From 415213c8049e75ad781634565ec6c227bedc3660 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Wed, 18 Mar 2026 17:14:16 +0000 Subject: [PATCH] Updating requirements.txt after change to `uv.lock` was pushed to `main` --- requirements/linux/requirements.txt | 270 +++++++++++++------------- requirements/macos/requirements.txt | 270 +++++++++++++------------- requirements/windows/requirements.txt | 270 +++++++++++++------------- 3 files changed, 405 insertions(+), 405 deletions(-) diff --git a/requirements/linux/requirements.txt b/requirements/linux/requirements.txt index 9e648b015..34a5c7883 100644 --- a/requirements/linux/requirements.txt +++ b/requirements/linux/requirements.txt @@ -5,60 +5,56 @@ alabaster==1.0.0 # via sphinx annotated-types==0.7.0 # via pydantic -anyio==4.10.0 +anyio==4.12.1 # via httpx appnope==0.1.4 ; sys_platform == 'darwin' # via ipykernel -asttokens==3.0.0 +asttokens==3.0.1 # via stack-data -babel==2.17.0 +babel==2.18.0 # via sphinx -bioio==3.0.0 +bioio==3.2.0 # via cellpack -bioio-base==3.0.0 +bioio-base==3.2.0 # via # bioio # bioio-ome-tiff bioio-ome-tiff==1.4.0 # via cellpack -black==25.1.0 -boto3==1.40.19 +black==26.3.1 +boto3==1.42.69 # via # cellpack # moto -botocore==1.40.19 +botocore==1.42.69 # via # boto3 # moto # s3transfer bumpver==2025.1131 -cachecontrol==0.14.3 +cachecontrol==0.14.4 # via firebase-admin -cachetools==5.5.2 - # via - # google-auth - # tox -certifi==2025.8.3 +cachetools==7.0.5 + # via tox +certifi==2026.2.25 # via # httpcore # httpx # requests -cffi==1.17.1 +cffi==2.0.0 # via # cryptography # pymunk # pyzmq -chardet==5.2.0 - # via tox -charset-normalizer==3.4.3 +charset-normalizer==3.4.6 # via requests -click==8.2.1 +click==8.3.1 # via # black # bumpver # dask # distributed -cloudpickle==3.1.1 +cloudpickle==3.1.2 # via # dask # distributed @@ -75,48 +71,48 @@ comm==0.2.3 # via ipykernel contourpy==1.3.3 # via matplotlib -coverage==7.10.5 +coverage==7.13.5 # via pytest-cov -crc32c==2.7.1 - # via numcodecs -cryptography==45.0.6 +cryptography==46.0.5 # via + # google-auth # moto # pyjwt cycler==0.12.1 # via matplotlib -dask==2025.9.1 +dask==2026.1.2 # via # bioio # bioio-base # bioio-ome-tiff # distributed -debugpy==1.8.16 +debugpy==1.8.20 # via ipykernel decorator==5.2.1 # via ipython distlib==0.4.0 # via virtualenv -distributed==2025.9.1 +distributed==2026.1.2 # via dask -docutils==0.21.2 +docutils==0.22.4 # via # myst-parser # sphinx # sphinx-rtd-theme donfig==0.8.1.post1 # via zarr -elementpath==5.0.4 +elementpath==5.1.1 # via xmlschema -executing==2.2.0 +executing==2.2.1 # via stack-data -filelock==3.19.1 +filelock==3.25.2 # via + # python-discovery # tox # virtualenv fire==0.7.1 # via cellpack -firebase-admin==7.1.0 +firebase-admin==7.2.0 # via cellpack flake8==7.3.0 # via flake8-debugger @@ -125,51 +121,53 @@ flexcache==0.3 # via pint flexparser==0.4 # via pint -fonttools==4.59.2 +fonttools==4.62.1 # via matplotlib -fsspec==2025.9.0 +fsspec==2026.2.0 # via # bioio-base # bioio-ome-tiff # dask # kerchunk # tifffile -google-api-core==2.25.1 +google-api-core==2.30.0 # via # firebase-admin # google-cloud-core # google-cloud-firestore # google-cloud-storage -google-auth==2.40.3 +google-auth==2.49.1 # via # google-api-core # google-cloud-core # google-cloud-firestore # google-cloud-storage -google-cloud-core==2.4.3 +google-cloud-core==2.5.0 # via # google-cloud-firestore # google-cloud-storage -google-cloud-firestore==2.21.0 ; platform_python_implementation != 'PyPy' +google-cloud-firestore==2.25.0 ; platform_python_implementation != 'PyPy' # via firebase-admin -google-cloud-storage==3.3.0 +google-cloud-storage==3.9.0 # via firebase-admin -google-crc32c==1.7.1 +google-crc32c==1.8.0 # via # google-cloud-storage # google-resumable-media -google-resumable-media==2.7.2 + # zarr +google-resumable-media==2.8.0 # via google-cloud-storage -googleapis-common-protos==1.70.0 +googleapis-common-protos==1.73.0 # via # google-api-core # grpcio-status -grpcio==1.74.0 +grpcio==1.78.0 # via # cellpack # google-api-core + # google-cloud-firestore # grpcio-status -grpcio-status==1.74.0 +grpcio-status==1.78.0 # via google-api-core h11==0.16.0 # via httpcore @@ -183,21 +181,21 @@ httpx==0.28.1 # via firebase-admin hyperframe==6.1.0 # via h2 -idna==3.10 +idna==3.11 # via # anyio # httpx # requests -imagecodecs==2025.8.2 +imagecodecs==2026.3.6 # via bioio-ome-tiff -imagesize==1.4.1 +imagesize==2.0.0 # via sphinx -importlib-metadata==8.7.0 +importlib-metadata==8.7.1 # via dask -iniconfig==2.1.0 +iniconfig==2.3.0 # via pytest -ipykernel==6.30.1 -ipython==9.4.0 +ipykernel==7.2.0 +ipython==9.10.0 # via ipykernel ipython-pygments-lexers==1.1.1 # via ipython @@ -209,40 +207,40 @@ jinja2==3.1.6 # moto # myst-parser # sphinx -jmespath==1.0.1 +jmespath==1.1.0 # via # boto3 # botocore -jupyter-client==8.6.3 +jupyter-client==8.8.0 # via ipykernel -jupyter-core==5.8.1 +jupyter-core==5.9.1 # via # ipykernel # jupyter-client kerchunk==0.2.9 # via tifffile -kiwisolver==1.4.9 +kiwisolver==1.5.0 # via matplotlib lexid==2021.1006 # via bumpver -linkify-it-py==2.0.3 +linkify-it-py==2.1.0 locket==1.0.0 # via # distributed # partd lxml==6.0.2 # via ome-types -markdown-it-py==3.0.0 +markdown-it-py==4.0.0 # via # mdit-py-plugins # myst-parser -markupsafe==3.0.2 +markupsafe==3.0.3 # via # jinja2 # werkzeug -matplotlib==3.10.5 +matplotlib==3.10.8 # via cellpack -matplotlib-inline==0.1.7 +matplotlib-inline==0.2.1 # via # ipykernel # ipython @@ -252,25 +250,25 @@ mdit-py-plugins==0.5.0 # via myst-parser mdurl==0.1.2 # via markdown-it-py -mdutils==1.8.0 +mdutils==1.8.1 # via cellpack -moto==5.1.11 -msgpack==1.1.1 +moto==5.1.22 +msgpack==1.1.2 # via # cachecontrol # distributed mypy-extensions==1.1.0 # via black -myst-parser==4.0.1 -narwhals==2.2.0 +myst-parser==5.0.0 +narwhals==2.18.0 # via plotly nest-asyncio==1.6.0 # via ipykernel -numcodecs==0.16.3 +numcodecs==0.16.5 # via # kerchunk # zarr -numpy==2.3.2 +numpy==2.4.3 # via # bioio # bioio-base @@ -290,12 +288,12 @@ numpy==2.3.2 # trimesh # xarray # zarr -ome-types==0.6.1 +ome-types==0.6.3 # via # bioio # bioio-base # bioio-ome-tiff -packaging==25.0 +packaging==26.0 # via # black # dask @@ -307,33 +305,38 @@ packaging==25.0 # pytest # sphinx # tox + # wheel # xarray # zarr -pandas==2.3.2 +pandas==3.0.1 # via # cellpack # simulariumio # xarray -parso==0.8.5 +parso==0.8.6 # via jedi partd==1.4.2 # via dask -pathspec==0.12.1 +pathspec==1.0.4 # via black pexpect==4.9.0 ; sys_platform != 'emscripten' and sys_platform != 'win32' # via ipython -pillow==11.3.0 +pillow==12.1.1 # via matplotlib -pint==0.25 - # via simulariumio -platformdirs==4.4.0 +pint==0.25.2 + # via + # bioio-base + # ome-types + # simulariumio +platformdirs==4.9.4 # via # black # jupyter-core # pint + # python-discovery # tox # virtualenv -plotly==6.3.0 +plotly==6.6.0 # via cellpack pluggy==1.6.0 # via @@ -342,18 +345,18 @@ pluggy==1.6.0 # tox prompt-toolkit==3.0.52 # via ipython -proto-plus==1.26.1 +proto-plus==1.27.1 # via # google-api-core # google-cloud-firestore -protobuf==6.32.0 +protobuf==6.33.5 # via # google-api-core # google-cloud-firestore # googleapis-common-protos # grpcio-status # proto-plus -psutil==7.0.0 +psutil==7.2.2 # via # distributed # ipykernel @@ -361,28 +364,26 @@ ptyprocess==0.7.0 ; sys_platform != 'emscripten' and sys_platform != 'win32' # via pexpect pure-eval==0.2.3 # via stack-data -pyasn1==0.6.1 - # via - # pyasn1-modules - # rsa +pyasn1==0.6.3 + # via pyasn1-modules pyasn1-modules==0.4.2 # via google-auth pycodestyle==2.14.0 # via # flake8 # flake8-debugger -pycollada==0.9.2 +pycollada==0.9.3 # via cellpack -pycparser==2.22 +pycparser==3.0 ; implementation_name != 'PyPy' # via cffi -pydantic==2.11.9 +pydantic==2.12.5 # via # bioio-ome-tiff # ome-types # pydantic-extra-types -pydantic-core==2.33.2 +pydantic-core==2.41.5 # via pydantic -pydantic-extra-types==2.10.5 +pydantic-extra-types==2.11.1 # via ome-types pyflakes==3.4.0 # via flake8 @@ -392,19 +393,19 @@ pygments==2.19.2 # ipython-pygments-lexers # pytest # sphinx -pyjwt==2.10.1 +pyjwt==2.12.1 # via firebase-admin -pymunk==7.1.0 +pymunk==7.2.0 # via cellpack -pyparsing==3.2.3 +pyparsing==3.3.2 # via matplotlib -pyproject-api==1.9.1 +pyproject-api==1.10.0 # via tox -pytest==8.4.1 +pytest==9.0.2 # via # pytest-cov # pytest-raises -pytest-cov==6.2.1 +pytest-cov==7.0.0 pytest-raises==0.11 python-dateutil==2.9.0.post0 # via @@ -414,13 +415,13 @@ python-dateutil==2.9.0.post0 # moto # pandas # pycollada -python-dotenv==1.1.1 +python-discovery==1.1.3 + # via virtualenv +python-dotenv==1.2.2 # via cellpack -pytz==2025.2 - # via pandas -pywin32==311 ; platform_python_implementation != 'PyPy' and sys_platform == 'win32' - # via jupyter-core -pyyaml==6.0.2 +pytokens==0.4.1 + # via black +pyyaml==6.0.3 # via # bioio-ome-tiff # dask @@ -428,7 +429,7 @@ pyyaml==6.0.2 # donfig # myst-parser # responses -pyzmq==27.0.2 +pyzmq==27.1.0 # via # ipykernel # jupyter-client @@ -440,17 +441,15 @@ requests==2.32.5 # moto # responses # sphinx -responses==0.25.8 +responses==0.26.0 # via moto -roman-numerals-py==3.1.0 +roman-numerals==4.1.0 # via sphinx -rsa==4.9.1 - # via google-auth rtree==1.4.1 # via cellpack -s3transfer==0.13.1 +s3transfer==0.16.0 # via boto3 -scipy==1.16.1 +scipy==1.17.1 # via cellpack semver==3.0.4 # via bioio @@ -458,18 +457,16 @@ simulariumio==1.13.0 # via cellpack six==1.17.0 # via python-dateutil -sniffio==1.3.1 - # via anyio snowballstemmer==3.0.1 # via sphinx sortedcontainers==2.4.0 # via distributed -sphinx==8.2.3 +sphinx==9.0.4 # via # myst-parser # sphinx-rtd-theme # sphinxcontrib-jquery -sphinx-rtd-theme==3.0.2 +sphinx-rtd-theme==3.1.0 sphinxcontrib-applehelp==2.0.0 # via sphinx sphinxcontrib-devhelp==2.0.0 @@ -486,28 +483,30 @@ sphinxcontrib-serializinghtml==2.0.0 # via sphinx stack-data==0.6.3 # via ipython -tblib==3.1.0 +tblib==3.2.2 # via distributed -termcolor==3.1.0 +termcolor==3.3.0 # via fire -tifffile==2025.9.20 +tifffile==2026.3.3 # via bioio-ome-tiff toml==0.10.2 # via bumpver -tomli==2.2.1 ; python_full_version <= '3.11' +tomli==2.4.0 ; python_full_version <= '3.11' # via coverage -toolz==1.0.0 +tomli-w==1.2.0 + # via tox +toolz==1.1.0 # via # dask # distributed # partd -tornado==6.5.2 +tornado==6.5.5 # via # distributed # ipykernel # jupyter-client -tox==4.27.0 -tqdm==4.67.1 +tox==4.50.0 +tqdm==4.67.3 # via cellpack traitlets==5.14.3 # via @@ -516,13 +515,14 @@ traitlets==5.14.3 # jupyter-client # jupyter-core # matplotlib-inline -trimesh==4.7.4 +trimesh==4.11.3 # via cellpack typing-extensions==4.15.0 # via # anyio # flexcache # flexparser + # grpcio # ipython # numcodecs # pint @@ -532,38 +532,38 @@ typing-extensions==4.15.0 # typing-inspection # xsdata # zarr -typing-inspection==0.4.1 +typing-inspection==0.4.2 # via pydantic -tzdata==2025.2 +tzdata==2025.3 ; sys_platform == 'emscripten' or sys_platform == 'win32' # via pandas -uc-micro-py==1.0.3 +uc-micro-py==2.0.0 # via linkify-it-py -ujson==5.11.0 +ujson==5.12.0 # via kerchunk -urllib3==2.5.0 +urllib3==2.6.3 # via # botocore # distributed # requests # responses -virtualenv==20.34.0 +virtualenv==21.2.0 # via tox -wcwidth==0.2.13 +wcwidth==0.6.0 # via prompt-toolkit -werkzeug==3.1.3 +werkzeug==3.1.6 # via moto -wheel==0.45.1 -xarray==2025.9.0 +wheel==0.46.3 +xarray==2026.2.0 # via # bioio-base # bioio-ome-tiff -xmlschema==4.1.0 +xmlschema==4.3.1 # via bioio-ome-tiff -xmltodict==0.14.2 +xmltodict==1.0.4 # via moto -xsdata==24.3.1 +xsdata==26.2 # via ome-types -zarr==3.1.3 +zarr==3.1.5 # via # kerchunk # tifffile diff --git a/requirements/macos/requirements.txt b/requirements/macos/requirements.txt index 81e319ed7..9277df9ff 100644 --- a/requirements/macos/requirements.txt +++ b/requirements/macos/requirements.txt @@ -5,60 +5,56 @@ alabaster==1.0.0 # via sphinx annotated-types==0.7.0 # via pydantic -anyio==4.10.0 +anyio==4.12.1 # via httpx appnope==0.1.4 ; sys_platform == 'darwin' # via ipykernel -asttokens==3.0.0 +asttokens==3.0.1 # via stack-data -babel==2.17.0 +babel==2.18.0 # via sphinx -bioio==3.0.0 +bioio==3.2.0 # via cellpack -bioio-base==3.0.0 +bioio-base==3.2.0 # via # bioio # bioio-ome-tiff bioio-ome-tiff==1.4.0 # via cellpack -black==25.1.0 -boto3==1.40.19 +black==26.3.1 +boto3==1.42.69 # via # cellpack # moto -botocore==1.40.19 +botocore==1.42.69 # via # boto3 # moto # s3transfer bumpver==2025.1131 -cachecontrol==0.14.3 +cachecontrol==0.14.4 # via firebase-admin -cachetools==5.5.2 - # via - # google-auth - # tox -certifi==2025.8.3 +cachetools==7.0.5 + # via tox +certifi==2026.2.25 # via # httpcore # httpx # requests -cffi==1.17.1 +cffi==2.0.0 # via # cryptography # pymunk # pyzmq -chardet==5.2.0 - # via tox -charset-normalizer==3.4.3 +charset-normalizer==3.4.6 # via requests -click==8.2.1 +click==8.3.1 # via # black # bumpver # dask # distributed -cloudpickle==3.1.1 +cloudpickle==3.1.2 # via # dask # distributed @@ -75,48 +71,48 @@ comm==0.2.3 # via ipykernel contourpy==1.3.3 # via matplotlib -coverage==7.10.5 +coverage==7.13.5 # via pytest-cov -crc32c==2.7.1 - # via numcodecs -cryptography==45.0.6 +cryptography==46.0.5 # via + # google-auth # moto # pyjwt cycler==0.12.1 # via matplotlib -dask==2025.9.1 +dask==2026.1.2 # via # bioio # bioio-base # bioio-ome-tiff # distributed -debugpy==1.8.16 +debugpy==1.8.20 # via ipykernel decorator==5.2.1 # via ipython distlib==0.4.0 # via virtualenv -distributed==2025.9.1 +distributed==2026.1.2 # via dask -docutils==0.21.2 +docutils==0.22.4 # via # myst-parser # sphinx # sphinx-rtd-theme donfig==0.8.1.post1 # via zarr -elementpath==5.0.4 +elementpath==5.1.1 # via xmlschema -executing==2.2.0 +executing==2.2.1 # via stack-data -filelock==3.19.1 +filelock==3.25.2 # via + # python-discovery # tox # virtualenv fire==0.7.1 # via cellpack -firebase-admin==7.1.0 +firebase-admin==7.2.0 # via cellpack flake8==7.3.0 # via flake8-debugger @@ -125,51 +121,53 @@ flexcache==0.3 # via pint flexparser==0.4 # via pint -fonttools==4.59.2 +fonttools==4.62.1 # via matplotlib -fsspec==2025.9.0 +fsspec==2026.2.0 # via # bioio-base # bioio-ome-tiff # dask # kerchunk # tifffile -google-api-core==2.25.1 +google-api-core==2.30.0 # via # firebase-admin # google-cloud-core # google-cloud-firestore # google-cloud-storage -google-auth==2.40.3 +google-auth==2.49.1 # via # google-api-core # google-cloud-core # google-cloud-firestore # google-cloud-storage -google-cloud-core==2.4.3 +google-cloud-core==2.5.0 # via # google-cloud-firestore # google-cloud-storage -google-cloud-firestore==2.21.0 ; platform_python_implementation != 'PyPy' +google-cloud-firestore==2.25.0 ; platform_python_implementation != 'PyPy' # via firebase-admin -google-cloud-storage==3.3.0 +google-cloud-storage==3.9.0 # via firebase-admin -google-crc32c==1.7.1 +google-crc32c==1.8.0 # via # google-cloud-storage # google-resumable-media -google-resumable-media==2.7.2 + # zarr +google-resumable-media==2.8.0 # via google-cloud-storage -googleapis-common-protos==1.70.0 +googleapis-common-protos==1.73.0 # via # google-api-core # grpcio-status -grpcio==1.74.0 +grpcio==1.78.0 # via # cellpack # google-api-core + # google-cloud-firestore # grpcio-status -grpcio-status==1.74.0 +grpcio-status==1.78.0 # via google-api-core h11==0.16.0 # via httpcore @@ -183,21 +181,21 @@ httpx==0.28.1 # via firebase-admin hyperframe==6.1.0 # via h2 -idna==3.10 +idna==3.11 # via # anyio # httpx # requests -imagecodecs==2025.8.2 +imagecodecs==2026.3.6 # via bioio-ome-tiff -imagesize==1.4.1 +imagesize==2.0.0 # via sphinx -importlib-metadata==8.7.0 +importlib-metadata==8.7.1 # via dask -iniconfig==2.1.0 +iniconfig==2.3.0 # via pytest -ipykernel==6.30.1 -ipython==9.4.0 +ipykernel==7.2.0 +ipython==9.10.0 # via ipykernel ipython-pygments-lexers==1.1.1 # via ipython @@ -209,40 +207,40 @@ jinja2==3.1.6 # moto # myst-parser # sphinx -jmespath==1.0.1 +jmespath==1.1.0 # via # boto3 # botocore -jupyter-client==8.6.3 +jupyter-client==8.8.0 # via ipykernel -jupyter-core==5.8.1 +jupyter-core==5.9.1 # via # ipykernel # jupyter-client kerchunk==0.2.9 # via tifffile -kiwisolver==1.4.9 +kiwisolver==1.5.0 # via matplotlib lexid==2021.1006 # via bumpver -linkify-it-py==2.0.3 +linkify-it-py==2.1.0 locket==1.0.0 # via # distributed # partd lxml==6.0.2 # via ome-types -markdown-it-py==3.0.0 +markdown-it-py==4.0.0 # via # mdit-py-plugins # myst-parser -markupsafe==3.0.2 +markupsafe==3.0.3 # via # jinja2 # werkzeug -matplotlib==3.10.5 +matplotlib==3.10.8 # via cellpack -matplotlib-inline==0.1.7 +matplotlib-inline==0.2.1 # via # ipykernel # ipython @@ -252,25 +250,25 @@ mdit-py-plugins==0.5.0 # via myst-parser mdurl==0.1.2 # via markdown-it-py -mdutils==1.8.0 +mdutils==1.8.1 # via cellpack -moto==5.1.11 -msgpack==1.1.1 +moto==5.1.22 +msgpack==1.1.2 # via # cachecontrol # distributed mypy-extensions==1.1.0 # via black -myst-parser==4.0.1 -narwhals==2.2.0 +myst-parser==5.0.0 +narwhals==2.18.0 # via plotly nest-asyncio==1.6.0 # via ipykernel -numcodecs==0.16.3 +numcodecs==0.16.5 # via # kerchunk # zarr -numpy==2.3.2 +numpy==2.4.3 # via # bioio # bioio-base @@ -290,12 +288,12 @@ numpy==2.3.2 # trimesh # xarray # zarr -ome-types==0.6.1 +ome-types==0.6.3 # via # bioio # bioio-base # bioio-ome-tiff -packaging==25.0 +packaging==26.0 # via # black # dask @@ -307,33 +305,38 @@ packaging==25.0 # pytest # sphinx # tox + # wheel # xarray # zarr -pandas==2.3.2 +pandas==3.0.1 # via # cellpack # simulariumio # xarray -parso==0.8.5 +parso==0.8.6 # via jedi partd==1.4.2 # via dask -pathspec==0.12.1 +pathspec==1.0.4 # via black pexpect==4.9.0 ; sys_platform != 'emscripten' and sys_platform != 'win32' # via ipython -pillow==11.3.0 +pillow==12.1.1 # via matplotlib -pint==0.25 - # via simulariumio -platformdirs==4.4.0 +pint==0.25.2 + # via + # bioio-base + # ome-types + # simulariumio +platformdirs==4.9.4 # via # black # jupyter-core # pint + # python-discovery # tox # virtualenv -plotly==6.3.0 +plotly==6.6.0 # via cellpack pluggy==1.6.0 # via @@ -342,18 +345,18 @@ pluggy==1.6.0 # tox prompt-toolkit==3.0.52 # via ipython -proto-plus==1.26.1 +proto-plus==1.27.1 # via # google-api-core # google-cloud-firestore -protobuf==6.32.0 +protobuf==6.33.5 # via # google-api-core # google-cloud-firestore # googleapis-common-protos # grpcio-status # proto-plus -psutil==7.0.0 +psutil==7.2.2 # via # distributed # ipykernel @@ -361,28 +364,26 @@ ptyprocess==0.7.0 ; sys_platform != 'emscripten' and sys_platform != 'win32' # via pexpect pure-eval==0.2.3 # via stack-data -pyasn1==0.6.1 - # via - # pyasn1-modules - # rsa +pyasn1==0.6.3 + # via pyasn1-modules pyasn1-modules==0.4.2 # via google-auth pycodestyle==2.14.0 # via # flake8 # flake8-debugger -pycollada==0.9.2 +pycollada==0.9.3 # via cellpack -pycparser==2.22 +pycparser==3.0 ; implementation_name != 'PyPy' # via cffi -pydantic==2.11.9 +pydantic==2.12.5 # via # bioio-ome-tiff # ome-types # pydantic-extra-types -pydantic-core==2.33.2 +pydantic-core==2.41.5 # via pydantic -pydantic-extra-types==2.10.5 +pydantic-extra-types==2.11.1 # via ome-types pyflakes==3.4.0 # via flake8 @@ -392,19 +393,19 @@ pygments==2.19.2 # ipython-pygments-lexers # pytest # sphinx -pyjwt==2.10.1 +pyjwt==2.12.1 # via firebase-admin -pymunk==7.1.0 +pymunk==7.2.0 # via cellpack -pyparsing==3.2.3 +pyparsing==3.3.2 # via matplotlib -pyproject-api==1.9.1 +pyproject-api==1.10.0 # via tox -pytest==8.4.1 +pytest==9.0.2 # via # pytest-cov # pytest-raises -pytest-cov==6.2.1 +pytest-cov==7.0.0 pytest-raises==0.11 python-dateutil==2.9.0.post0 # via @@ -414,13 +415,13 @@ python-dateutil==2.9.0.post0 # moto # pandas # pycollada -python-dotenv==1.1.1 +python-discovery==1.1.3 + # via virtualenv +python-dotenv==1.2.2 # via cellpack -pytz==2025.2 - # via pandas -pywin32==311 ; platform_python_implementation != 'PyPy' and sys_platform == 'win32' - # via jupyter-core -pyyaml==6.0.2 +pytokens==0.4.1 + # via black +pyyaml==6.0.3 # via # bioio-ome-tiff # dask @@ -428,7 +429,7 @@ pyyaml==6.0.2 # donfig # myst-parser # responses -pyzmq==27.0.2 +pyzmq==27.1.0 # via # ipykernel # jupyter-client @@ -440,17 +441,15 @@ requests==2.32.5 # moto # responses # sphinx -responses==0.25.8 +responses==0.26.0 # via moto -roman-numerals-py==3.1.0 +roman-numerals==4.1.0 # via sphinx -rsa==4.9.1 - # via google-auth rtree==1.4.1 # via cellpack -s3transfer==0.13.1 +s3transfer==0.16.0 # via boto3 -scipy==1.16.1 +scipy==1.17.1 # via cellpack semver==3.0.4 # via bioio @@ -458,18 +457,16 @@ simulariumio==1.13.0 # via cellpack six==1.17.0 # via python-dateutil -sniffio==1.3.1 - # via anyio snowballstemmer==3.0.1 # via sphinx sortedcontainers==2.4.0 # via distributed -sphinx==8.2.3 +sphinx==9.0.4 # via # myst-parser # sphinx-rtd-theme # sphinxcontrib-jquery -sphinx-rtd-theme==3.0.2 +sphinx-rtd-theme==3.1.0 sphinxcontrib-applehelp==2.0.0 # via sphinx sphinxcontrib-devhelp==2.0.0 @@ -486,28 +483,30 @@ sphinxcontrib-serializinghtml==2.0.0 # via sphinx stack-data==0.6.3 # via ipython -tblib==3.1.0 +tblib==3.2.2 # via distributed -termcolor==3.1.0 +termcolor==3.3.0 # via fire -tifffile==2025.9.20 +tifffile==2026.3.3 # via