From 61669e031e8fdb12a5f5aad379be9a531c33b128 Mon Sep 17 00:00:00 2001 From: ritvikvasan Date: Fri, 13 Oct 2023 00:44:20 +0000 Subject: [PATCH] Updating lock files and requirements --- requirements/linux/all-requirements.txt | 155 ++-- requirements/linux/docs-requirements.txt | 155 ++-- requirements/linux/equiv-requirements.txt | 131 ++- requirements/linux/omnipose-requirements.txt | 135 ++- requirements/linux/pdm.lock | 836 ++++++----------- requirements/linux/requirements.txt | 152 ++-- requirements/linux/spharm-requirements.txt | 127 ++- requirements/linux/test-requirements.txt | 156 ++-- .../linux/torchserve-requirements.txt | 127 ++- requirements/macos/all-requirements.txt | 150 ++-- requirements/macos/docs-requirements.txt | 150 ++-- requirements/macos/equiv-requirements.txt | 126 ++- requirements/macos/omnipose-requirements.txt | 130 ++- requirements/macos/pdm.lock | 831 ++++++----------- requirements/macos/requirements.txt | 124 +-- requirements/macos/spharm-requirements.txt | 122 +-- requirements/macos/test-requirements.txt | 151 ++-- .../macos/torchserve-requirements.txt | 122 +-- requirements/windows/all-requirements.txt | 152 ++-- requirements/windows/docs-requirements.txt | 152 ++-- requirements/windows/equiv-requirements.txt | 128 ++- .../windows/omnipose-requirements.txt | 132 ++- requirements/windows/pdm.lock | 838 ++++++------------ requirements/windows/requirements.txt | 126 +-- requirements/windows/spharm-requirements.txt | 124 +-- requirements/windows/test-requirements.txt | 153 ++-- .../windows/torchserve-requirements.txt | 124 +-- 27 files changed, 2203 insertions(+), 3606 deletions(-) diff --git a/requirements/linux/all-requirements.txt b/requirements/linux/all-requirements.txt index 90fe503c4..74717b82c 100644 --- a/requirements/linux/all-requirements.txt +++ b/requirements/linux/all-requirements.txt @@ -5,119 +5,108 @@ aicscytoparam==0.1.9 aicsimageio==4.11.0 aicsshparam==0.1.7 aiobotocore==2.4.2 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 autograd==1.6.2 autopage==0.5.1 -backoff==2.2.1 -beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 boto3==1.24.4 botocore==1.27.59 cellpose-omni==0.9.1 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 cmaes==0.10.0 -cmake==3.27.4.1 +cmake==3.27.6 cmd2==2.4.3 colorama==0.4.6 colorlog==6.7.0 -contourpy==1.1.0 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 Deprecated==1.2.14 distributed==2023.5.0 docker==6.1.3 e3nn==0.5.1 edt==2.3.1 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -escnn==1.0.7 -exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 +escnn==1.0.11 +fasteners==0.19 fastremap==1.14.0 -filelock==3.12.3 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 future==0.18.3 geomloss==0.2.6 gitdb==4.0.10 -gitpython==3.1.35 +gitpython==3.1.37 gorilla==0.4.0 -greenlet==2.0.2 +greenlet==3.0.0 gunicorn==21.2.0 -h11==0.14.0 -h5py==3.9.0 -huggingface-hub==0.16.4 +h5py==3.10.0 +huggingface-hub==0.17.3 humanize==4.8.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 -igraph==0.10.6 +igraph==0.11.2 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 importlib-metadata==6.8.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 lie-learn @ git+https://github.com/colobas/lie_learn.git@d5be2ab -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 -lit==16.0.6 -llvmlite==0.40.1 +lit==17.0.2 +llvmlite==0.41.0 locket==1.0.0 lxml==4.9.3 mahotas==1.4.13 Mako==1.2.4 -markdown==3.4.4 +markdown==3.5 markdown-it-py==3.0.0 MarkupSafe==2.1.3 -matplotlib==3.7.2 +matplotlib==3.7.3 mdurl==0.1.2 mgen==1.2.1 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 ncolor==1.2.1 networkx==3.1 nibabel==5.1.0 -Ninja==1.11.1 -numba==0.57.1 -numcodecs==0.11.0 +Ninja==1.11.1.1 +numba==0.58.0 +numcodecs==0.12.0 numpy==1.24.4 nvidia-cublas-cu11==11.10.3.66 nvidia-cuda-cupti-cu11==11.7.101 @@ -132,108 +121,98 @@ nvidia-nccl-cu11==2.14.3 nvidia-nvtx-cu11==11.7.91 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 omnipose @ git+https://github.com/kevinjohncutler/omnipose.git@ce2e9aa -opencv-python-headless==4.8.0.76 +opencv-python-headless==4.8.1.78 opt-einsum==3.3.0 opt-einsum-fx==0.1.4 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 peakdetect==1.2 -pillow==10.0.0 -platformdirs==3.10.0 -point-cloud-utils==0.29.6 +pillow==10.0.1 +platformdirs==3.11.0 +point-cloud-utils==0.30.0 pooch==1.7.0 -PrettyTable==3.8.0 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 -py3nj==0.2.1 +py3nj==0.1.2 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 +pydantic==2.4.2 +pydantic-core==2.10.1 pyerfa==2.0.0.3 pygments==2.16.1 pyjwt==2.8.0 -pymanopt==2.1.1 +pymanopt==2.2.0 pyntcloud==0.3.1 -pyparsing==3.0.9 +pyparsing==3.1.1 pyperclip==1.8.2 pyshtools==4.10.3 python-dateutil==2.8.2 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytorch-ranger==0.1.1 pytz==2023.3.post1 PyWavelets==1.4.1 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 +rich==13.6.0 s3fs==2023.3.0 s3transfer==0.6.2 -safetensors==0.3.3 +safetensors==0.4.0 scikit-image==0.21.0 -scikit-learn==1.3.0 -scipy==1.10.1 -setuptools==68.2.0 +scikit-learn==1.3.1 +scipy==1.9.3 +scyjava==1.9.1 +setuptools==68.2.2 shellingham==1.5.3 -SimpleITK==2.2.1 +SimpleITK==2.3.0 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 sortedcontainers==2.4.0 -soupsieve==2.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 tblib==2.0.0 termcolor==2.3.0 -texttable==1.6.7 +texttable==1.7.0 threadpoolctl==3.2.0 tifffile==2023.7.10 timm==0.9.7 toolz==0.12.0 torch==2.0.1 -torch-geometric==2.3.1 +torch-geometric==2.4.0 torch-optimizer==0.3.0 torchio==0.19.1 -torchmetrics==1.1.1 -torchserve==0.8.2 +torchmetrics==1.2.0 +torchserve==0.9.0 torchvf==0.1.3 torchvision==0.15.2 tornado==6.3.3 tqdm==4.66.1 -traitlets==5.9.0 triton==2.0.0 typer==0.9.0 -typing-extensions==4.7.1 +typing-extensions==4.8.0 universal-pathlib==0.1.3 -urllib3==1.26.16 -uvicorn==0.23.2 +urllib3==1.26.17 vtk==9.2.6 -wcwidth==0.2.6 -websocket-client==1.6.2 -websockets==11.0.3 -Werkzeug==2.3.7 +wcwidth==0.2.8 +websocket-client==1.6.4 +Werkzeug==3.0.0 wheel==0.41.2 wrapt==1.15.0 xarray==2023.1.0 -xmlschema==2.4.0 +xmlschema==2.5.0 xsdata==23.8 yarl==1.9.2 zarr==2.16.1 zict==3.0.0 -zipp==3.16.2 +zipp==3.17.0 diff --git a/requirements/linux/docs-requirements.txt b/requirements/linux/docs-requirements.txt index 568d6c15e..2d5db8a11 100644 --- a/requirements/linux/docs-requirements.txt +++ b/requirements/linux/docs-requirements.txt @@ -5,126 +5,116 @@ aicscytoparam==0.1.9 aicsimageio==4.11.0 aicsshparam==0.1.7 aiobotocore==2.4.2 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alabaster==0.7.13 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 autograd==1.6.2 autopage==0.5.1 -babel==2.12.1 -backoff==2.2.1 +babel==2.13.0 beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 boto3==1.24.4 botocore==1.27.59 cellpose-omni==0.9.1 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 cmaes==0.10.0 -cmake==3.27.4.1 +cmake==3.27.6 cmd2==2.4.3 colorama==0.4.6 colorlog==6.7.0 -contourpy==1.1.0 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 Deprecated==1.2.14 distributed==2023.5.0 docker==6.1.3 docutils==0.19 e3nn==0.5.1 edt==2.3.1 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -escnn==1.0.7 -exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 +escnn==1.0.11 +fasteners==0.19 fastremap==1.14.0 -filelock==3.12.3 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 furo==2023.3.23 future==0.18.3 geomloss==0.2.6 gitdb==4.0.10 -gitpython==3.1.35 +gitpython==3.1.37 gorilla==0.4.0 -greenlet==2.0.2 +greenlet==3.0.0 gunicorn==21.2.0 -h11==0.14.0 -h5py==3.9.0 -huggingface-hub==0.16.4 +h5py==3.10.0 +huggingface-hub==0.17.3 humanize==4.8.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 -igraph==0.10.6 +igraph==0.11.2 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 imagesize==1.4.1 importlib-metadata==6.8.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 lie-learn @ git+https://github.com/colobas/lie_learn.git@d5be2ab -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 -lit==16.0.6 -llvmlite==0.40.1 +lit==17.0.2 +llvmlite==0.41.0 locket==1.0.0 lxml==4.9.3 m2r2==0.3.3.post2 mahotas==1.4.13 Mako==1.2.4 -markdown==3.4.4 +markdown==3.5 markdown-it-py==3.0.0 MarkupSafe==2.1.3 -matplotlib==3.7.2 +matplotlib==3.7.3 mdurl==0.1.2 mgen==1.2.1 mistune==0.8.4 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 ncolor==1.2.1 networkx==3.1 nibabel==5.1.0 -Ninja==1.11.1 -numba==0.57.1 -numcodecs==0.11.0 +Ninja==1.11.1.1 +numba==0.58.0 +numcodecs==0.12.0 numpy==1.24.4 nvidia-cublas-cu11==11.10.3.66 nvidia-cuda-cupti-cu11==11.7.101 @@ -139,64 +129,60 @@ nvidia-nccl-cu11==2.14.3 nvidia-nvtx-cu11==11.7.91 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 omnipose @ git+https://github.com/kevinjohncutler/omnipose.git@ce2e9aa -opencv-python-headless==4.8.0.76 +opencv-python-headless==4.8.1.78 opt-einsum==3.3.0 opt-einsum-fx==0.1.4 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 peakdetect==1.2 -pillow==10.0.0 -platformdirs==3.10.0 -point-cloud-utils==0.29.6 +pillow==10.0.1 +platformdirs==3.11.0 +point-cloud-utils==0.30.0 pooch==1.7.0 -PrettyTable==3.8.0 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 -py3nj==0.2.1 +py3nj==0.1.2 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 +pydantic==2.4.2 +pydantic-core==2.10.1 pyerfa==2.0.0.3 pygments==2.16.1 pyjwt==2.8.0 -pymanopt==2.1.1 +pymanopt==2.2.0 pyntcloud==0.3.1 -pyparsing==3.0.9 +pyparsing==3.1.1 pyperclip==1.8.2 pyshtools==4.10.3 python-dateutil==2.8.2 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytorch-ranger==0.1.1 pytz==2023.3.post1 PyWavelets==1.4.1 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 +rich==13.6.0 s3fs==2023.3.0 s3transfer==0.6.2 -safetensors==0.3.3 +safetensors==0.4.0 scikit-image==0.21.0 -scikit-learn==1.3.0 -scipy==1.10.1 -setuptools==68.2.0 +scikit-learn==1.3.1 +scipy==1.9.3 +scyjava==1.9.1 +setuptools==68.2.2 shellingham==1.5.3 -SimpleITK==2.2.1 +SimpleITK==2.3.0 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 snowballstemmer==2.2.0 sortedcontainers==2.4.0 soupsieve==2.5 @@ -208,48 +194,43 @@ sphinxcontrib-htmlhelp==2.0.1 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==1.0.3 sphinxcontrib-serializinghtml==1.1.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 tblib==2.0.0 termcolor==2.3.0 -texttable==1.6.7 +texttable==1.7.0 threadpoolctl==3.2.0 tifffile==2023.7.10 timm==0.9.7 toolz==0.12.0 torch==2.0.1 -torch-geometric==2.3.1 +torch-geometric==2.4.0 torch-optimizer==0.3.0 torchio==0.19.1 -torchmetrics==1.1.1 -torchserve==0.8.2 +torchmetrics==1.2.0 +torchserve==0.9.0 torchvf==0.1.3 torchvision==0.15.2 tornado==6.3.3 tqdm==4.66.1 -traitlets==5.9.0 triton==2.0.0 typer==0.9.0 -typing-extensions==4.7.1 +typing-extensions==4.8.0 universal-pathlib==0.1.3 -urllib3==1.26.16 -uvicorn==0.23.2 +urllib3==1.26.17 vtk==9.2.6 -wcwidth==0.2.6 -websocket-client==1.6.2 -websockets==11.0.3 -Werkzeug==2.3.7 +wcwidth==0.2.8 +websocket-client==1.6.4 +Werkzeug==3.0.0 wheel==0.41.2 wrapt==1.15.0 xarray==2023.1.0 -xmlschema==2.4.0 +xmlschema==2.5.0 xsdata==23.8 yarl==1.9.2 zarr==2.16.1 zict==3.0.0 -zipp==3.16.2 +zipp==3.17.0 diff --git a/requirements/linux/equiv-requirements.txt b/requirements/linux/equiv-requirements.txt index 1102847d1..73db1eb2d 100644 --- a/requirements/linux/equiv-requirements.txt +++ b/requirements/linux/equiv-requirements.txt @@ -3,100 +3,87 @@ aicsimageio==4.11.0 aiobotocore==2.4.2 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 async-timeout==4.0.3 attrs==23.1.0 autograd==1.6.2 autopage==0.5.1 -backoff==2.2.1 -beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 botocore==1.27.59 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 cmaes==0.10.0 -cmake==3.27.4.1 +cmake==3.27.6 cmd2==2.4.3 colorlog==6.7.0 -contourpy==1.1.0 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 e3nn==0.5.1 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -escnn==1.0.7 -exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 -filelock==3.12.3 +escnn==1.0.11 +fasteners==0.19 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 future==0.18.3 gitdb==4.0.10 -gitpython==3.1.35 -greenlet==2.0.2 +gitpython==3.1.37 +greenlet==3.0.0 gunicorn==21.2.0 -h11==0.14.0 -h5py==3.9.0 +h5py==3.10.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 importlib-metadata==6.8.