
# via rich
markupsafe==2.1.5
# via jinja2
# via nbconvert
matplotlib==3.9.2
# via scanpy
# via seaborn
matplotlib-inline==0.1.7
# via ipykernel
# via ipython
mdit-py-plugins==0.4.1
# via myst-parser
mdurl==0.1.2
# via markdown-it-py
mistune==3.0.2
# via nbconvert
more-itertools==10.4.0
# via jaraco-classes
# via jaraco-functools
msgpack==1.0.8
# via distributed
multidict==6.0.5
# via aiohttp
# via yarl
mypy-extensions==1.0.0
# via black
myst-nb==1.1.1
# via angelolab-vitessce
myst-parser==4.0.0
# via myst-nb
natsort==8.4.0
# via anndata
# via scanpy
nbclient==0.10.0
# via jupyter-cache
# via myst-nb
# via nbconvert
nbconvert==7.16.4
# via jupyter-server
nbformat==5.10.4
# via jupyter-cache
# via jupyter-server
# via myst-nb
# via nbclient
# via nbconvert
negspy==0.2.24
# via vitessce
nest-asyncio==1.6.0
# via ipykernel
networkx==3.3
# via scanpy
# via scikit-image
nh3==0.2.18
# via readme-renderer
nodeenv==1.9.1
# via pre-commit
numba==0.60.0
# via pynndescent
# via scanpy
# via umap-learn
numcodecs==0.13.0
# via vitessce
# via zarr
numpy==1.26.4
# via anndata
# via bokeh
# via contourpy
# via dask
# via dask-image
# via h5py
# via imageio
# via matplotlib
# via numba
# via numcodecs
# via ome-zarr
# via pandas
# via patsy
# via pims
# via pyarrow
# via pywavelets
# via scanpy
# via scikit-image
# via scikit-learn
# via scipy
# via seaborn
# via statsmodels
# via tifffile
# via umap-learn
# via vitessce
# via zarr
ome-zarr==0.8.3
# via vitessce
overrides==7.7.0
# via jupyter-server
packaging==24.1
# via anndata
# via black
# via bokeh
# via buckaroo
# via dask
# via distributed
# via ipykernel
# via jupyter-server
# via lazy-loader
# via matplotlib
# via nbconvert
# via pims
# via pydata-sphinx-theme
# via pytest
# via scanpy
# via scikit-image
# via sphinx
# via statsmodels
pandas==2.2.2
# via angelolab-vitessce
# via anndata
# via bokeh
# via dask
# via dask-expr
# via dask-image
# via scanpy
# via seaborn
# via statsmodels
# via vitessce
pandocfilters==1.5.1
# via nbconvert
parso==0.8.4
# via jedi
partd==1.4.2
# via dask
pathspec==0.12.1
# via black
patsy==0.5.6
# via scanpy
# via statsmodels
pexpect==4.9.0
# via ipython
pillow==10.4.0
# via bokeh
# via imageio
# via matplotlib
# via scikit-image
pims==0.7
# via dask-image
pkginfo==1.10.0
# via twine
platformdirs==4.2.2
# via black
# via jupyter-core
# via virtualenv
pluggy==1.5.0
# via pytest
pre-commit==3.8.0
# via angelolab-vitessce
prometheus-client==0.20.0
# via jupyter-server
prompt-toolkit==3.0.47
# via ipython
psutil==6.0.0
# via distributed
# via ipykernel
psygnal==0.11.1
# via anywidget
ptyprocess==0.7.0
# via pexpect
# via terminado
pure-eval==0.2.3
# via stack-data
pyarrow==17.0.0
# via dask
# via dask-expr
pyarrow-hotfix==0.6
# via dask
pybtex==0.24.0
# via pybtex-docutils
# via sphinxcontrib-bibtex
pybtex-docutils==1.0.3
# via sphinxcontrib-bibtex
pycparser==2.22
# via cffi
pydata-sphinx-theme==0.15.4
# via sphinx-book-theme
pygments==2.18.0
# via accessible-pygments
# via ipython
# via nbconvert
# via pydata-sphinx-theme
# via readme-renderer
# via rich
# via sphinx
pynndescent==0.5.13
# via scanpy
# via umap-learn
pyparsing==3.1.2
# via matplotlib
pytest==8.3.2
# via angelolab-vitessce
python-dateutil==2.9.0.post0
# via arrow
# via botocore
# via jupyter-client
# via matplotlib
# via pandas
python-json-logger==2.0.7
# via jupyter-events
pytz==2024.1
# via pandas
pywavelets==1.7.0
# via scikit-image
pyyaml==6.0.2
# via bokeh
# via dask
# via distributed
# via jupyter-cache
# via jupyter-events
# via myst-nb
# via myst-parser
# via pre-commit
# via pybtex
pyzmq==26.2.0
# via ipykernel
# via jupyter-client
# via jupyter-server
readme-renderer==44.0
# via twine
referencing==0.35.1
# via jsonschema
# via jsonschema-specifications
# via jupyter-events
requests==2.32.3
# via ome-zarr
# via requests-toolbelt
# via sphinx
# via twine
requests-toolbelt==1.0.0