bioio-ome-tiff toml==0.10.2 # via bumpver -tomli==2.2.1 ; python_full_version <= '3.11' +tomli==2.4.0 ; python_full_version <= '3.11' # via coverage -toolz==1.0.0 +tomli-w==1.2.0 + # via tox +toolz==1.1.0 # via # dask # distributed # partd -tornado==6.5.2 +tornado==6.5.5 # via # distributed # ipykernel # jupyter-client -tox==4.27.0 -tqdm==4.67.1 +tox==4.50.0 +tqdm==4.67.3 # via cellpack traitlets==5.14.3 # via @@ -516,13 +515,14 @@ traitlets==5.14.3 # jupyter-client # jupyter-core # matplotlib-inline -trimesh==4.7.4 +trimesh==4.11.3 # via cellpack typing-extensions==4.15.0 # via # anyio # flexcache # flexparser + # grpcio # ipython # numcodecs # pint @@ -532,38 +532,38 @@ typing-extensions==4.15.0 # typing-inspection # xsdata # zarr -typing-inspection==0.4.1 +typing-inspection==0.4.2 # via pydantic -tzdata==2025.2 +tzdata==2025.3 ; sys_platform == 'emscripten' or sys_platform == 'win32' # via pandas -uc-micro-py==1.0.3 +uc-micro-py==2.0.0 # via linkify-it-py -ujson==5.11.0 +ujson==5.12.0 # via kerchunk -urllib3==2.5.0 +urllib3==2.6.3 # via # botocore # distributed # requests # responses -virtualenv==20.34.0 +virtualenv==21.2.0 # via tox -wcwidth==0.2.13 +wcwidth==0.6.0 # via prompt-toolkit -werkzeug==3.1.3 +werkzeug==3.1.6 # via moto -wheel==0.45.1 -xarray==2025.9.0 +wheel==0.46.3 +xarray==2026.2.0 # via # bioio-base # bioio-ome-tiff -xmlschema==4.1.0 +xmlschema==4.3.1 # via bioio-ome-tiff -xmltodict==0.14.2 +xmltodict==1.0.4 # via moto -xsdata==24.3.1 +xsdata==26.2 # via ome-types -zarr==3.1.3 +zarr==3.1.5 # via # kerchunk # tifffile diff --git a/requirements/windows/requirements.txt b/requirements/windows/requirements.txt index 3ceddc6f6..302ea01f0 100644 --- a/requirements/windows/requirements.txt +++ b/requirements/windows/requirements.txt @@ -5,60 +5,56 @@ alabaster==1.0.0 # via sphinx annotated-types==0.7.0 # via pydantic -anyio==4.10.0 +anyio==4.12.1 # via httpx appnope==0.1.4 ; sys_platform == 'darwin' # via ipykernel -asttokens==3.0.0 +asttokens==3.0.1 # via stack-data -babel==2.17.0 +babel==2.18.0 # via sphinx -bioio==3.0.0 +bioio==3.2.0 # via cellpack -bioio-base==3.0.0 +bioio-base==3.2.0 # via # bioio # bioio-ome-tiff bioio-ome-tiff==1.4.0 # via cellpack -black==25.1.0 -boto3==1.40.19 +black==26.3.1 +boto3==1.42.69 # via # cellpack # moto -botocore==1.40.19 +botocore==1.42.69 # via # boto3 # moto # s3transfer bumpver==2025.1131 -cachecontrol==0.14.3 +cachecontrol==0.14.4 # via firebase-admin -cachetools==5.5.2 - # via - # google-auth - # tox -certifi==2025.8.3 +cachetools==7.0.5 + # via tox +certifi==2026.2.25 # via # httpcore # httpx # requests -cffi==1.17.1 +cffi==2.0.0 # via # cryptography # pymunk # pyzmq -chardet==5.2.0 - # via tox -charset-normalizer==3.4.3 +charset-normalizer==3.4.6 # via requests -click==8.2.1 +click==8.3.1 # via # black # bumpver # dask # distributed -cloudpickle==3.1.1 +cloudpickle==3.1.2 # via # dask # distributed @@ -75,48 +71,48 @@ comm==0.2.3 # via ipykernel contourpy==1.3.3 # via matplotlib -coverage==7.10.5 +coverage==7.13.5 # via pytest-cov -crc32c==2.7.1 - # via numcodecs -cryptography==45.0.6 +cryptography==46.0.5 # via + # google-auth # moto # pyjwt cycler==0.12.1 # via matplotlib -dask==2025.9.1 +dask==2026.1.2 # via # bioio # bioio-base # bioio-ome-tiff # distributed -debugpy==1.8.16 +debugpy==1.8.20 # via ipykernel decorator==5.2.1 # via ipython distlib==0.4.0 # via virtualenv -distributed==2025.9.1 +distributed==2026.1.2 # via dask -docutils==0.21.2 +docutils==0.22.4 # via # myst-parser # sphinx # sphinx-rtd-theme donfig==0.8.1.post1 # via zarr -elementpath==5.0.4 +elementpath==5.1.1 # via xmlschema -executing==2.2.0 +executing==2.2.1 # via stack-data -filelock==3.19.1 +filelock==3.25.2 # via + # python-discovery # tox # virtualenv fire==0.7.1 # via cellpack -firebase-admin==7.1.0 +firebase-admin==7.2.0 # via cellpack flake8==7.3.0 # via flake8-debugger @@ -125,51 +121,53 @@ flexcache==0.3 # via pint flexparser==0.4 # via pint -fonttools==4.59.2 +fonttools==4.62.1 # via matplotlib -fsspec==2025.9.0 +fsspec==2026.2.0 # via # bioio-base # bioio-ome-tiff # dask # kerchunk # tifffile -google-api-core==2.25.1 +google-api-core==2.30.0 # via # firebase-admin # google-cloud-core # google-cloud-firestore # google-cloud-storage -google-auth==2.40.3 +google-auth==2.49.1 # via # google-api-core # google-cloud-core # google-cloud-firestore # google-cloud-storage -google-cloud-core==2.4.3 +google-cloud-core==2.5.0 # via # google-cloud-firestore # google-cloud-storage -google-cloud-firestore==2.21.0 ; platform_python_implementation != 'PyPy' +google-cloud-firestore==2.25.0 ; platform_python_implementation != 'PyPy' # via firebase-admin -google-cloud-storage==3.3.0 +google-cloud-storage==3.9.0 # via firebase-admin -google-crc32c==1.7.1 +google-crc32c==1.8.0 # via # google-cloud-storage # google-resumable-media -google-resumable-media==2.7.2 + # zarr +google-resumable-media==2.8.0 # via google-cloud-storage -googleapis-common-protos==1.70.0 +googleapis-common-protos==1.73.0 # via # google-api-core # grpcio-status -grpcio==1.74.0 +grpcio==1.78.0 # via # cellpack # google-api-core + # google-cloud-firestore # grpcio-status -grpcio-status==1.74.0 +grpcio-status==1.78.0 # via google-api-core h11==0.16.0 # via httpcore @@ -183,21 +181,21 @@ httpx==0.28.1 # via firebase-admin hyperframe==6.1.0 # via h2 -idna==3.10 +idna==3.11 # via # anyio # httpx # requests -imagecodecs==2025.8.2 +imagecodecs==2026.3.6 # via bioio-ome-tiff -imagesize==1.4.1 +imagesize==2.0.0 # via sphinx -importlib-metadata==8.7.0 +importlib-metadata==8.7.1 # via dask -iniconfig==2.1.0 +iniconfig==2.3.0 # via pytest -ipykernel==6.30.1 -ipython==9.4.0 +ipykernel==7.2.0 +ipython==9.10.0 # via ipykernel ipython-pygments-lexers==1.1.1 # via ipython @@ -209,40 +207,40 @@ jinja2==3.1.6 # moto # myst-parser # sphinx -jmespath==1.0.1 +jmespath==1.1.0 # via # boto3 # botocore -jupyter-client==8.6.3 +jupyter-client==8.8.0 # via ipykernel -jupyter-core==5.8.1 +jupyter-core==5.9.1 # via # ipykernel # jupyter-client kerchunk==0.2.9 # via tifffile -kiwisolver==1.4.9 +kiwisolver==1.5.0 # via matplotlib lexid==2021.1006 # via bumpver -linkify-it-py==2.0.3 +linkify-it-py==2.1.0 locket==1.0.0 # via # distributed # partd lxml==6.0.2 # via ome-types -markdown-it-py==3.0.0 +markdown-it-py==4.0.0 # via # mdit-py-plugins # myst-parser -markupsafe==3.0.2 +markupsafe==3.0.3 # via # jinja2 # werkzeug -matplotlib==3.10.5 +matplotlib==3.10.8 # via cellpack -matplotlib-inline==0.1.7 +matplotlib-inline==0.2.1 # via # ipykernel # ipython @@ -252,25 +250,25 @@ mdit-py-plugins==0.5.0 # via myst-parser mdurl==0.1.2 # via markdown-it-py -mdutils==1.8.0 +mdutils==1.8.1 # via cellpack -moto==5.1.11 -msgpack==1.1.1 +moto==5.1.22 +msgpack==1.1.2 # via # cachecontrol # distributed mypy-extensions==1.1.0 # via black -myst-parser==4.0.1 -narwhals==2.2.0 +myst-parser==5.0.0 +narwhals==2.18.0 # via plotly nest-asyncio==1.6.0 # via ipykernel -numcodecs==0.16.3 +numcodecs==0.16.5 # via # kerchunk # zarr -numpy==2.3.2 +numpy==2.4.3 # via # bioio # bioio-base @@ -290,12 +288,12 @@ numpy==2.3.2 # trimesh # xarray # zarr -ome-types==0.6.1 +ome-types==0.6.3 # via # bioio # bioio-base # bioio-ome-tiff -packaging==25.0 +packaging==26.0 # via # black # dask @@ -307,33 +305,38 @@ packaging==25.0 # pytest # sphinx # tox + # wheel # xarray # zarr -pandas==2.3.2 +pandas==3.0.1 # via # cellpack # simulariumio # xarray -parso==0.8.5 +parso==0.8.6 # via jedi partd==1.4.2 # via dask -pathspec==0.12.1 +pathspec==1.0.4 # via black pexpect==4.9.0 ; sys_platform != 'emscripten' and sys_platform != 'win32' # via ipython -pillow==11.3.0 +pillow==12.1.1 # via matplotlib -pint==0.25 - # via simulariumio -platformdirs==4.4.0 +pint==0.25.2 + # via + # bioio-base + # ome-types + # simulariumio +platformdirs==4.9.4 # via # black # jupyter-core # pint + # python-discovery # tox # virtualenv -plotly==6.3.0 +plotly==6.6.0 # via cellpack pluggy==1.6.0 # via @@ -342,18 +345,18 @@ pluggy==1.6.0 # tox prompt-toolkit==3.0.52 # via ipython -proto-plus==1.26.1 +proto-plus==1.27.1 # via # google-api-core # google-cloud-firestore -protobuf==6.32.0 +protobuf==6.33.5 # via # google-api-core # google-cloud-firestore # googleapis-common-protos # grpcio-status # proto-plus -psutil==7.0.0 +psutil==7.2.2 # via # distributed # ipykernel @@ -361,28 +364,26 @@ ptyprocess==0.7.0 ; sys_platform != 'emscripten' and sys_platform != 