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 lie-learn @ git+https://github.com/colobas/lie_learn.git@d5be2ab -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 -lit==16.0.6 +lit==17.0.2 locket==1.0.0 lxml==4.9.3 Mako==1.2.4 -markdown==3.4.4 -markdown-it-py==3.0.0 +markdown==3.5 MarkupSafe==2.1.3 -matplotlib==3.7.2 -mdurl==0.1.2 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +matplotlib==3.7.3 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.11.0 +numcodecs==0.12.0 numpy==1.24.4 nvidia-cublas-cu11==11.10.3.66 nvidia-cuda-cupti-cu11==11.7.101 @@ -111,56 +98,47 @@ nvidia-nccl-cu11==2.14.3 nvidia-nvtx-cu11==11.7.91 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 opt-einsum==3.3.0 opt-einsum-fx==0.1.4 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 -pillow==10.0.0 -PrettyTable==3.8.0 +pillow==10.0.1 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 -py3nj==0.2.1 +py3nj==0.1.2 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 -pygments==2.16.1 +pydantic==2.4.2 +pydantic-core==2.10.1 pyjwt==2.8.0 -pymanopt==2.1.1 -pyparsing==3.0.9 +pymanopt==2.2.0 +pyparsing==3.1.1 pyperclip==1.8.2 python-dateutil==2.8.2 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytz==2023.3.post1 PyWavelets==1.4.1 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 s3fs==2023.3.0 scikit-image==0.21.0 -scikit-learn==1.3.0 -scipy==1.10.1 -setuptools==68.2.0 +scikit-learn==1.3.1 +scipy==1.9.3 +scyjava==1.9.1 +setuptools==68.2.2 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 sortedcontainers==2.4.0 -soupsieve==2.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 @@ -170,25 +148,22 @@ threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 torch==2.0.1 -torchmetrics==1.1.1 +torchmetrics==1.2.0 tornado==6.3.3 tqdm==4.66.1 -traitlets==5.9.0 triton==2.0.0 -typing-extensions==4.7.1 +typing-extensions==4.8.0 universal-pathlib==0.1.3 -urllib3==1.26.16 -uvicorn==0.23.2 -wcwidth==0.2.6 -websocket-client==1.6.2 -websockets==11.0.3 -Werkzeug==2.3.7 +urllib3==1.26.17 +wcwidth==0.2.8 +websocket-client==1.6.4 +Werkzeug==3.0.0 wheel==0.41.2 wrapt==1.15.0 xarray==2023.1.0 -xmlschema==2.4.0 +xmlschema==2.5.0 xsdata==23.8 yarl==1.9.2 zarr==2.16.1 zict==3.0.0 -zipp==3.16.2 +zipp==3.17.0 diff --git a/requirements/linux/omnipose-requirements.txt b/requirements/linux/omnipose-requirements.txt index 7b99b0a34..18efff9cc 100644 --- a/requirements/linux/omnipose-requirements.txt +++ b/requirements/linux/omnipose-requirements.txt @@ -3,104 +3,91 @@ aicsimageio==4.11.0 aiobotocore==2.4.2 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 async-timeout==4.0.3 attrs==23.1.0 autopage==0.5.1 -backoff==2.2.1 -beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 botocore==1.27.59 cellpose-omni==0.9.1 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 cmaes==0.10.0 -cmake==3.27.4.1 +cmake==3.27.6 cmd2==2.4.3 colorlog==6.7.0 -contourpy==1.1.0 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 edt==2.3.1 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 +fasteners==0.19 fastremap==1.14.0 -filelock==3.12.3 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 gitdb==4.0.10 -gitpython==3.1.35 -greenlet==2.0.2 +gitpython==3.1.37 +greenlet==3.0.0 gunicorn==21.2.0 -h11==0.14.0 -h5py==3.9.0 +h5py==3.10.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 -igraph==0.10.6 +igraph==0.11.2 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 importlib-metadata==6.8.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 -lit==16.0.6 -llvmlite==0.40.1 +lit==17.0.2 +llvmlite==0.41.0 locket==1.0.0 lxml==4.9.3 mahotas==1.4.13 Mako==1.2.4 -markdown==3.4.4 -markdown-it-py==3.0.0 +markdown==3.5 MarkupSafe==2.1.3 -matplotlib==3.7.2 -mdurl==0.1.2 +matplotlib==3.7.3 mgen==1.2.1 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 ncolor==1.2.1 networkx==3.1 -numba==0.57.1 -numcodecs==0.11.0 +numba==0.58.0 +numcodecs==0.12.0 numpy==1.24.4 nvidia-cublas-cu11==11.10.3.66 nvidia-cuda-cupti-cu11==11.7.101 @@ -115,88 +102,76 @@ nvidia-nccl-cu11==2.14.3 nvidia-nvtx-cu11==11.7.91 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 omnipose @ git+https://github.com/kevinjohncutler/omnipose.git@ce2e9aa -opencv-python-headless==4.8.0.76 +opencv-python-headless==4.8.1.78 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 peakdetect==1.2 -pillow==10.0.0 -PrettyTable==3.8.0 +pillow==10.0.1 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 -pygments==2.16.1 +pydantic==2.4.2 +pydantic-core==2.10.1 pyjwt==2.8.0 -pyparsing==3.0.9 +pyparsing==3.1.1 pyperclip==1.8.2 python-dateutil==2.8.2 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytorch-ranger==0.1.1 pytz==2023.3.post1 PyWavelets==1.4.1 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 s3fs==2023.3.0 scikit-image==0.21.0 -scikit-learn==1.3.0 -scipy==1.10.1 -setuptools==68.2.0 +scikit-learn==1.3.1 +scipy==1.9.3 +scyjava==1.9.1 +setuptools==68.2.2 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 sortedcontainers==2.4.0 -soupsieve==2.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 tblib==2.0.0 termcolor==2.3.0 -texttable==1.6.7 +texttable==1.7.0 threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 torch==2.0.1 torch-optimizer==0.3.0 -torchmetrics==1.1.1 +torchmetrics==1.2.0 torchvf==0.1.3 torchvision==0.15.2 tornado==6.3.3 tqdm==4.66.1 -traitlets==5.9.0 triton==2.0.0 -typing-extensions==4.7.1 +typing-extensions==4.8.0 universal-pathlib==0.1.3 -urllib3==1.26.16 -uvicorn==0.23.2 -wcwidth==0.2.6 -websocket-client==1.6.2 -websockets==11.0.3 -Werkzeug==2.3.7 +urllib3==1.26.17 +wcwidth==0.2.8 +websocket-client==1.6.4 +Werkzeug==3.0.0 wheel==0.41.2 wrapt==1.15.0 xarray==2023.1.0 -xmlschema==2.4.0 +xmlschema==2.5.0 xsdata==23.8 yarl==1.9.2 zarr==2.16.1 zict==3.0.0 -zipp==3.16.2 +zipp==3.17.0 diff --git a/requirements/linux/pdm.lock b/requirements/linux/pdm.lock index a75749ef5..9cc059da4 100644 --- a/requirements/linux/pdm.lock +++ b/requirements/linux/pdm.lock @@ -6,7 +6,7 @@ groups = ["default", "all", "docs", "equiv", "omnipose", "pcloud", "s3", "spharm cross_platform = false static_urls = false lock_version = "4.3" -content_hash = "sha256:2ee3b0f492ef4c233c7454749aa28a2ea58edb7605b0bc866176c370107009f5" +content_hash = "sha256:e37073446848e15bbc0ccb7f651dad85c6d46e07816b4b1fe870c7ee6aa14abd" [[package]] name = "aicscytoparam" @@ -88,7 +88,7 @@ files = [ [[package]] name = "aiohttp" -version = "3.8.5" +version = "3.8.6" requires_python = ">=3.6" summary = "Async http client/server framework (asyncio)" dependencies = [ @@ -101,8 +101,8 @@ dependencies = [ "yarl<2.0,>=1.0", ] files = [ - {file = "aiohttp-3.8.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:df72ac063b97837a80d80dec8d54c241af059cc9bb42c4de68bd5b61ceb37caa"}, - {file = "aiohttp-3.8.5.tar.gz", hash = "sha256:b9552ec52cc147dbf1944ac7ac98af7602e51ea2dcd076ed194ca3c0d1c7d0bc"}, + {file = "aiohttp-3.8.6-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:0fa375b3d34e71ccccf172cab401cd94a72de7a8cc01847a7b3386204093bb47"}, + {file = "aiohttp-3.8.6.tar.gz", hash = "sha256:b0cf2a4501bff9330a8a5248b4ce951851e415bdcce9dc158e76cfd55e15085c"}, ] [[package]] @@ -173,12 +173,12 @@ files = [ [[package]] name = "annotated-types" -version = "0.5.0" -requires_python = ">=3.7" +version = "0.6.0" +requires_python = ">=3.8" summary = "Reusable constraint types to use with typing.Annotated" files = [ - {file = "annotated_types-0.5.0-py3-none-any.whl", hash = "sha256:58da39888f92c276ad970249761ebea80ba544b77acddaa1a4d6cf78287d45fd"}, - {file = "annotated_types-0.5.0.tar.gz", hash = "sha256:47cdc3490d9ac1506ce92c7aaa76c579dc3509ff11e098fc867e5130ab7be802"}, + {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"}, + {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"}, ] [[package]] @@ -189,34 +189,6 @@ files = [ {file = "antlr4-python3-runtime-4.9.3.tar.gz", hash = "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"}, ] -[[package]] -name = "anyio" -version = "3.7.1" -requires_python = ">=3.7" -summary = "High level compatibility layer for multiple asynchronous event loop implementations" -dependencies = [ - "exceptiongroup; python_version < \"3.11\"", - "idna>=2.8", - "sniffio>=1.1", -] -files = [ - {file = "anyio-3.7.1-py3-none-any.whl", hash = "sha256:91dee416e570e92c64041bd18b900d1d6fa78dff7048769ce5ac5ddad004fbb5"}, - {file = "anyio-3.7.1.tar.gz", hash = "sha256:44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780"}, -] - -[[package]] -name = "arrow" -version = "1.2.3" -requires_python = ">=3.6" -summary = "Better dates & times for Python" -dependencies = [ - "python-dateutil>=2.7.0", -] -files = [ - {file = "arrow-1.2.3-py3-none-any.whl", hash = "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"}, - {file = "arrow-1.2.3.tar.gz", hash = "sha256:3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1"}, -] - [[package]] name = "asciitree" version = "0.3.3" @@ -286,22 +258,12 @@ files = [ [[package]] name = "babel" -version = "2.12.1" +version = "2.13.0" requires_python = ">=3.7" summary = "Internationalization utilities" files = [ - {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"}, - {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"}, -] - -[[package]] -name = "backoff" -version = "2.2.1" -requires_python = ">=3.7,<4.0" -summary = "Function decoration for backoff and retry" -files = [ - {file = "backoff-2.2.1-py3-none-any.whl", hash = "sha256:63579f9a0628e06278f7e47b7d7d5b6ce20dc65c5e96a6f3ca99a6adca0396e8"}, - {file = "backoff-2.2.1.tar.gz", hash = "sha256:03f829f5bb1923180821643f8753b0502c3b682293992485b0eef2807afa5cba"}, + {file = "Babel-2.13.0-py3-none-any.whl", hash = "sha256:fbfcae1575ff78e26c7449136f1abbefc3c13ce542eeb13d43d50d8b047216ec"}, + {file = "Babel-2.13.0.tar.gz", hash = "sha256:04c3e2d28d2b7681644508f836be388ae49e0cfe91465095340395b60d00f210"}, ] [[package]] @@ -319,43 +281,31 @@ files = [ [[package]] name = "bfio" -version = "2.3.0" -requires_python = ">=3.6" +version = "2.3.1" +requires_python = ">=3.7" summary = "Simple reading and writing classes for tiled tiffs using Bioformats." dependencies = [ "imagecodecs>=2021.2.26", - "lxml", + "jpype1", "numpy>=1.20.1", - "ome-types>=0.2.10", - "tifffile>=2021.8.30", -] -files = [ - {file = "bfio-2.3.0-py2.py3-none-any.whl", hash = "sha256:df343233add10e592a047254397d167c4c22496415287ff5ab4cdb0cb94c110a"}, - {file = "bfio-2.3.0.tar.gz", hash = "sha256:963a56aed17cf0fcbcac3995daf61dd75b8d68d8358b144003d79cf17dce16fe"}, -] - -[[package]] -name = "blessed" -version = "1.20.0" -requires_python = ">=2.7" -summary = "Easy, practical library for making terminal apps, by providing an elegant, 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application library." dependencies = [ "MarkupSafe>=2.1.1", ] files = [ - {file = "werkzeug-2.3.7-py3-none-any.whl", hash = "sha256:effc12dba7f3bd72e605ce49807bbe692bd729c3bb122a3b91747a6ae77df528"}, - {file = "werkzeug-2.3.7.tar.gz", hash = "sha256:2b8c0e447b4b9dbcc85dd97b6eeb4dcbaf6c8b6c3be0bd654e25553e0a2157d8"}, + {file = "werkzeug-3.0.0-py3-none-any.whl", hash = "sha256:cbb2600f7eabe51dbc0502f58be0b3e1b96b893b05695ea2b35b43d4de2d9962"}, + {file = "werkzeug-3.0.0.tar.gz", hash = "sha256:3ffff4dcc32db52ef3cc94dff3000a3c2846890f3a5a51800a27b909c5e770f0"}, ] [[package]] @@ -3427,15 +3171,15 @@ files = [ [[package]] name = "xmlschema" -version = "2.4.0" +version = "2.5.0" requires_python = ">=3.7" summary = "An XML Schema validator and decoder" dependencies = [ "elementpath<5.0.0,>=4.1.5", ] files = [ - {file = "xmlschema-2.4.0-py3-none-any.whl", hash = "sha256:dc87be0caaa61f42649899189aab2fd8e0d567f2cf548433ba7b79278d231a4a"}, - {file = "xmlschema-2.4.0.tar.gz", hash = "sha256:d74cd0c10866ac609e1ef94a5a69b018ad16e39077bc6393408b40c6babee793"}, + {file = "xmlschema-2.5.0-py3-none-any.whl", hash = "sha256:f2b29c45485fac414cc1fdb38d18a220c5987d7d3aa996e6df6ff35ee94d5a63"}, + {file = "xmlschema-2.5.0.tar.gz", hash = "sha256:276a03e0fd3c94c148d528bff4d9482f9b99bf8c7b4056a2e8e703d28149d454"}, ] [[package]] @@ -3493,10 +3237,10 @@ files = [ [[package]] name = "zipp" -version = "3.16.2" +version = "3.17.0" requires_python = ">=3.8" summary = "Backport of pathlib-compatible object wrapper for zip files" files = [ - {file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"}, - {file = "zipp-3.16.2.tar.gz", hash = "sha256:ebc15946aa78bd63458992fc81ec3b6f7b1e92d51c35e6de1c3804e73b799147"}, + {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"}, + {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"}, ] diff --git a/requirements/linux/requirements.txt b/requirements/linux/requirements.txt index 8f9787cca..3eff70296 100644 --- a/requirements/linux/requirements.txt +++ b/requirements/linux/requirements.txt @@ -3,155 +3,131 @@ aicsimageio==4.11.0 aiobotocore==2.5.4 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 async-timeout==4.0.3 attrs==23.1.0 autopage==0.5.1 -backoff==2.2.1 -beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 botocore==1.31.17 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 cmaes==0.10.0 -cmake==3.27.4.1 cmd2==2.4.3 colorlog==6.7.0 -contourpy==1.1.0 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 -filelock==3.12.3 +fasteners==0.19 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 -fsspec==2023.9.0 +fsspec==2023.9.2 gitdb==4.0.10 -gitpython==3.1.35 -greenlet==2.0.2 +gitpython==3.1.37 +greenlet==3.0.0 gunicorn==21.2.0 -h11==0.14.0 -h5py==3.9.0 +h5py==3.10.