# via twine
rfc3339-validator==0.1.4
# via jsonschema
# via jupyter-events
rfc3986==2.0.0
# via twine
rfc3986-validator==0.1.1
# via jsonschema
# via jupyter-events
rich==13.7.1
# via twine
rpds-py==0.20.0
# via jsonschema
# via referencing
s3fs==2024.6.1
# via fsspec
scanpy==1.10.2
# via vitessce
scikit-image==0.20.0
# via ome-zarr
scikit-learn==1.5.1
# via pynndescent
# via scanpy
# via umap-learn
scipy==1.14.1
# via anndata
# via dask-image
# via pynndescent
# via scanpy
# via scikit-image
# via scikit-learn
# via statsmodels
# via umap-learn
# via vitessce
seaborn==0.13.2
# via scanpy
send2trash==1.8.3
# via jupyter-server
session-info==1.0.0
# via angelolab-vitessce
# via scanpy
setuptools==73.0.1
# via angelolab-vitessce
simpervisor==1.0.0
# via jupyter-server-proxy
six==1.16.0
# via asttokens
# via bleach
# via patsy
# via pybtex
# via python-dateutil
# via rfc3339-validator
slicerator==1.1.0
# via pims
sniffio==1.3.1
# via anyio
snowballstemmer==2.2.0
# via sphinx
sortedcontainers==2.4.0
# via distributed
soupsieve==2.6
# via beautifulsoup4
sphinx==8.0.2
# via angelolab-vitessce
# via myst-nb
# via myst-parser
# via pydata-sphinx-theme
# via sphinx-autodoc-typehints
# via sphinx-book-theme
# via sphinx-copybutton
# via sphinxcontrib-bibtex
# via sphinxext-opengraph
sphinx-autodoc-typehints==2.2.3
# via angelolab-vitessce
sphinx-book-theme==1.1.3
# via angelolab-vitessce
sphinx-copybutton==0.5.2
# via angelolab-vitessce
sphinxcontrib-applehelp==2.0.0
# via sphinx
sphinxcontrib-bibtex==2.6.2
# via angelolab-vitessce
sphinxcontrib-devhelp==2.0.0
# via sphinx
sphinxcontrib-htmlhelp==2.1.0
# via sphinx
sphinxcontrib-jsmath==1.0.1
# via sphinx
sphinxcontrib-qthelp==2.0.0
# via sphinx
sphinxcontrib-serializinghtml==2.0.0
# via sphinx
sphinxext-opengraph==0.9.1
# via angelolab-vitessce
sqlalchemy==2.0.32
# via jupyter-cache
stack-data==0.6.3
# via ipython
starlette==0.14.0
# via vitessce
statsmodels==0.14.2
# via scanpy
stdlib-list==0.10.0
# via session-info
tabulate==0.9.0
# via jupyter-cache
tblib==3.0.0
# via distributed
terminado==0.18.1
# via jupyter-server
# via jupyter-server-terminals
threadpoolctl==3.5.0
# via scikit-learn
tifffile==2020.10.1
# via dask-image
# via generate-tiff-offsets
# via pims
# via scikit-image
# via vitessce
tinycss2==1.3.0
# via nbconvert
toolz==0.12.1
# via dask
# via distributed
# via ome-zarr
# via partd
tornado==6.4.1
# via bokeh
# via distributed
# via ipykernel
# via jupyter-client
# via jupyter-server
# via jupyter-server-proxy
# via terminado
tqdm==4.66.5
# via scanpy
# via umap-learn
# via vitessce
traitlets==5.14.3
# via comm
# via ipykernel
# via ipython
# via ipywidgets
# via jupyter-client
# via jupyter-core
# via jupyter-events
# via jupyter-server
# via jupyter-server-proxy
# via matplotlib-inline
# via nbclient
# via nbconvert
# via nbformat
twine==5.1.1
# via angelolab-vitessce
types-python-dateutil==2.9.0.20240821
# via arrow
typing-extensions==4.12.2
# via anywidget
# via ipython
# via myst-nb
# via pydata-sphinx-theme
# via sqlalchemy
tzdata==2024.1
# via pandas
ujson==5.10.0
# via vitessce
umap-learn==0.5.6
# via scanpy
universal-pathlib==0.2.2
# via angelolab-vitessce
uri-template==1.3.0
# via jsonschema
urllib3==2.2.2
# via botocore
# via distributed
# via requests
# via twine
uvicorn==0.30.6
# via vitessce
virtualenv==20.26.3
# via pre-commit
vitessce==3.3.1
# via angelolab-vitessce
wcwidth==0.2.13
# via prompt-toolkit
webcolors==24.8.0
# via jsonschema
webencodings==0.5.1
# via bleach
# via tinycss2
websocket-client==1.8.0
# via jupyter-server
widgetsnbextension==4.0.13
# via ipywidgets
wrapt==1.16.0
# via aiobotocore
xyzservices==2024.6.0
# via bokeh
yarl==1.9.4
# via aiohttp
zarr==2.18.2
# via ome-zarr
# via vitessce
zict==3.0.0
# via distributed
zipp==3.20.0
# via importlib-metadata