'win32' # via pexpect pure-eval==0.2.3 # via stack-data -pyasn1==0.6.1 - # via - # pyasn1-modules - # rsa +pyasn1==0.6.3 + # via pyasn1-modules pyasn1-modules==0.4.2 # via google-auth pycodestyle==2.14.0 # via # flake8 # flake8-debugger -pycollada==0.9.2 +pycollada==0.9.3 # via cellpack -pycparser==2.22 +pycparser==3.0 ; implementation_name != 'PyPy' # via cffi -pydantic==2.11.9 +pydantic==2.12.5 # via # bioio-ome-tiff # ome-types # pydantic-extra-types -pydantic-core==2.33.2 +pydantic-core==2.41.5 # via pydantic -pydantic-extra-types==2.10.5 +pydantic-extra-types==2.11.1 # via ome-types pyflakes==3.4.0 # via flake8 @@ -392,19 +393,19 @@ pygments==2.19.2 # ipython-pygments-lexers # pytest # sphinx -pyjwt==2.10.1 +pyjwt==2.12.1 # via firebase-admin -pymunk==7.1.0 +pymunk==7.2.0 # via cellpack -pyparsing==3.2.3 +pyparsing==3.3.2 # via matplotlib -pyproject-api==1.9.1 +pyproject-api==1.10.0 # via tox -pytest==8.4.1 +pytest==9.0.2 # via # pytest-cov # pytest-raises -pytest-cov==6.2.1 +pytest-cov==7.0.0 pytest-raises==0.11 python-dateutil==2.9.0.post0 # via @@ -414,13 +415,13 @@ python-dateutil==2.9.0.post0 # moto # pandas # pycollada -python-dotenv==1.1.1 +python-discovery==1.1.3 + # via virtualenv +python-dotenv==1.2.2 # via cellpack -pytz==2025.2 - # via pandas -pywin32==311 ; platform_python_implementation != 'PyPy' and sys_platform == 'win32' - # via jupyter-core -pyyaml==6.0.2 +pytokens==0.4.1 + # via black +pyyaml==6.0.3 # via # bioio-ome-tiff # dask @@ -428,7 +429,7 @@ pyyaml==6.0.2 # donfig # myst-parser # responses -pyzmq==27.0.2 +pyzmq==27.1.0 # via # ipykernel # jupyter-client @@ -440,17 +441,15 @@ requests==2.32.5 # moto # responses # sphinx -responses==0.25.8 +responses==0.26.0 # via moto -roman-numerals-py==3.1.0 +roman-numerals==4.1.0 # via sphinx -rsa==4.9.1 - # via google-auth rtree==1.4.1 # via cellpack -s3transfer==0.13.1 +s3transfer==0.16.0 # via boto3 -scipy==1.16.1 +scipy==1.17.1 # via cellpack semver==3.0.4 # via bioio @@ -458,18 +457,16 @@ simulariumio==1.13.0 # via cellpack six==1.17.0 # via python-dateutil -sniffio==1.3.1 - # via anyio snowballstemmer==3.0.1 # via sphinx sortedcontainers==2.4.0 # via distributed -sphinx==8.2.3 +sphinx==9.0.4 # via # myst-parser # sphinx-rtd-theme # sphinxcontrib-jquery -sphinx-rtd-theme==3.0.2 +sphinx-rtd-theme==3.1.0 sphinxcontrib-applehelp==2.0.0 # via sphinx sphinxcontrib-devhelp==2.0.0 @@ -486,28 +483,30 @@ sphinxcontrib-serializinghtml==2.0.0 # via sphinx stack-data==0.6.3 # via ipython -tblib==3.1.0 +tblib==3.2.2 # via distributed -termcolor==3.1.0 +termcolor==3.3.0 # via fire -tifffile==2025.9.20 +tifffile==2026.3.3 # via bioio-ome-tiff toml==0.10.2 # via bumpver -tomli==2.2.1 ; python_full_version <= '3.11' +tomli==2.4.0 ; python_full_version <= '3.11' # via coverage -toolz==1.0.0 +tomli-w==1.2.0 + # via tox +toolz==1.1.0 # via # dask # distributed # partd -tornado==6.5.2 +tornado==6.5.5 # via # distributed # ipykernel # jupyter-client -tox==4.27.0 -tqdm==4.67.1 +tox==4.50.0 +tqdm==4.67.3 # via cellpack traitlets==5.14.3 # via @@ -516,13 +515,14 @@ traitlets==5.14.3 # jupyter-client # jupyter-core # matplotlib-inline -trimesh==4.7.4 +trimesh==4.11.3 # via cellpack typing-extensions==4.15.0 # via # anyio # flexcache # flexparser + # grpcio # ipython # numcodecs # pint @@ -532,38 +532,38 @@ typing-extensions==4.15.0 # typing-inspection # xsdata # zarr -typing-inspection==0.4.1 +typing-inspection==0.4.2 # via pydantic -tzdata==2025.2 +tzdata==2025.3 ; sys_platform == 'emscripten' or sys_platform == 'win32' # via pandas -uc-micro-py==1.0.3 +uc-micro-py==2.0.0 # via linkify-it-py -ujson==5.11.0 +ujson==5.12.0 # via kerchunk -urllib3==2.5.0 +urllib3==2.6.3 # via # botocore # distributed # requests # responses -virtualenv==20.34.0 +virtualenv==21.2.0 # via tox -wcwidth==0.2.13 +wcwidth==0.6.0 # via prompt-toolkit -werkzeug==3.1.3 +werkzeug==3.1.6 # via moto -wheel==0.45.1 -xarray==2025.9.0 +wheel==0.46.3 +xarray==2026.2.0 # via # bioio-base # bioio-ome-tiff -xmlschema==4.1.0 +xmlschema==4.3.1 # via bioio-ome-tiff -xmltodict==0.14.2 +xmltodict==1.0.4 # via moto -xsdata==24.3.1 +xsdata==26.2 # via ome-types -zarr==3.1.3 +zarr==3.1.5 # via # kerchunk # tifffile