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 importlib-metadata==6.8.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 -lit==16.0.6 locket==1.0.0 lxml==4.9.3 Mako==1.2.4 -markdown==3.4.4 -markdown-it-py==3.0.0 +markdown==3.5 MarkupSafe==2.1.3 -matplotlib==3.7.2 -mdurl==0.1.2 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +matplotlib==3.7.3 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.11.0 +numcodecs==0.12.0 numpy==1.24.4 -nvidia-cublas-cu11==11.10.3.66 -nvidia-cuda-cupti-cu11==11.7.101 -nvidia-cuda-nvrtc-cu11==11.7.99 -nvidia-cuda-runtime-cu11==11.7.99 -nvidia-cudnn-cu11==8.5.0.96 -nvidia-cufft-cu11==10.9.0.58 -nvidia-curand-cu11==10.2.10.91 -nvidia-cusolver-cu11==11.4.0.1 -nvidia-cusparse-cu11==11.7.4.91 -nvidia-nccl-cu11==2.14.3 -nvidia-nvtx-cu11==11.7.91 +nvidia-cublas-cu12==12.1.3.1 +nvidia-cuda-cupti-cu12==12.1.105 +nvidia-cuda-nvrtc-cu12==12.1.105 +nvidia-cuda-runtime-cu12==12.1.105 +nvidia-cudnn-cu12==8.9.2.26 +nvidia-cufft-cu12==11.0.2.54 +nvidia-curand-cu12==10.3.2.106 +nvidia-cusolver-cu12==11.4.5.107 +nvidia-cusparse-cu12==12.1.0.106 +nvidia-nccl-cu12==2.18.1 +nvidia-nvjitlink-cu12==12.2.140 +nvidia-nvtx-cu12==12.1.105 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 -pillow==10.0.0 -PrettyTable==3.8.0 +pillow==10.0.1 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 -pygments==2.16.1 +pydantic==2.4.2 +pydantic-core==2.10.1 pyjwt==2.8.0 -pyparsing==3.0.9 +pyparsing==3.1.1 pyperclip==1.8.2 python-dateutil==2.8.2 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytz==2023.3.post1 PyWavelets==1.4.1 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 -s3fs==2023.9.0 +s3fs==2023.9.2 scikit-image==0.21.0 -scikit-learn==1.3.0 +scikit-learn==1.3.1 scipy==1.10.1 -setuptools==68.2.0 +scyjava==1.9.1 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 sortedcontainers==2.4.0 -soupsieve==2.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 @@ -160,26 +136,22 @@ termcolor==2.3.0 threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 -torch==2.0.1 -torchmetrics==1.1.1 +torch==2.1.0 +torchmetrics==1.2.0 tornado==6.3.3 tqdm==4.66.1 -traitlets==5.9.0 -triton==2.0.0 -typing-extensions==4.7.1 +triton==2.1.0 +typing-extensions==4.8.0 universal-pathlib==0.1.3 -urllib3==1.26.16 -uvicorn==0.23.2 -wcwidth==0.2.6 -websocket-client==1.6.2 -websockets==11.0.3 -Werkzeug==2.3.7 -wheel==0.41.2 +urllib3==1.26.17 +wcwidth==0.2.8 +websocket-client==1.6.4 +Werkzeug==3.0.0 wrapt==1.15.0 xarray==2023.1.0 -xmlschema==2.4.0 +xmlschema==2.5.0 xsdata==23.8 yarl==1.9.2 zarr==2.16.1 zict==3.0.0 -zipp==3.16.2 +zipp==3.17.0 diff --git a/requirements/linux/spharm-requirements.txt b/requirements/linux/spharm-requirements.txt index 5ba94dadb..1d3331d66 100644 --- a/requirements/linux/spharm-requirements.txt +++ b/requirements/linux/spharm-requirements.txt @@ -5,96 +5,83 @@ aicscytoparam==0.1.9 aicsimageio==4.11.0 aicsshparam==0.1.7 aiobotocore==2.4.2 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 autopage==0.5.1 -backoff==2.2.1 -beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 botocore==1.27.59 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 cmaes==0.10.0 -cmake==3.27.4.1 +cmake==3.27.6 cmd2==2.4.3 colorlog==6.7.0 -contourpy==1.1.0 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 -filelock==3.12.3 +fasteners==0.19 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 gitdb==4.0.10 -gitpython==3.1.35 -greenlet==2.0.2 +gitpython==3.1.37 +greenlet==3.0.0 gunicorn==21.2.0 -h11==0.14.0 -h5py==3.9.0 +h5py==3.10.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 importlib-metadata==6.8.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 -lit==16.0.6 +lit==17.0.2 locket==1.0.0 lxml==4.9.3 Mako==1.2.4 -markdown==3.4.4 -markdown-it-py==3.0.0 +markdown==3.5 MarkupSafe==2.1.3 -matplotlib==3.7.2 -mdurl==0.1.2 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +matplotlib==3.7.3 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.11.0 +numcodecs==0.12.0 numpy==1.24.4 nvidia-cublas-cu11==11.10.3.66 nvidia-cuda-cupti-cu11==11.7.101 @@ -109,56 +96,47 @@ nvidia-nccl-cu11==2.14.3 nvidia-nvtx-cu11==11.7.91 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 -pillow==10.0.0 -platformdirs==3.10.0 +pillow==10.0.1 +platformdirs==3.11.0 pooch==1.7.0 -PrettyTable==3.8.0 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 +pydantic==2.4.2 +pydantic-core==2.10.1 pyerfa==2.0.0.3 -pygments==2.16.1 pyjwt==2.8.0 -pyparsing==3.0.9 +pyparsing==3.1.1 pyperclip==1.8.2 pyshtools==4.10.3 python-dateutil==2.8.2 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytz==2023.3.post1 PyWavelets==1.4.1 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 s3fs==2023.3.0 scikit-image==0.21.0 -scikit-learn==1.3.0 -scipy==1.10.1 -setuptools==68.2.0 +scikit-learn==1.3.1 +scipy==1.9.3 +scyjava==1.9.1 +setuptools==68.2.2 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 sortedcontainers==2.4.0 -soupsieve==2.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 @@ -168,26 +146,23 @@ threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 torch==2.0.1 -torchmetrics==1.1.1 +torchmetrics==1.2.0 tornado==6.3.3 tqdm==4.66.1 -traitlets==5.9.0 triton==2.0.0 -typing-extensions==4.7.1 +typing-extensions==4.8.0 universal-pathlib==0.1.3 -urllib3==1.26.16 -uvicorn==0.23.2 +urllib3==1.26.17 vtk==9.2.6 -wcwidth==0.2.6 -websocket-client==1.6.2 -websockets==11.0.3 -Werkzeug==2.3.7 +wcwidth==0.2.8 +websocket-client==1.6.4 +Werkzeug==3.0.0 wheel==0.41.2 wrapt==1.15.0 xarray==2023.1.0 -xmlschema==2.4.0 +xmlschema==2.5.0 xsdata==23.8 yarl==1.9.2 zarr==2.16.1 zict==3.0.0 -zipp==3.16.2 +zipp==3.17.0 diff --git a/requirements/linux/test-requirements.txt b/requirements/linux/test-requirements.txt index 66ca16930..b854fd7d8 100644 --- a/requirements/linux/test-requirements.txt +++ b/requirements/linux/test-requirements.txt @@ -5,121 +5,111 @@ aicscytoparam==0.1.9 aicsimageio==4.11.0 aicsshparam==0.1.7 aiobotocore==2.4.2 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 autograd==1.6.2 autopage==0.5.1 -backoff==2.2.1 -beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 boto3==1.24.4 botocore==1.27.59 cellpose-omni==0.9.1 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 cmaes==0.10.0 -cmake==3.27.4.1 +cmake==3.27.6 cmd2==2.4.3 colorama==0.4.6 colorlog==6.7.0 -contourpy==1.1.0 -coverage==7.3.1 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +coverage==7.3.2 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 Deprecated==1.2.14 distributed==2023.5.0 docker==6.1.3 e3nn==0.5.1 edt==2.3.1 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -escnn==1.0.7 +escnn==1.0.11 exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 +fasteners==0.19 fastremap==1.14.0 -filelock==3.12.3 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 future==0.18.3 geomloss==0.2.6 gitdb==4.0.10 -gitpython==3.1.35 +gitpython==3.1.37 gorilla==0.4.0 -greenlet==2.0.2 +greenlet==3.0.0 gunicorn==21.2.0 -h11==0.14.0 -h5py==3.9.0 -huggingface-hub==0.16.4 +h5py==3.10.0 +huggingface-hub==0.17.3 humanize==4.8.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 -igraph==0.10.6 +igraph==0.11.2 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 importlib-metadata==6.8.0 iniconfig==2.0.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 lie-learn @ git+https://github.com/colobas/lie_learn.git@d5be2ab -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 -lit==16.0.6 -llvmlite==0.40.1 +lit==17.0.2 +llvmlite==0.41.0 locket==1.0.0 lxml==4.9.3 mahotas==1.4.13 Mako==1.2.4 -markdown==3.4.4 +markdown==3.5 markdown-it-py==3.0.0 MarkupSafe==2.1.3 -matplotlib==3.7.2 +matplotlib==3.7.3 mdurl==0.1.2 mgen==1.2.1 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 ncolor==1.2.1 networkx==3.1 nibabel==5.1.0 -Ninja==1.11.1 -numba==0.57.1 -numcodecs==0.11.0 +Ninja==1.11.1.1 +numba==0.58.0 +numcodecs==0.12.0 numpy==1.24.4 nvidia-cublas-cu11==11.10.3.66 nvidia-cuda-cupti-cu11==11.7.101 @@ -134,38 +124,37 @@ nvidia-nccl-cu11==2.14.3 nvidia-nvtx-cu11==11.7.91 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 omnipose @ git+https://github.com/kevinjohncutler/omnipose.git@ce2e9aa -opencv-python-headless==4.8.0.76 +opencv-python-headless==4.8.1.78 opt-einsum==3.3.0 opt-einsum-fx==0.1.4 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 peakdetect==1.2 -pillow==10.0.0 -platformdirs==3.10.0 +pillow==10.0.1 +platformdirs==3.11.0 pluggy==1.3.0 -point-cloud-utils==0.29.6 +point-cloud-utils==0.30.0 pooch==1.7.0 -PrettyTable==3.8.0 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 -py3nj==0.2.1 +py3nj==0.1.2 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 +pydantic==2.4.2 +pydantic-core==2.10.1 pyerfa==2.0.0.3 pygments==2.16.1 pyjwt==2.8.0 -pymanopt==2.1.1 +pymanopt==2.2.0 pyntcloud==0.3.1 -pyparsing==3.0.9 +pyparsing==3.1.1 pyperclip==1.8.2 pyrootutils==1.0.4 pyshtools==4.10.3 @@ -173,75 +162,66 @@ pytest==7.4.2 pytest-cov==4.1.0 python-dateutil==2.8.2 python-dotenv==1.0.0 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytorch-ranger==0.1.1 pytz==2023.3.post1 PyWavelets==1.4.1 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 +rich==13.6.0 s3fs==2023.3.0 s3transfer==0.6.2 -safetensors==0.3.3 +safetensors==0.4.0 scikit-image==0.21.0 -scikit-learn==1.3.0 -scipy==1.10.1 -setuptools==68.2.0 +scikit-learn==1.3.1 +scipy==1.9.3 +scyjava==1.9.1 +setuptools==68.2.2 shellingham==1.5.3 -SimpleITK==2.2.1 +SimpleITK==2.3.0 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 sortedcontainers==2.4.0 -soupsieve==2.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 tblib==2.0.0 termcolor==2.3.0 -texttable==1.6.7 +texttable==1.7.0 threadpoolctl==3.2.0 tifffile==2023.7.10 timm==0.9.7 tomli==2.0.1 toolz==0.12.0 torch==2.0.1 -torch-geometric==2.3.1 +torch-geometric==2.4.0 torch-optimizer==0.3.0 torchio==0.19.1 -torchmetrics==1.1.1 -torchserve==0.8.2 +torchmetrics==1.2.0 +torchserve==0.9.0 torchvf==0.1.3 torchvision==0.15.2 tornado==6.3.3 tqdm==4.66.1 -traitlets==5.9.0 triton==2.0.0 typer==0.9.0 -typing-extensions==4.7.1 +typing-extensions==4.8.0 universal-pathlib==0.1.3 -urllib3==1.26.16 -uvicorn==0.23.2 +urllib3==1.26.17 vtk==9.2.6 -wcwidth==0.2.6 -websocket-client==1.6.2 -websockets==11.0.3 -Werkzeug==2.3.7 +wcwidth==0.2.8 +websocket-client==1.6.4 +Werkzeug==3.0.0 wheel==0.41.2 wrapt==1.15.0 xarray==2023.1.0 -xmlschema==2.4.0 +xmlschema==2.5.0 xsdata==23.8 yarl==1.9.2 zarr==2.16.1 zict==3.0.0 -zipp==3.16.2 +zipp==3.17.0 diff --git a/requirements/linux/torchserve-requirements.txt b/requirements/linux/torchserve-requirements.txt index 27027d800..fde59e71a 100644 --- a/requirements/linux/torchserve-requirements.txt +++ b/requirements/linux/torchserve-requirements.txt @@ -3,96 +3,83 @@ aicsimageio==4.11.0 aiobotocore==2.4.2 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 async-timeout==4.0.3 attrs==23.1.0 autopage==0.5.1 -backoff==2.2.1 -beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 botocore==1.27.59 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 cmaes==0.10.0 -cmake==3.27.4.1 +cmake==3.27.6 cmd2==2.4.3 colorlog==6.7.0 -contourpy==1.1.0 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 -filelock==3.12.3 +fasteners==0.19 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 gitdb==4.0.10 -gitpython==3.1.35 +gitpython==3.1.37 gorilla==0.4.0 -greenlet==2.0.2 +greenlet==3.0.0 gunicorn==21.2.0 -h11==0.14.0 -h5py==3.9.0 +h5py==3.10.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 importlib-metadata==6.8.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 -lit==16.0.6 +lit==17.0.2 locket==1.0.0 lxml==4.9.3 Mako==1.2.4 -markdown==3.4.4 -markdown-it-py==3.0.0 +markdown==3.5 MarkupSafe==2.1.3 -matplotlib==3.7.2 -mdurl==0.1.2 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +matplotlib==3.7.3 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.11.0 +numcodecs==0.12.0 numpy==1.24.4 nvidia-cublas-cu11==11.10.3.66 nvidia-cuda-cupti-cu11==11.7.101 @@ -107,52 +94,43 @@ nvidia-nccl-cu11==2.14.3 nvidia-nvtx-cu11==11.7.91 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 -pillow==10.0.0 -PrettyTable==3.8.0 +pillow==10.0.1 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 -pygments==2.16.1 +pydantic==2.4.2 +pydantic-core==2.10.1 pyjwt==2.8.0 -pyparsing==3.0.9 +pyparsing==3.1.1 pyperclip==1.8.2 python-dateutil==2.8.2 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytz==2023.3.post1 PyWavelets==1.4.1 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 s3fs==2023.3.0 scikit-image==0.21.0 -scikit-learn==1.3.0 -scipy==1.10.1 -setuptools==68.2.0 +scikit-learn==1.3.1 +scipy==1.9.3 +scyjava==1.9.1 +setuptools==68.2.2 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 sortedcontainers==2.4.0 -soupsieve==2.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 @@ -162,26 +140,23 @@ threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 torch==2.0.1 -torchmetrics==1.1.1 -torchserve==0.8.2 +torchmetrics==1.2.0 +torchserve==0.9.0 tornado==6.3.3 tqdm==4.66.1 -traitlets==5.9.0 triton==2.0.0 -typing-extensions==4.7.1 +typing-extensions==4.8.0 universal-pathlib==0.1.3 -urllib3==1.26.16 -uvicorn==0.23.2 -wcwidth==0.2.6 -websocket-client==1.6.2 -websockets==11.0.3 -Werkzeug==2.3.7 +urllib3==1.26.17 +wcwidth==0.2.8 +websocket-client==1.6.4 +Werkzeug==3.0.0 wheel==0.41.2 wrapt==1.15.0 xarray==2023.1.0 -xmlschema==2.4.0 +xmlschema==2.5.0 xsdata==23.8 yarl==1.9.2 zarr==2.16.1 zict==3.0.0 -zipp==3.16.2 +zipp==3.17.0 diff --git a/requirements/macos/all-requirements.txt b/requirements/macos/all-requirements.txt index 08e7316e8..5b60d24a4 100644 --- a/requirements/macos/all-requirements.txt +++ b/requirements/macos/all-requirements.txt @@ -5,31 +5,26 @@ aicscytoparam==0.1.9 aicsimageio==4.11.0 aicsshparam==0.1.7 aiobotocore==2.4.2 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 autograd==1.6.2 autopage==0.5.1 -backoff==2.2.1 -beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 boto3==1.24.4 botocore==1.27.59 cellpose-omni==0.9.1 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 @@ -37,189 +32,172 @@ cmaes==0.10.0 cmd2==2.4.3 colorama==0.4.6 colorlog==6.7.0 -contourpy==1.1.0 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 Deprecated==1.2.14 distributed==2023.5.0 docker==6.1.3 e3nn==0.5.1 edt==2.3.1 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -escnn==1.0.7 -exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 +escnn==1.0.11 +fasteners==0.19 fastremap==1.14.0 -filelock==3.12.3 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 future==0.18.3 geomloss==0.2.6 gitdb==4.0.10 -gitpython==3.1.35 +gitpython==3.1.37 gorilla==0.4.0 -greenlet==2.0.2 +greenlet==3.0.0 gunicorn==21.2.0 -h11==0.14.0 -h5py==3.9.0 -huggingface-hub==0.16.4 +h5py==3.10.0 +huggingface-hub==0.17.3 humanize==4.8.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 -igraph==0.10.6 +igraph==0.11.2 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 importlib-metadata==6.8.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 lie-learn @ git+https://github.com/colobas/lie_learn.git@d5be2ab -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 -llvmlite==0.40.1 +llvmlite==0.41.0 locket==1.0.0 lxml==4.9.3 mahotas==1.4.13 Mako==1.2.4 -markdown==3.4.4 +markdown==3.5 markdown-it-py==3.0.0 MarkupSafe==2.1.3 -matplotlib==3.7.2 +matplotlib==3.7.3 mdurl==0.1.2 mgen==1.2.1 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 ncolor==1.2.1 networkx==3.1 nibabel==5.1.0 -Ninja==1.11.1 -numba==0.57.1 -numcodecs==0.11.0 +Ninja==1.11.1.1 +numba==0.58.0 +numcodecs==0.12.0 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 omnipose @ git+https://github.com/kevinjohncutler/omnipose.git@ce2e9aa -opencv-python-headless==4.8.0.76 +opencv-python-headless==4.8.1.78 opt-einsum==3.3.0 opt-einsum-fx==0.1.4 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 peakdetect==1.2 -pillow==10.0.0 -platformdirs==3.10.0 -point-cloud-utils==0.29.6 +pillow==10.0.1 +platformdirs==3.11.0 +point-cloud-utils==0.30.0 pooch==1.7.0 -PrettyTable==3.8.0 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 -py3nj==0.2.1 +py3nj==0.1.2 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 +pydantic==2.4.2 +pydantic-core==2.10.1 pyerfa==2.0.0.3 pygments==2.16.1 pyjwt==2.8.0 -pymanopt==2.1.1 +pymanopt==2.2.0 pyntcloud==0.3.1 -pyparsing==3.0.9 +pyparsing==3.1.1 pyperclip==1.8.2 pyshtools==4.10.3 python-dateutil==2.8.2 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytorch-ranger==0.1.1 pytz==2023.3.post1 PyWavelets==1.4.1 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 +rich==13.6.0 s3fs==2023.3.0 s3transfer==0.6.2 -safetensors==0.3.3 +safetensors==0.4.0 scikit-image==0.21.0 -scikit-learn==1.3.0 -scipy==1.10.1 -setuptools==68.2.0 +scikit-learn==1.3.1 +scipy==1.9.3 +scyjava==1.9.1 shellingham==1.5.3 -SimpleITK==2.2.1 +SimpleITK==2.3.0 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 sortedcontainers==2.4.0 -soupsieve==2.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 tblib==2.0.0 termcolor==2.3.0 -texttable==1.6.7 +texttable==1.7.0 threadpoolctl==3.2.0 tifffile==2023.7.10 timm==0.9.7 toolz==0.12.0 torch==2.0.1 -torch-geometric==2.3.1 +torch-geometric==2.4.0 torch-optimizer==0.3.0 torchio==0.19.1 -torchmetrics==1.1.1 -torchserve==0.8.2 +torchmetrics==1.2.0 +torchserve==0.9.0 torchvf==0.1.3 torchvision==0.15.2 tornado==6.3.3 tqdm==4.66.1 -traitlets==5.9.0 typer==0.9.0 -typing-extensions==4.7.1 +typing-extensions==4.8.0 universal-pathlib==0.1.3 -urllib3==1.26.16 -uvicorn==0.23.2 +urllib3==1.26.17 vtk==9.2.6 -wcwidth==0.2.6 -websocket-client==1.6.2 -websockets==11.0.3 -Werkzeug==2.3.7 +wcwidth==0.2.8 +websocket-client==1.6.4 +Werkzeug==3.0.0 wheel==0.41.2 wrapt==1.15.0 xarray==2023.1.0 -xmlschema==2.4.0 +xmlschema==2.5.0 xsdata==23.8 yarl==1.9.2 zarr==2.16.1 zict==3.0.0 -zipp==3.16.2 +zipp==3.17.0 diff --git a/requirements/macos/docs-requirements.txt b/requirements/macos/docs-requirements.txt index 274c64c45..79140e07c 100644 --- a/requirements/macos/docs-requirements.txt +++ b/requirements/macos/docs-requirements.txt @@ -5,33 +5,29 @@ aicscytoparam==0.1.9 aicsimageio==4.11.0 aicsshparam==0.1.7 aiobotocore==2.4.2 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alabaster==0.7.13 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 autograd==1.6.2 autopage==0.5.1 -babel==2.12.1 -backoff==2.2.1 +babel==2.13.0 beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 boto3==1.24.4 botocore==1.27.59 cellpose-omni==0.9.1 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 @@ -39,151 +35,140 @@ cmaes==0.10.0 cmd2==2.4.3 colorama==0.4.6 colorlog==6.7.0 -contourpy==1.1.0 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 Deprecated==1.2.14 distributed==2023.5.0 docker==6.1.3 docutils==0.19 e3nn==0.5.1 edt==2.3.1 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -escnn==1.0.7 -exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 +escnn==1.0.11 +fasteners==0.19 fastremap==1.14.0 -filelock==3.12.3 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 furo==2023.3.23 future==0.18.3 geomloss==0.2.6 gitdb==4.0.10 -gitpython==3.1.35 +gitpython==3.1.37 gorilla==0.4.0 -greenlet==2.0.2 +greenlet==3.0.0 gunicorn==21.2.0 -h11==0.14.0 -h5py==3.9.0 -huggingface-hub==0.16.4 +h5py==3.10.0 +huggingface-hub==0.17.3 humanize==4.8.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 -igraph==0.10.6 +igraph==0.11.2 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 imagesize==1.4.1 importlib-metadata==6.8.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 lie-learn @ git+https://github.com/colobas/lie_learn.git@d5be2ab -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 -llvmlite==0.40.1 +llvmlite==0.41.0 locket==1.0.0 lxml==4.9.3 m2r2==0.3.3.post2 mahotas==1.4.13 Mako==1.2.4 -markdown==3.4.4 +markdown==3.5 markdown-it-py==3.0.0 MarkupSafe==2.1.3 -matplotlib==3.7.2 +matplotlib==3.7.3 mdurl==0.1.2 mgen==1.2.1 mistune==0.8.4 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 ncolor==1.2.1 networkx==3.1 nibabel==5.1.0 -Ninja==1.11.1 -numba==0.57.1 -numcodecs==0.11.0 +Ninja==1.11.1.1 +numba==0.58.0 +numcodecs==0.12.0 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 omnipose @ git+https://github.com/kevinjohncutler/omnipose.git@ce2e9aa -opencv-python-headless==4.8.0.76 +opencv-python-headless==4.8.1.78 opt-einsum==3.3.0 opt-einsum-fx==0.1.4 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 peakdetect==1.2 -pillow==10.0.0 -platformdirs==3.10.0 -point-cloud-utils==0.29.6 +pillow==10.0.1 +platformdirs==3.11.0 +point-cloud-utils==0.30.0 pooch==1.7.0 -PrettyTable==3.8.0 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 -py3nj==0.2.1 +py3nj==0.1.2 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 +pydantic==2.4.2 +pydantic-core==2.10.1 pyerfa==2.0.0.3 pygments==2.16.1 pyjwt==2.8.0 -pymanopt==2.1.1 +pymanopt==2.2.0 pyntcloud==0.3.1 -pyparsing==3.0.9 +pyparsing==3.1.1 pyperclip==1.8.2 pyshtools==4.10.3 python-dateutil==2.8.2 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytorch-ranger==0.1.1 pytz==2023.3.post1 PyWavelets==1.4.1 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 +rich==13.6.0 s3fs==2023.3.0 s3transfer==0.6.2 -safetensors==0.3.3 +safetensors==0.4.0 scikit-image==0.21.0 -scikit-learn==1.3.0 -scipy==1.10.1 -setuptools==68.2.0 +scikit-learn==1.3.1 +scipy==1.9.3 +scyjava==1.9.1 shellingham==1.5.3 -SimpleITK==2.2.1 +SimpleITK==2.3.0 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 snowballstemmer==2.2.0 sortedcontainers==2.4.0 soupsieve==2.5 @@ -195,47 +180,42 @@ sphinxcontrib-htmlhelp==2.0.1 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==1.0.3 sphinxcontrib-serializinghtml==1.1.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 tblib==2.0.0 termcolor==2.3.0 -texttable==1.6.7 +texttable==1.7.0 threadpoolctl==3.2.0 tifffile==2023.7.10 timm==0.9.7 toolz==0.12.0 torch==2.0.1 -torch-geometric==2.3.1 +torch-geometric==2.4.0 torch-optimizer==0.3.0 torchio==0.19.1 -torchmetrics==1.1.1 -torchserve==0.8.2 +torchmetrics==1.2.0 +torchserve==0.9.0 torchvf==0.1.3 torchvision==0.15.2 tornado==6.3.3 tqdm==4.66.1 -traitlets==5.9.0 typer==0.9.0 -typing-extensions==4.7.1 +typing-extensions==4.8.0 universal-pathlib==0.1.3 -urllib3==1.26.16 -uvicorn==0.23.2 +urllib3==1.26.17 vtk==9.2.6 -wcwidth==0.2.6 -websocket-client==1.6.2 -websockets==11.0.3 -Werkzeug==2.3.7 +wcwidth==0.2.8 +websocket-client==1.6.4 +Werkzeug==3.0.0 wheel==0.41.2 wrapt==1.15.0 xarray==2023.1.0 -xmlschema==2.4.0 +xmlschema==2.5.0 xsdata==23.8 yarl==1.9.2 zarr==2.16.1 zict==3.0.0 -zipp==3.16.2 +zipp==3.17.0 diff --git a/requirements/macos/equiv-requirements.txt b/requirements/macos/equiv-requirements.txt index aa92bfc42..c1d701be0 100644 --- a/requirements/macos/equiv-requirements.txt +++ b/requirements/macos/equiv-requirements.txt @@ -3,151 +3,128 @@ aicsimageio==4.11.0 aiobotocore==2.4.2 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 async-timeout==4.0.3 attrs==23.1.0 autograd==1.6.2 autopage==0.5.1 -backoff==2.2.1 -beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 botocore==1.27.59 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 cmaes==0.10.0 cmd2==2.4.3 colorlog==6.7.0 -contourpy==1.1.0 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 e3nn==0.5.1 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -escnn==1.0.7 -exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 -filelock==3.12.3 +escnn==1.0.11 +fasteners==0.19 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 future==0.18.3 gitdb==4.0.10 -gitpython==3.1.35 -greenlet==2.0.2 +gitpython==3.1.37 +greenlet==3.0.0 gunicorn==21.2.0 -h11==0.14.0 -h5py==3.9.0 +h5py==3.10.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 importlib-metadata==6.8.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 lie-learn @ git+https://github.com/colobas/lie_learn.git@d5be2ab -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 locket==1.0.0 lxml==4.9.3 Mako==1.2.4 -markdown==3.4.4 -markdown-it-py==3.0.0 +markdown==3.5 MarkupSafe==2.1.3 -matplotlib==3.7.2 -mdurl==0.1.2 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +matplotlib==3.7.3 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.11.0 +numcodecs==0.12.0 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 opt-einsum==3.3.0 opt-einsum-fx==0.1.4 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 -pillow==10.0.0 -PrettyTable==3.8.0 +pillow==10.0.1 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 -py3nj==0.2.1 +py3nj==0.1.2 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 -pygments==2.16.1 +pydantic==2.4.2 +pydantic-core==2.10.1 pyjwt==2.8.0 -pymanopt==2.1.1 -pyparsing==3.0.9 +pymanopt==2.2.0 +pyparsing==3.1.1 pyperclip==1.8.2 python-dateutil==2.8.2 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytz==2023.3.post1 PyWavelets==1.4.1 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 s3fs==2023.3.0 scikit-image==0.21.0 -scikit-learn==1.3.0 -scipy==1.10.1 -setuptools==68.2.0 +scikit-learn==1.3.1 +scipy==1.9.3 +scyjava==1.9.1 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 sortedcontainers==2.4.0 -soupsieve==2.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 @@ -157,23 +134,20 @@ threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 torch==2.0.1 -torchmetrics==1.1.1 +torchmetrics==1.2.0 tornado==6.3.3 tqdm==4.66.1 -traitlets==5.9.0 -typing-extensions==4.7.1 +typing-extensions==4.8.0 universal-pathlib==0.1.3 -urllib3==1.26.16 -uvicorn==0.23.2 -wcwidth==0.2.6 -websocket-client==1.6.2 -websockets==11.0.3 -Werkzeug==2.3.7 +urllib3==1.26.17 +wcwidth==0.2.8 +websocket-client==1.6.4 +Werkzeug==3.0.0 wrapt==1.15.0 xarray==2023.1.0 -xmlschema==2.4.0 +xmlschema==2.5.0 xsdata==23.8 yarl==1.9.2 zarr==2.16.1 zict==3.0.0 -zipp==3.16.2 +zipp==3.17.0 diff --git a/requirements/macos/omnipose-requirements.txt b/requirements/macos/omnipose-requirements.txt index aa056e08c..ec861339e 100644 --- a/requirements/macos/omnipose-requirements.txt +++ b/requirements/macos/omnipose-requirements.txt @@ -3,185 +3,159 @@ aicsimageio==4.11.0 aiobotocore==2.4.2 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 async-timeout==4.0.3 attrs==23.1.0 autopage==0.5.1 -backoff==2.2.1 -beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 botocore==1.27.59 cellpose-omni==0.9.1 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 cmaes==0.10.0 cmd2==2.4.3 colorlog==6.7.0 -contourpy==1.1.0 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 edt==2.3.1 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 +fasteners==0.19 fastremap==1.14.0 -filelock==3.12.3 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 gitdb==4.0.10 -gitpython==3.1.35 -greenlet==2.0.2 +gitpython==3.1.37 +greenlet==3.0.0 gunicorn==21.2.0 -h11==0.14.0 -h5py==3.9.0 +h5py==3.10.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 -igraph==0.10.6 +igraph==0.11.2 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 importlib-metadata==6.8.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 -llvmlite==0.40.1 +llvmlite==0.41.0 locket==1.0.0 lxml==4.9.3 mahotas==1.4.13 Mako==1.2.4 -markdown==3.4.4 -markdown-it-py==3.0.0 +markdown==3.5 MarkupSafe==2.1.3 -matplotlib==3.7.2 -mdurl==0.1.2 +matplotlib==3.7.3 mgen==1.2.1 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 ncolor==1.2.1 networkx==3.1 -numba==0.57.1 -numcodecs==0.11.0 +numba==0.58.0 +numcodecs==0.12.0 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 omnipose @ git+https://github.com/kevinjohncutler/omnipose.git@ce2e9aa -opencv-python-headless==4.8.0.76 +opencv-python-headless==4.8.1.78 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 peakdetect==1.2 -pillow==10.0.0 -PrettyTable==3.8.0 +pillow==10.0.1 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 -pygments==2.16.1 +pydantic==2.4.2 +pydantic-core==2.10.1 pyjwt==2.8.0 -pyparsing==3.0.9 +pyparsing==3.1.1 pyperclip==1.8.2 python-dateutil==2.8.2 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytorch-ranger==0.1.1 pytz==2023.3.post1 PyWavelets==1.4.1 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 s3fs==2023.3.0 scikit-image==0.21.0 -scikit-learn==1.3.0 -scipy==1.10.1 -setuptools==68.2.0 +scikit-learn==1.3.1 +scipy==1.9.3 +scyjava==1.9.1 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 sortedcontainers==2.4.0 -soupsieve==2.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 tblib==2.0.0 termcolor==2.3.0 -texttable==1.6.7 +texttable==1.7.0 threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 torch==2.0.1 torch-optimizer==0.3.0 -torchmetrics==1.1.1 +torchmetrics==1.2.0 torchvf==0.1.3 torchvision==0.15.2 tornado==6.3.3 tqdm==4.66.1 -traitlets==5.9.0 -typing-extensions==4.7.1 +typing-extensions==4.8.0 universal-pathlib==0.1.3 -urllib3==1.26.16 -uvicorn==0.23.2 -wcwidth==0.2.6 -websocket-client==1.6.2 -websockets==11.0.3 -Werkzeug==2.3.7 +urllib3==1.26.17 +wcwidth==0.2.8 +websocket-client==1.6.4 +Werkzeug==3.0.0 wrapt==1.15.0 xarray==2023.1.0 -xmlschema==2.4.0 +xmlschema==2.5.0 xsdata==23.8 yarl==1.9.2 zarr==2.16.1 zict==3.0.0 -zipp==3.16.2 +zipp==3.17.0 diff --git a/requirements/macos/pdm.lock b/requirements/macos/pdm.lock index 9d7ee5a7c..efab9c2ce 100644 --- a/requirements/macos/pdm.lock +++ b/requirements/macos/pdm.lock @@ -6,7 +6,7 @@ groups = ["default", "all", "docs", "equiv", "omnipose", "pcloud", "s3", "spharm cross_platform = false static_urls = false lock_version = "4.3" -content_hash = "sha256:2ee3b0f492ef4c233c7454749aa28a2ea58edb7605b0bc866176c370107009f5" +content_hash = "sha256:e37073446848e15bbc0ccb7f651dad85c6d46e07816b4b1fe870c7ee6aa14abd" [[package]] name = "aicscytoparam" @@ -88,7 +88,7 @@ files = [ [[package]] name = "aiohttp" -version = "3.8.5" +version = "3.8.6" requires_python = ">=3.6" summary = "Async http client/server framework (asyncio)" dependencies = [ @@ -101,9 +101,9 @@ dependencies = [ "yarl<2.0,>=1.0", ] files = [ - {file = "aiohttp-3.8.5-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:a94159871304770da4dd371f4291b20cac04e8c94f11bdea1c3478e557fbe0d8"}, - {file = "aiohttp-3.8.5-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:13bf85afc99ce6f9ee3567b04501f18f9f8dbbb2ea11ed1a2e079670403a7c84"}, - {file = "aiohttp-3.8.5.tar.gz", hash = "sha256:b9552ec52cc147dbf1944ac7ac98af7602e51ea2dcd076ed194ca3c0d1c7d0bc"}, + {file = "aiohttp-3.8.6-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:41d55fc043954cddbbd82503d9cc3f4814a40bcef30b3569bc7b5e34130718c1"}, + {file = "aiohttp-3.8.6-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:1d84166673694841d8953f0a8d0c90e1087739d24632fe86b1a08819168b4566"}, + {file = "aiohttp-3.8.6.tar.gz", hash = "sha256:b0cf2a4501bff9330a8a5248b4ce951851e415bdcce9dc158e76cfd55e15085c"}, ] [[package]] @@ -174,12 +174,12 @@ files = [ [[package]] name = "annotated-types" -version = "0.5.0" -requires_python = ">=3.7" +version = "0.6.0" +requires_python = ">=3.8" summary = "Reusable constraint types to use with typing.Annotated" files = [ - {file = "annotated_types-0.5.0-py3-none-any.whl", hash = "sha256:58da39888f92c276ad970249761ebea80ba544b77acddaa1a4d6cf78287d45fd"}, - {file = "annotated_types-0.5.0.tar.gz", hash = "sha256:47cdc3490d9ac1506ce92c7aaa76c579dc3509ff11e098fc867e5130ab7be802"}, + {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"}, + {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"}, ] [[package]] @@ -190,34 +190,6 @@ files = [ {file = "antlr4-python3-runtime-4.9.3.tar.gz", hash = "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"}, ] -[[package]] -name = "anyio" -version = "3.7.1" -requires_python = ">=3.7" -summary = "High level compatibility layer for multiple asynchronous event loop implementations" -dependencies = [ - "exceptiongroup; python_version < \"3.11\"", - "idna>=2.8", - "sniffio>=1.1", -] -files = [ - {file = "anyio-3.7.1-py3-none-any.whl", hash = "sha256:91dee416e570e92c64041bd18b900d1d6fa78dff7048769ce5ac5ddad004fbb5"}, - {file = "anyio-3.7.1.tar.gz", hash = "sha256:44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780"}, -] - -[[package]] -name = "arrow" -version = "1.2.3" -requires_python = ">=3.6" -summary = "Better dates & times for Python" -dependencies = [ - "python-dateutil>=2.7.0", -] -files = [ - {file = "arrow-1.2.3-py3-none-any.whl", hash = "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"}, - {file = "arrow-1.2.3.tar.gz", hash = "sha256:3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1"}, -] - [[package]] name = "asciitree" version = "0.3.3" @@ -287,22 +259,12 @@ files = [ [[package]] name = "babel" -version = "2.12.1" +version = "2.13.0" requires_python = ">=3.7" summary = "Internationalization utilities" files = [ - {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"}, - {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"}, -] - -[[package]] -name = "backoff" -version = "2.2.1" -requires_python = ">=3.7,<4.0" -summary = "Function decoration for backoff and retry" -files = [ - {file = "backoff-2.2.1-py3-none-any.whl", 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= "1.6.2" +version = "1.6.3" requires_python = ">=3.7" summary = "Fast, simple object-to-object and broadcast signaling" files = [ - {file = "blinker-1.6.2-py3-none-any.whl", hash = "sha256:c3d739772abb7bc2860abf5f2ec284223d9ad5c76da018234f6f50d6f31ab1f0"}, - {file = "blinker-1.6.2.tar.gz", hash = "sha256:4afd3de66ef3a9f8067559fb7a1cbe555c17dcbe15971b05d1b625c3e7abe213"}, + {file = "blinker-1.6.3-py3-none-any.whl", hash = "sha256:296320d6c28b006eb5e32d4712202dbcdcbf5dc482da298c2f44881c43884aaa"}, + {file = "blinker-1.6.3.tar.gz", hash = "sha256:152090d27c1c5c722ee7e48504b02d76502811ce02e1523553b4cf8c8b3d3a8d"}, ] [[package]] @@ -440,14 +390,14 @@ files = [ [[package]] name = "charset-normalizer" -version = "3.2.0" +version = "3.3.0" requires_python = ">=3.7.0" summary = "The Real First Universal Charset Detector. 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"websockets-11.0.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:d67ac60a307f760c6e65dad586f556dde58e683fab03323221a4e530ead6f74d"}, - {file = "websockets-11.0.3-py3-none-any.whl", hash = "sha256:6681ba9e7f8f3b19440921e99efbb40fc89f26cd71bf539e45d8c8a25c976dc6"}, - {file = "websockets-11.0.3.tar.gz", hash = "sha256:88fc51d9a26b10fc331be344f1781224a375b78488fc343620184e95a4b27016"}, + {file = "websocket-client-1.6.4.tar.gz", hash = "sha256:b3324019b3c28572086c4a319f91d1dcd44e6e11cd340232978c684a7650d0df"}, + {file = "websocket_client-1.6.4-py3-none-any.whl", hash = "sha256:084072e0a7f5f347ef2ac3d8698a5e0b4ffbfcab607628cadabc650fc9a83a24"}, ] [[package]] name = "werkzeug" -version = "2.3.7" +version = "3.0.0" requires_python = ">=3.8" summary = "The comprehensive WSGI web application library." dependencies = [ "MarkupSafe>=2.1.1", ] files = [ - {file = "werkzeug-2.3.7-py3-none-any.whl", hash = "sha256:effc12dba7f3bd72e605ce49807bbe692bd729c3bb122a3b91747a6ae77df528"}, - {file = "werkzeug-2.3.7.tar.gz", hash = "sha256:2b8c0e447b4b9dbcc85dd97b6eeb4dcbaf6c8b6c3be0bd654e25553e0a2157d8"}, + {file = "werkzeug-3.0.0-py3-none-any.whl", hash = "sha256:cbb2600f7eabe51dbc0502f58be0b3e1b96b893b05695ea2b35b43d4de2d9962"}, + {file = "werkzeug-3.0.0.tar.gz", hash = "sha256:3ffff4dcc32db52ef3cc94dff3000a3c2846890f3a5a51800a27b909c5e770f0"}, ] [[package]] @@ -3265,15 +2996,15 @@ files = [ [[package]] name = "xmlschema" -version = "2.4.0" +version = "2.5.0" requires_python = ">=3.7" summary = "An XML Schema validator and decoder" dependencies = [ "elementpath<5.0.0,>=4.1.5", ] files = [ - {file = "xmlschema-2.4.0-py3-none-any.whl", hash = "sha256:dc87be0caaa61f42649899189aab2fd8e0d567f2cf548433ba7b79278d231a4a"}, - {file = "xmlschema-2.4.0.tar.gz", hash = "sha256:d74cd0c10866ac609e1ef94a5a69b018ad16e39077bc6393408b40c6babee793"}, + {file = "xmlschema-2.5.0-py3-none-any.whl", hash = "sha256:f2b29c45485fac414cc1fdb38d18a220c5987d7d3aa996e6df6ff35ee94d5a63"}, + {file = "xmlschema-2.5.0.tar.gz", hash = "sha256:276a03e0fd3c94c148d528bff4d9482f9b99bf8c7b4056a2e8e703d28149d454"}, ] [[package]] @@ -3332,10 +3063,10 @@ files = [ [[package]] name = "zipp" -version = "3.16.2" +version = "3.17.0" requires_python = ">=3.8" summary = "Backport of pathlib-compatible object wrapper for zip files" files = [ - {file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"}, - {file = "zipp-3.16.2.tar.gz", hash = "sha256:ebc15946aa78bd63458992fc81ec3b6f7b1e92d51c35e6de1c3804e73b799147"}, + {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"}, + {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"}, ] diff --git a/requirements/macos/requirements.txt b/requirements/macos/requirements.txt index d2d6f24c2..adeaf1652 100644 --- a/requirements/macos/requirements.txt +++ b/requirements/macos/requirements.txt @@ -3,142 +3,119 @@ aicsimageio==4.11.0 aiobotocore==2.5.4 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 async-timeout==4.0.3 attrs==23.1.0 autopage==0.5.1 -backoff==2.2.1 -beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 botocore==1.31.17 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 cmaes==0.10.0 cmd2==2.4.3 colorlog==6.7.0 -contourpy==1.1.0 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 -filelock==3.12.3 +fasteners==0.19 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 -fsspec==2023.9.0 +fsspec==2023.9.2 gitdb==4.0.10 -gitpython==3.1.35 -greenlet==2.0.2 +gitpython==3.1.37 +greenlet==3.0.0 gunicorn==21.2.0 -h11==0.14.0 -h5py==3.9.0 +h5py==3.10.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 importlib-metadata==6.8.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 locket==1.0.0 lxml==4.9.3 Mako==1.2.4 -markdown==3.4.4 -markdown-it-py==3.0.0 +markdown==3.5 MarkupSafe==2.1.3 -matplotlib==3.7.2 -mdurl==0.1.2 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +matplotlib==3.7.3 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.11.0 +numcodecs==0.12.0 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 -pillow==10.0.0 -PrettyTable==3.8.0 +pillow==10.0.1 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 -pygments==2.16.1 +pydantic==2.4.2 +pydantic-core==2.10.1 pyjwt==2.8.0 -pyparsing==3.0.9 +pyparsing==3.1.1 pyperclip==1.8.2 python-dateutil==2.8.2 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytz==2023.3.post1 PyWavelets==1.4.1 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 -s3fs==2023.9.0 +s3fs==2023.9.2 scikit-image==0.21.0 -scikit-learn==1.3.0 +scikit-learn==1.3.1 scipy==1.10.1 -setuptools==68.2.0 +scyjava==1.9.1 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 sortedcontainers==2.4.0 -soupsieve==2.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 @@ -147,24 +124,21 @@ termcolor==2.3.0 threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 -torch==2.0.1 -torchmetrics==1.1.1 +torch==2.1.0 +torchmetrics==1.2.0 tornado==6.3.3 tqdm==4.66.1 -traitlets==5.9.0 -typing-extensions==4.7.1 +typing-extensions==4.8.0 universal-pathlib==0.1.3 -urllib3==1.26.16 -uvicorn==0.23.2 -wcwidth==0.2.6 -websocket-client==1.6.2 -websockets==11.0.3 -Werkzeug==2.3.7 +urllib3==1.26.17 +wcwidth==0.2.8 +websocket-client==1.6.4 +Werkzeug==3.0.0 wrapt==1.15.0 xarray==2023.1.0 -xmlschema==2.4.0 +xmlschema==2.5.0 xsdata==23.8 yarl==1.9.2 zarr==2.16.1 zict==3.0.0 -zipp==3.16.2 +zipp==3.17.0 diff --git a/requirements/macos/spharm-requirements.txt b/requirements/macos/spharm-requirements.txt index e4ad0e380..5e3de1915 100644 --- a/requirements/macos/spharm-requirements.txt +++ b/requirements/macos/spharm-requirements.txt @@ -5,147 +5,124 @@ aicscytoparam==0.1.9 aicsimageio==4.11.0 aicsshparam==0.1.7 aiobotocore==2.4.2 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 autopage==0.5.1 -backoff==2.2.1 -beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 botocore==1.27.59 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 cmaes==0.10.0 cmd2==2.4.3 colorlog==6.7.0 -contourpy==1.1.0 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 -filelock==3.12.3 +fasteners==0.19 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 gitdb==4.0.10 -gitpython==3.1.35 -greenlet==2.0.2 +gitpython==3.1.37 +greenlet==3.0.0 gunicorn==21.2.0 -h11==0.14.0 -h5py==3.9.0 +h5py==3.10.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 importlib-metadata==6.8.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 locket==1.0.0 lxml==4.9.3 Mako==1.2.4 -markdown==3.4.4 -markdown-it-py==3.0.0 +markdown==3.5 MarkupSafe==2.1.3 -matplotlib==3.7.2 -mdurl==0.1.2 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +matplotlib==3.7.3 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.11.0 +numcodecs==0.12.0 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 -pillow==10.0.0 -platformdirs==3.10.0 +pillow==10.0.1 +platformdirs==3.11.0 pooch==1.7.0 -PrettyTable==3.8.0 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 +pydantic==2.4.2 +pydantic-core==2.10.1 pyerfa==2.0.0.3 -pygments==2.16.1 pyjwt==2.8.0 -pyparsing==3.0.9 +pyparsing==3.1.1 pyperclip==1.8.2 pyshtools==4.10.3 python-dateutil==2.8.2 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytz==2023.3.post1 PyWavelets==1.4.1 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 s3fs==2023.3.0 scikit-image==0.21.0 -scikit-learn==1.3.0 -scipy==1.10.1 -setuptools==68.2.0 +scikit-learn==1.3.1 +scipy==1.9.3 +scyjava==1.9.1 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 sortedcontainers==2.4.0 -soupsieve==2.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 @@ -155,24 +132,21 @@ threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 torch==2.0.1 -torchmetrics==1.1.1 +torchmetrics==1.2.0 tornado==6.3.3 tqdm==4.66.1 -traitlets==5.9.0 -typing-extensions==4.7.1 +typing-extensions==4.8.0 universal-pathlib==0.1.3 -urllib3==1.26.16 -uvicorn==0.23.2 +urllib3==1.26.17 vtk==9.2.6 -wcwidth==0.2.6 -websocket-client==1.6.2 -websockets==11.0.3 -Werkzeug==2.3.7 +wcwidth==0.2.8 +websocket-client==1.6.4 +Werkzeug==3.0.0 wrapt==1.15.0 xarray==2023.1.0 -xmlschema==2.4.0 +xmlschema==2.5.0 xsdata==23.8 yarl==1.9.2 zarr==2.16.1 zict==3.0.0 -zipp==3.16.2 +zipp==3.17.0 diff --git a/requirements/macos/test-requirements.txt b/requirements/macos/test-requirements.txt index 2c58a886c..d68b0f324 100644 --- a/requirements/macos/test-requirements.txt +++ b/requirements/macos/test-requirements.txt @@ -5,31 +5,26 @@ aicscytoparam==0.1.9 aicsimageio==4.11.0 aicsshparam==0.1.7 aiobotocore==2.4.2 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 autograd==1.6.2 autopage==0.5.1 -backoff==2.2.1 -beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 boto3==1.24.4 botocore==1.27.59 cellpose-omni==0.9.1 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 @@ -37,122 +32,116 @@ cmaes==0.10.0 cmd2==2.4.3 colorama==0.4.6 colorlog==6.7.0 -contourpy==1.1.0 -coverage==7.3.1 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +coverage==7.3.2 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 Deprecated==1.2.14 distributed==2023.5.0 docker==6.1.3 e3nn==0.5.1 edt==2.3.1 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -escnn==1.0.7 +escnn==1.0.11 exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 +fasteners==0.19 fastremap==1.14.0 -filelock==3.12.3 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 future==0.18.3 geomloss==0.2.6 gitdb==4.0.10 -gitpython==3.1.35 +gitpython==3.1.37 gorilla==0.4.0 -greenlet==2.0.2 +greenlet==3.0.0 gunicorn==21.2.0 -h11==0.14.0 -h5py==3.9.0 -huggingface-hub==0.16.4 +h5py==3.10.0 +huggingface-hub==0.17.3 humanize==4.8.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 -igraph==0.10.6 +igraph==0.11.2 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 importlib-metadata==6.8.0 iniconfig==2.0.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 lie-learn @ git+https://github.com/colobas/lie_learn.git@d5be2ab -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 -llvmlite==0.40.1 +llvmlite==0.41.0 locket==1.0.0 lxml==4.9.3 mahotas==1.4.13 Mako==1.2.4 -markdown==3.4.4 +markdown==3.5 markdown-it-py==3.0.0 MarkupSafe==2.1.3 -matplotlib==3.7.2 +matplotlib==3.7.3 mdurl==0.1.2 mgen==1.2.1 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 ncolor==1.2.1 networkx==3.1 nibabel==5.1.0 -Ninja==1.11.1 -numba==0.57.1 -numcodecs==0.11.0 +Ninja==1.11.1.1 +numba==0.58.0 +numcodecs==0.12.0 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 omnipose @ git+https://github.com/kevinjohncutler/omnipose.git@ce2e9aa -opencv-python-headless==4.8.0.76 +opencv-python-headless==4.8.1.78 opt-einsum==3.3.0 opt-einsum-fx==0.1.4 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 peakdetect==1.2 -pillow==10.0.0 -platformdirs==3.10.0 +pillow==10.0.1 +platformdirs==3.11.0 pluggy==1.3.0 -point-cloud-utils==0.29.6 +point-cloud-utils==0.30.0 pooch==1.7.0 -PrettyTable==3.8.0 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 -py3nj==0.2.1 +py3nj==0.1.2 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 +pydantic==2.4.2 +pydantic-core==2.10.1 pyerfa==2.0.0.3 pygments==2.16.1 pyjwt==2.8.0 -pymanopt==2.1.1 +pymanopt==2.2.0 pyntcloud==0.3.1 -pyparsing==3.0.9 +pyparsing==3.1.1 pyperclip==1.8.2 pyrootutils==1.0.4 pyshtools==4.10.3 @@ -160,74 +149,64 @@ pytest==7.4.2 pytest-cov==4.1.0 python-dateutil==2.8.2 python-dotenv==1.0.0 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytorch-ranger==0.1.1 pytz==2023.3.post1 PyWavelets==1.4.1 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 +rich==13.6.0 s3fs==2023.3.0 s3transfer==0.6.2 -safetensors==0.3.3 +safetensors==0.4.0 scikit-image==0.21.0 -scikit-learn==1.3.0 -scipy==1.10.1 -setuptools==68.2.0 +scikit-learn==1.3.1 +scipy==1.9.3 +scyjava==1.9.1 shellingham==1.5.3 -SimpleITK==2.2.1 +SimpleITK==2.3.0 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 sortedcontainers==2.4.0 -soupsieve==2.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 tblib==2.0.0 termcolor==2.3.0 -texttable==1.6.7 +texttable==1.7.0 threadpoolctl==3.2.0 tifffile==2023.7.10 timm==0.9.7 tomli==2.0.1 toolz==0.12.0 torch==2.0.1 -torch-geometric==2.3.1 +torch-geometric==2.4.0 torch-optimizer==0.3.0 torchio==0.19.1 -torchmetrics==1.1.1 -torchserve==0.8.2 +torchmetrics==1.2.0 +torchserve==0.9.0 torchvf==0.1.3 torchvision==0.15.2 tornado==6.3.3 tqdm==4.66.1 -traitlets==5.9.0 typer==0.9.0 -typing-extensions==4.7.1 +typing-extensions==4.8.0 universal-pathlib==0.1.3 -urllib3==1.26.16 -uvicorn==0.23.2 +urllib3==1.26.17 vtk==9.2.6 -wcwidth==0.2.6 -websocket-client==1.6.2 -websockets==11.0.3 -Werkzeug==2.3.7 +wcwidth==0.2.8 +websocket-client==1.6.4 +Werkzeug==3.0.0 wheel==0.41.2 wrapt==1.15.0 xarray==2023.1.0 -xmlschema==2.4.0 +xmlschema==2.5.0 xsdata==23.8 yarl==1.9.2 zarr==2.16.1 zict==3.0.0 -zipp==3.16.2 +zipp==3.17.0 diff --git a/requirements/macos/torchserve-requirements.txt b/requirements/macos/torchserve-requirements.txt index dbe7db526..beb5bd4f3 100644 --- a/requirements/macos/torchserve-requirements.txt +++ b/requirements/macos/torchserve-requirements.txt @@ -3,143 +3,120 @@ aicsimageio==4.11.0 aiobotocore==2.4.2 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 async-timeout==4.0.3 attrs==23.1.0 autopage==0.5.1 -backoff==2.2.1 -beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 botocore==1.27.59 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 cmaes==0.10.0 cmd2==2.4.3 colorlog==6.7.0 -contourpy==1.1.0 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 -filelock==3.12.3 +fasteners==0.19 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 gitdb==4.0.10 -gitpython==3.1.35 +gitpython==3.1.37 gorilla==0.4.0 -greenlet==2.0.2 +greenlet==3.0.0 gunicorn==21.2.0 -h11==0.14.0 -h5py==3.9.0 +h5py==3.10.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 importlib-metadata==6.8.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 locket==1.0.0 lxml==4.9.3 Mako==1.2.4 -markdown==3.4.4 -markdown-it-py==3.0.0 +markdown==3.5 MarkupSafe==2.1.3 -matplotlib==3.7.2 -mdurl==0.1.2 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +matplotlib==3.7.3 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.11.0 +numcodecs==0.12.0 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 -pillow==10.0.0 -PrettyTable==3.8.0 +pillow==10.0.1 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 -pygments==2.16.1 +pydantic==2.4.2 +pydantic-core==2.10.1 pyjwt==2.8.0 -pyparsing==3.0.9 +pyparsing==3.1.1 pyperclip==1.8.2 python-dateutil==2.8.2 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytz==2023.3.post1 PyWavelets==1.4.1 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 s3fs==2023.3.0 scikit-image==0.21.0 -scikit-learn==1.3.0 -scipy==1.10.1 -setuptools==68.2.0 +scikit-learn==1.3.1 +scipy==1.9.3 +scyjava==1.9.1 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 sortedcontainers==2.4.0 -soupsieve==2.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 @@ -149,25 +126,22 @@ threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 torch==2.0.1 -torchmetrics==1.1.1 -torchserve==0.8.2 +torchmetrics==1.2.0 +torchserve==0.9.0 tornado==6.3.3 tqdm==4.66.1 -traitlets==5.9.0 -typing-extensions==4.7.1 +typing-extensions==4.8.0 universal-pathlib==0.1.3 -urllib3==1.26.16 -uvicorn==0.23.2 -wcwidth==0.2.6 -websocket-client==1.6.2 -websockets==11.0.3 -Werkzeug==2.3.7 +urllib3==1.26.17 +wcwidth==0.2.8 +websocket-client==1.6.4 +Werkzeug==3.0.0 wheel==0.41.2 wrapt==1.15.0 xarray==2023.1.0 -xmlschema==2.4.0 +xmlschema==2.5.0 xsdata==23.8 yarl==1.9.2 zarr==2.16.1 zict==3.0.0 -zipp==3.16.2 +zipp==3.17.0 diff --git a/requirements/windows/all-requirements.txt b/requirements/windows/all-requirements.txt index 1210b3f01..13c24483f 100644 --- a/requirements/windows/all-requirements.txt +++ b/requirements/windows/all-requirements.txt @@ -5,32 +5,26 @@ aicscytoparam==0.1.9 aicsimageio==4.11.0 aicsshparam==0.1.7 aiobotocore==2.4.2 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 -ansicon==1.89.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 autograd==1.6.2 autopage==0.5.1 -backoff==2.2.1 -beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 boto3==1.24.4 botocore==1.27.59 cellpose-omni==0.9.1 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 @@ -38,192 +32,174 @@ cmaes==0.10.0 cmd2==2.4.3 colorama==0.4.6 colorlog==6.7.0 -contourpy==1.1.0 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 Deprecated==1.2.14 distributed==2023.5.0 docker==6.1.3 e3nn==0.5.1 edt==2.3.1 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -escnn==1.0.7 -exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 +escnn==1.0.11 +fasteners==0.19 fastremap==1.14.0 -filelock==3.12.3 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 future==0.18.3 geomloss==0.2.6 gitdb==4.0.10 -gitpython==3.1.35 +gitpython==3.1.37 gorilla==0.4.0 -greenlet==2.0.2 -h11==0.14.0 -h5py==3.9.0 -huggingface-hub==0.16.4 +greenlet==3.0.0 +h5py==3.10.0 +huggingface-hub==0.17.3 humanize==4.8.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 -igraph==0.10.6 +igraph==0.11.2 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 importlib-metadata==6.8.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 -jinxed==1.2.0 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 lie-learn @ git+https://github.com/colobas/lie_learn.git@d5be2ab -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 -llvmlite==0.40.1 +llvmlite==0.41.0 locket==1.0.0 lxml==4.9.3 mahotas==1.4.13 Mako==1.2.4 -markdown==3.4.4 +markdown==3.5 markdown-it-py==3.0.0 MarkupSafe==2.1.3 -matplotlib==3.7.2 +matplotlib==3.7.3 mdurl==0.1.2 mgen==1.2.1 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 ncolor==1.2.1 networkx==3.1 nibabel==5.1.0 -Ninja==1.11.1 -numba==0.57.1 -numcodecs==0.11.0 +Ninja==1.11.1.1 +numba==0.58.0 +numcodecs==0.12.0 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 omnipose @ git+https://github.com/kevinjohncutler/omnipose.git@ce2e9aa -opencv-python-headless==4.8.0.76 +opencv-python-headless==4.8.1.78 opt-einsum==3.3.0 opt-einsum-fx==0.1.4 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 peakdetect==1.2 -pillow==10.0.0 -platformdirs==3.10.0 -point-cloud-utils==0.29.6 +pillow==10.0.1 +platformdirs==3.11.0 +point-cloud-utils==0.30.0 pooch==1.7.0 -PrettyTable==3.8.0 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 -py3nj==0.2.1 +py3nj==0.1.2 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 +pydantic==2.4.2 +pydantic-core==2.10.1 pyerfa==2.0.0.3 pygments==2.16.1 pyjwt==2.8.0 -pymanopt==2.1.1 +pymanopt==2.2.0 pyntcloud==0.3.1 -pyparsing==3.0.9 +pyparsing==3.1.1 pyperclip==1.8.2 pyreadline3==3.4.1 pyshtools==4.10.3 python-dateutil==2.8.2 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytorch-ranger==0.1.1 pytz==2023.3.post1 PyWavelets==1.4.1 pywin32==306 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 +rich==13.6.0 s3fs==2023.3.0 s3transfer==0.6.2 -safetensors==0.3.3 +safetensors==0.4.0 scikit-image==0.21.0 -scikit-learn==1.3.0 -scipy==1.10.1 -setuptools==68.2.0 +scikit-learn==1.3.1 +scipy==1.9.3 +scyjava==1.9.1 shellingham==1.5.3 -SimpleITK==2.2.1 +SimpleITK==2.3.0 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 sortedcontainers==2.4.0 -soupsieve==2.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 tblib==2.0.0 termcolor==2.3.0 -texttable==1.6.7 +texttable==1.7.0 threadpoolctl==3.2.0 tifffile==2023.7.10 timm==0.9.7 toolz==0.12.0 torch==2.0.1 -torch-geometric==2.3.1 +torch-geometric==2.4.0 torch-optimizer==0.3.0 torchio==0.19.1 -torchmetrics==1.1.1 -torchserve==0.8.2 +torchmetrics==1.2.0 +torchserve==0.9.0 torchvf==0.1.3 torchvision==0.15.2 tornado==6.3.3 tqdm==4.66.1 -traitlets==5.9.0 typer==0.9.0 -typing-extensions==4.7.1 +typing-extensions==4.8.0 universal-pathlib==0.1.3 -urllib3==1.26.16 -uvicorn==0.23.2 +urllib3==1.26.17 vtk==9.2.6 waitress==2.1.2 -wcwidth==0.2.6 -websocket-client==1.6.2 -websockets==11.0.3 -Werkzeug==2.3.7 +wcwidth==0.2.8 +websocket-client==1.6.4 +Werkzeug==3.0.0 wheel==0.41.2 wrapt==1.15.0 xarray==2023.1.0 -xmlschema==2.4.0 +xmlschema==2.5.0 xsdata==23.8 yarl==1.9.2 zarr==2.16.1 zict==3.0.0 -zipp==3.16.2 +zipp==3.17.0 diff --git a/requirements/windows/docs-requirements.txt b/requirements/windows/docs-requirements.txt index 5a777a951..0a419b3f5 100644 --- a/requirements/windows/docs-requirements.txt +++ b/requirements/windows/docs-requirements.txt @@ -5,34 +5,29 @@ aicscytoparam==0.1.9 aicsimageio==4.11.0 aicsshparam==0.1.7 aiobotocore==2.4.2 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alabaster==0.7.13 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 -ansicon==1.89.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 autograd==1.6.2 autopage==0.5.1 -babel==2.12.1 -backoff==2.2.1 +babel==2.13.0 beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 boto3==1.24.4 botocore==1.27.59 cellpose-omni==0.9.1 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 @@ -40,153 +35,141 @@ cmaes==0.10.0 cmd2==2.4.3 colorama==0.4.6 colorlog==6.7.0 -contourpy==1.1.0 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 Deprecated==1.2.14 distributed==2023.5.0 docker==6.1.3 docutils==0.19 e3nn==0.5.1 edt==2.3.1 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -escnn==1.0.7 -exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 +escnn==1.0.11 +fasteners==0.19 fastremap==1.14.0 -filelock==3.12.3 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 furo==2023.3.23 future==0.18.3 geomloss==0.2.6 gitdb==4.0.10 -gitpython==3.1.35 +gitpython==3.1.37 gorilla==0.4.0 -greenlet==2.0.2 -h11==0.14.0 -h5py==3.9.0 -huggingface-hub==0.16.4 +greenlet==3.0.0 +h5py==3.10.0 +huggingface-hub==0.17.3 humanize==4.8.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 -igraph==0.10.6 +igraph==0.11.2 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 imagesize==1.4.1 importlib-metadata==6.8.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 -jinxed==1.2.0 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 lie-learn @ git+https://github.com/colobas/lie_learn.git@d5be2ab -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 -llvmlite==0.40.1 +llvmlite==0.41.0 locket==1.0.0 lxml==4.9.3 m2r2==0.3.3.post2 mahotas==1.4.13 Mako==1.2.4 -markdown==3.4.4 +markdown==3.5 markdown-it-py==3.0.0 MarkupSafe==2.1.3 -matplotlib==3.7.2 +matplotlib==3.7.3 mdurl==0.1.2 mgen==1.2.1 mistune==0.8.4 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 ncolor==1.2.1 networkx==3.1 nibabel==5.1.0 -Ninja==1.11.1 -numba==0.57.1 -numcodecs==0.11.0 +Ninja==1.11.1.1 +numba==0.58.0 +numcodecs==0.12.0 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 omnipose @ git+https://github.com/kevinjohncutler/omnipose.git@ce2e9aa -opencv-python-headless==4.8.0.76 +opencv-python-headless==4.8.1.78 opt-einsum==3.3.0 opt-einsum-fx==0.1.4 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 peakdetect==1.2 -pillow==10.0.0 -platformdirs==3.10.0 -point-cloud-utils==0.29.6 +pillow==10.0.1 +platformdirs==3.11.0 +point-cloud-utils==0.30.0 pooch==1.7.0 -PrettyTable==3.8.0 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 -py3nj==0.2.1 +py3nj==0.1.2 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 +pydantic==2.4.2 +pydantic-core==2.10.1 pyerfa==2.0.0.3 pygments==2.16.1 pyjwt==2.8.0 -pymanopt==2.1.1 +pymanopt==2.2.0 pyntcloud==0.3.1 -pyparsing==3.0.9 +pyparsing==3.1.1 pyperclip==1.8.2 pyreadline3==3.4.1 pyshtools==4.10.3 python-dateutil==2.8.2 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytorch-ranger==0.1.1 pytz==2023.3.post1 PyWavelets==1.4.1 pywin32==306 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 +rich==13.6.0 s3fs==2023.3.0 s3transfer==0.6.2 -safetensors==0.3.3 +safetensors==0.4.0 scikit-image==0.21.0 -scikit-learn==1.3.0 -scipy==1.10.1 -setuptools==68.2.0 +scikit-learn==1.3.1 +scipy==1.9.3 +scyjava==1.9.1 shellingham==1.5.3 -SimpleITK==2.2.1 +SimpleITK==2.3.0 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 snowballstemmer==2.2.0 sortedcontainers==2.4.0 soupsieve==2.5 @@ -198,48 +181,43 @@ sphinxcontrib-htmlhelp==2.0.1 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==1.0.3 sphinxcontrib-serializinghtml==1.1.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 tblib==2.0.0 termcolor==2.3.0 -texttable==1.6.7 +texttable==1.7.0 threadpoolctl==3.2.0 tifffile==2023.7.10 timm==0.9.7 toolz==0.12.0 torch==2.0.1 -torch-geometric==2.3.1 +torch-geometric==2.4.0 torch-optimizer==0.3.0 torchio==0.19.1 -torchmetrics==1.1.1 -torchserve==0.8.2 +torchmetrics==1.2.0 +torchserve==0.9.0 torchvf==0.1.3 torchvision==0.15.2 tornado==6.3.3 tqdm==4.66.1 -traitlets==5.9.0 typer==0.9.0 -typing-extensions==4.7.1 +typing-extensions==4.8.0 universal-pathlib==0.1.3 -urllib3==1.26.16 -uvicorn==0.23.2 +urllib3==1.26.17 vtk==9.2.6 waitress==2.1.2 -wcwidth==0.2.6 -websocket-client==1.6.2 -websockets==11.0.3 -Werkzeug==2.3.7 +wcwidth==0.2.8 +websocket-client==1.6.4 +Werkzeug==3.0.0 wheel==0.41.2 wrapt==1.15.0 xarray==2023.1.0 -xmlschema==2.4.0 +xmlschema==2.5.0 xsdata==23.8 yarl==1.9.2 zarr==2.16.1 zict==3.0.0 -zipp==3.16.2 +zipp==3.17.0 diff --git a/requirements/windows/equiv-requirements.txt b/requirements/windows/equiv-requirements.txt index 58cce705f..354d23938 100644 --- a/requirements/windows/equiv-requirements.txt +++ b/requirements/windows/equiv-requirements.txt @@ -3,29 +3,23 @@ aicsimageio==4.11.0 aiobotocore==2.4.2 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 -ansicon==1.89.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 async-timeout==4.0.3 attrs==23.1.0 autograd==1.6.2 autopage==0.5.1 -backoff==2.2.1 -beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 botocore==1.27.59 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 @@ -33,125 +27,106 @@ cmaes==0.10.0 cmd2==2.4.3 colorama==0.4.6 colorlog==6.7.0 -contourpy==1.1.0 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 e3nn==0.5.1 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -escnn==1.0.7 -exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 -filelock==3.12.3 +escnn==1.0.11 +fasteners==0.19 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 future==0.18.3 gitdb==4.0.10 -gitpython==3.1.35 -greenlet==2.0.2 -h11==0.14.0 -h5py==3.9.0 +gitpython==3.1.37 +greenlet==3.0.0 +h5py==3.10.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 importlib-metadata==6.8.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 -jinxed==1.2.0 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 lie-learn @ git+https://github.com/colobas/lie_learn.git@d5be2ab -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 locket==1.0.0 lxml==4.9.3 Mako==1.2.4 -markdown==3.4.4 -markdown-it-py==3.0.0 +markdown==3.5 MarkupSafe==2.1.3 -matplotlib==3.7.2 -mdurl==0.1.2 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +matplotlib==3.7.3 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.11.0 +numcodecs==0.12.0 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 opt-einsum==3.3.0 opt-einsum-fx==0.1.4 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 -pillow==10.0.0 -PrettyTable==3.8.0 +pillow==10.0.1 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 -py3nj==0.2.1 +py3nj==0.1.2 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 -pygments==2.16.1 +pydantic==2.4.2 +pydantic-core==2.10.1 pyjwt==2.8.0 -pymanopt==2.1.1 -pyparsing==3.0.9 +pymanopt==2.2.0 +pyparsing==3.1.1 pyperclip==1.8.2 pyreadline3==3.4.1 python-dateutil==2.8.2 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytz==2023.3.post1 PyWavelets==1.4.1 pywin32==306 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 s3fs==2023.3.0 scikit-image==0.21.0 -scikit-learn==1.3.0 -scipy==1.10.1 -setuptools==68.2.0 +scikit-learn==1.3.1 +scipy==1.9.3 +scyjava==1.9.1 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 sortedcontainers==2.4.0 -soupsieve==2.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 @@ -161,24 +136,21 @@ threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 torch==2.0.1 -torchmetrics==1.1.1 +torchmetrics==1.2.0 tornado==6.3.3 tqdm==4.66.1 -traitlets==5.9.0 -typing-extensions==4.7.1 +typing-extensions==4.8.0 universal-pathlib==0.1.3 -urllib3==1.26.16 -uvicorn==0.23.2 +urllib3==1.26.17 waitress==2.1.2 -wcwidth==0.2.6 -websocket-client==1.6.2 -websockets==11.0.3 -Werkzeug==2.3.7 +wcwidth==0.2.8 +websocket-client==1.6.4 +Werkzeug==3.0.0 wrapt==1.15.0 xarray==2023.1.0 -xmlschema==2.4.0 +xmlschema==2.5.0 xsdata==23.8 yarl==1.9.2 zarr==2.16.1 zict==3.0.0 -zipp==3.16.2 +zipp==3.17.0 diff --git a/requirements/windows/omnipose-requirements.txt b/requirements/windows/omnipose-requirements.txt index 50462b217..981545c4b 100644 --- a/requirements/windows/omnipose-requirements.txt +++ b/requirements/windows/omnipose-requirements.txt @@ -3,29 +3,23 @@ aicsimageio==4.11.0 aiobotocore==2.4.2 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 -ansicon==1.89.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 async-timeout==4.0.3 attrs==23.1.0 autopage==0.5.1 -backoff==2.2.1 -beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 botocore==1.27.59 cellpose-omni==0.9.1 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 @@ -33,160 +27,138 @@ cmaes==0.10.0 cmd2==2.4.3 colorama==0.4.6 colorlog==6.7.0 -contourpy==1.1.0 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 edt==2.3.1 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 +fasteners==0.19 fastremap==1.14.0 -filelock==3.12.3 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 gitdb==4.0.10 -gitpython==3.1.35 -greenlet==2.0.2 -h11==0.14.0 -h5py==3.9.0 +gitpython==3.1.37 +greenlet==3.0.0 +h5py==3.10.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 -igraph==0.10.6 +igraph==0.11.2 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 importlib-metadata==6.8.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 -jinxed==1.2.0 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 -llvmlite==0.40.1 +llvmlite==0.41.0 locket==1.0.0 lxml==4.9.3 mahotas==1.4.13 Mako==1.2.4 -markdown==3.4.4 -markdown-it-py==3.0.0 +markdown==3.5 MarkupSafe==2.1.3 -matplotlib==3.7.2 -mdurl==0.1.2 +matplotlib==3.7.3 mgen==1.2.1 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 ncolor==1.2.1 networkx==3.1 -numba==0.57.1 -numcodecs==0.11.0 +numba==0.58.0 +numcodecs==0.12.0 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 omnipose @ git+https://github.com/kevinjohncutler/omnipose.git@ce2e9aa -opencv-python-headless==4.8.0.76 +opencv-python-headless==4.8.1.78 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 peakdetect==1.2 -pillow==10.0.0 -PrettyTable==3.8.0 +pillow==10.0.1 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 -pygments==2.16.1 +pydantic==2.4.2 +pydantic-core==2.10.1 pyjwt==2.8.0 -pyparsing==3.0.9 +pyparsing==3.1.1 pyperclip==1.8.2 pyreadline3==3.4.1 python-dateutil==2.8.2 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytorch-ranger==0.1.1 pytz==2023.3.post1 PyWavelets==1.4.1 pywin32==306 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 s3fs==2023.3.0 scikit-image==0.21.0 -scikit-learn==1.3.0 -scipy==1.10.1 -setuptools==68.2.0 +scikit-learn==1.3.1 +scipy==1.9.3 +scyjava==1.9.1 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 sortedcontainers==2.4.0 -soupsieve==2.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 tblib==2.0.0 termcolor==2.3.0 -texttable==1.6.7 +texttable==1.7.0 threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 torch==2.0.1 torch-optimizer==0.3.0 -torchmetrics==1.1.1 +torchmetrics==1.2.0 torchvf==0.1.3 torchvision==0.15.2 tornado==6.3.3 tqdm==4.66.1 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"aicscytoparam" @@ -88,7 +88,7 @@ files = [ [[package]] name = "aiohttp" -version = "3.8.5" +version = "3.8.6" requires_python = ">=3.6" summary = "Async http client/server framework (asyncio)" dependencies = [ @@ -101,8 +101,8 @@ dependencies = [ "yarl<2.0,>=1.0", ] files = [ - {file = "aiohttp-3.8.5-cp310-cp310-win_amd64.whl", hash = "sha256:6e4a280e4b975a2e7745573e3fc9c9ba0d1194a3738ce1cbaa80626cc9b4f4df"}, - {file = "aiohttp-3.8.5.tar.gz", hash = "sha256:b9552ec52cc147dbf1944ac7ac98af7602e51ea2dcd076ed194ca3c0d1c7d0bc"}, + {file = "aiohttp-3.8.6-cp310-cp310-win_amd64.whl", hash = "sha256:93c15c8e48e5e7b89d5cb4613479d144fda8344e2d886cf694fd36db4cc86865"}, + {file = "aiohttp-3.8.6.tar.gz", hash = "sha256:b0cf2a4501bff9330a8a5248b4ce951851e415bdcce9dc158e76cfd55e15085c"}, ] [[package]] @@ -173,21 +173,12 @@ files = [ [[package]] name = "annotated-types" -version = "0.5.0" -requires_python = ">=3.7" +version = "0.6.0" +requires_python = ">=3.8" summary = "Reusable constraint types to use with typing.Annotated" files = [ - {file = "annotated_types-0.5.0-py3-none-any.whl", hash = "sha256:58da39888f92c276ad970249761ebea80ba544b77acddaa1a4d6cf78287d45fd"}, - {file = "annotated_types-0.5.0.tar.gz", hash = "sha256:47cdc3490d9ac1506ce92c7aaa76c579dc3509ff11e098fc867e5130ab7be802"}, -] - -[[package]] -name = "ansicon" -version = "1.89.0" -summary = "Python wrapper for loading Jason Hood's ANSICON" -files = [ - {file = "ansicon-1.89.0-py2.py3-none-any.whl", hash = "sha256:f1def52d17f65c2c9682cf8370c03f541f410c1752d6a14029f97318e4b9dfec"}, - {file = "ansicon-1.89.0.tar.gz", hash = "sha256:e4d039def5768a47e4afec8e89e83ec3ae5a26bf00ad851f914d1240b444d2b1"}, + {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"}, + {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"}, ] [[package]] @@ -198,34 +189,6 @@ files = [ {file = 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{file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"}, + {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"}, ] diff --git a/requirements/windows/requirements.txt b/requirements/windows/requirements.txt index e47f1dc2c..7a8fa29d0 100644 --- a/requirements/windows/requirements.txt +++ b/requirements/windows/requirements.txt @@ -3,28 +3,22 @@ aicsimageio==4.11.0 aiobotocore==2.5.4 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 -ansicon==1.89.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 async-timeout==4.0.3 attrs==23.1.0 autopage==0.5.1 -backoff==2.2.1 -beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 botocore==1.31.17 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 @@ -32,117 +26,98 @@ cmaes==0.10.0 cmd2==2.4.3 colorama==0.4.6 colorlog==6.7.0 -contourpy==1.1.0 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 -filelock==3.12.3 +fasteners==0.19 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 -fsspec==2023.9.0 +fsspec==2023.9.2 gitdb==4.0.10 -gitpython==3.1.35 -greenlet==2.0.2 -h11==0.14.0 -h5py==3.9.0 +gitpython==3.1.37 +greenlet==3.0.0 +h5py==3.10.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 importlib-metadata==6.8.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 -jinxed==1.2.0 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 locket==1.0.0 lxml==4.9.3 Mako==1.2.4 -markdown==3.4.4 -markdown-it-py==3.0.0 +markdown==3.5 MarkupSafe==2.1.3 -matplotlib==3.7.2 -mdurl==0.1.2 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +matplotlib==3.7.3 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.11.0 +numcodecs==0.12.0 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 -pillow==10.0.0 -PrettyTable==3.8.0 +pillow==10.0.1 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 -pygments==2.16.1 +pydantic==2.4.2 +pydantic-core==2.10.1 pyjwt==2.8.0 -pyparsing==3.0.9 +pyparsing==3.1.1 pyperclip==1.8.2 pyreadline3==3.4.1 python-dateutil==2.8.2 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytz==2023.3.post1 PyWavelets==1.4.1 pywin32==306 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 -s3fs==2023.9.0 +s3fs==2023.9.2 scikit-image==0.21.0 -scikit-learn==1.3.0 +scikit-learn==1.3.1 scipy==1.10.1 -setuptools==68.2.0 +scyjava==1.9.1 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 sortedcontainers==2.4.0 -soupsieve==2.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 @@ -151,25 +126,22 @@ termcolor==2.3.0 threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 -torch==2.0.1 -torchmetrics==1.1.1 +torch==2.1.0 +torchmetrics==1.2.0 tornado==6.3.3 tqdm==4.66.1 -traitlets==5.9.0 -typing-extensions==4.7.1 +typing-extensions==4.8.0 universal-pathlib==0.1.3 -urllib3==1.26.16 -uvicorn==0.23.2 +urllib3==1.26.17 waitress==2.1.2 -wcwidth==0.2.6 -websocket-client==1.6.2 -websockets==11.0.3 -Werkzeug==2.3.7 +wcwidth==0.2.8 +websocket-client==1.6.4 +Werkzeug==3.0.0 wrapt==1.15.0 xarray==2023.1.0 -xmlschema==2.4.0 +xmlschema==2.5.0 xsdata==23.8 yarl==1.9.2 zarr==2.16.1 zict==3.0.0 -zipp==3.16.2 +zipp==3.17.0 diff --git a/requirements/windows/spharm-requirements.txt b/requirements/windows/spharm-requirements.txt index 09875a1fe..708ade3b9 100644 --- a/requirements/windows/spharm-requirements.txt +++ b/requirements/windows/spharm-requirements.txt @@ -5,29 +5,23 @@ aicscytoparam==0.1.9 aicsimageio==4.11.0 aicsshparam==0.1.7 aiobotocore==2.4.2 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 -ansicon==1.89.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 autopage==0.5.1 -backoff==2.2.1 -beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 botocore==1.27.59 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 @@ -35,121 +29,102 @@ cmaes==0.10.0 cmd2==2.4.3 colorama==0.4.6 colorlog==6.7.0 -contourpy==1.1.0 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 -filelock==3.12.3 +fasteners==0.19 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 gitdb==4.0.10 -gitpython==3.1.35 -greenlet==2.0.2 -h11==0.14.0 -h5py==3.9.0 +gitpython==3.1.37 +greenlet==3.0.0 +h5py==3.10.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 importlib-metadata==6.8.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 -jinxed==1.2.0 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 locket==1.0.0 lxml==4.9.3 Mako==1.2.4 -markdown==3.4.4 -markdown-it-py==3.0.0 +markdown==3.5 MarkupSafe==2.1.3 -matplotlib==3.7.2 -mdurl==0.1.2 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +matplotlib==3.7.3 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.11.0 +numcodecs==0.12.0 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 -pillow==10.0.0 -platformdirs==3.10.0 +pillow==10.0.1 +platformdirs==3.11.0 pooch==1.7.0 -PrettyTable==3.8.0 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 +pydantic==2.4.2 +pydantic-core==2.10.1 pyerfa==2.0.0.3 -pygments==2.16.1 pyjwt==2.8.0 -pyparsing==3.0.9 +pyparsing==3.1.1 pyperclip==1.8.2 pyreadline3==3.4.1 pyshtools==4.10.3 python-dateutil==2.8.2 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytz==2023.3.post1 PyWavelets==1.4.1 pywin32==306 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 s3fs==2023.3.0 scikit-image==0.21.0 -scikit-learn==1.3.0 -scipy==1.10.1 -setuptools==68.2.0 +scikit-learn==1.3.1 +scipy==1.9.3 +scyjava==1.9.1 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 sortedcontainers==2.4.0 -soupsieve==2.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 @@ -159,25 +134,22 @@ threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 torch==2.0.1 -torchmetrics==1.1.1 +torchmetrics==1.2.0 tornado==6.3.3 tqdm==4.66.1 -traitlets==5.9.0 -typing-extensions==4.7.1 +typing-extensions==4.8.0 universal-pathlib==0.1.3 -urllib3==1.26.16 -uvicorn==0.23.2 +urllib3==1.26.17 vtk==9.2.6 waitress==2.1.2 -wcwidth==0.2.6 -websocket-client==1.6.2 -websockets==11.0.3 -Werkzeug==2.3.7 +wcwidth==0.2.8 +websocket-client==1.6.4 +Werkzeug==3.0.0 wrapt==1.15.0 xarray==2023.1.0 -xmlschema==2.4.0 +xmlschema==2.5.0 xsdata==23.8 yarl==1.9.2 zarr==2.16.1 zict==3.0.0 -zipp==3.16.2 +zipp==3.17.0 diff --git a/requirements/windows/test-requirements.txt b/requirements/windows/test-requirements.txt index 120521037..950ed3b19 100644 --- a/requirements/windows/test-requirements.txt +++ b/requirements/windows/test-requirements.txt @@ -5,32 +5,26 @@ aicscytoparam==0.1.9 aicsimageio==4.11.0 aicsshparam==0.1.7 aiobotocore==2.4.2 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 -ansicon==1.89.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 autograd==1.6.2 autopage==0.5.1 -backoff==2.2.1 -beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 boto3==1.24.4 botocore==1.27.59 cellpose-omni==0.9.1 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 @@ -38,122 +32,115 @@ cmaes==0.10.0 cmd2==2.4.3 colorama==0.4.6 colorlog==6.7.0 -contourpy==1.1.0 -coverage==7.3.1 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +coverage==7.3.2 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 Deprecated==1.2.14 distributed==2023.5.0 docker==6.1.3 e3nn==0.5.1 edt==2.3.1 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -escnn==1.0.7 +escnn==1.0.11 exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 +fasteners==0.19 fastremap==1.14.0 -filelock==3.12.3 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 future==0.18.3 geomloss==0.2.6 gitdb==4.0.10 -gitpython==3.1.35 +gitpython==3.1.37 gorilla==0.4.0 -greenlet==2.0.2 -h11==0.14.0 -h5py==3.9.0 -huggingface-hub==0.16.4 +greenlet==3.0.0 +h5py==3.10.0 +huggingface-hub==0.17.3 humanize==4.8.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 -igraph==0.10.6 +igraph==0.11.2 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 importlib-metadata==6.8.0 iniconfig==2.0.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 -jinxed==1.2.0 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 lie-learn @ git+https://github.com/colobas/lie_learn.git@d5be2ab -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 -llvmlite==0.40.1 +llvmlite==0.41.0 locket==1.0.0 lxml==4.9.3 mahotas==1.4.13 Mako==1.2.4 -markdown==3.4.4 +markdown==3.5 markdown-it-py==3.0.0 MarkupSafe==2.1.3 -matplotlib==3.7.2 +matplotlib==3.7.3 mdurl==0.1.2 mgen==1.2.1 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 ncolor==1.2.1 networkx==3.1 nibabel==5.1.0 -Ninja==1.11.1 -numba==0.57.1 -numcodecs==0.11.0 +Ninja==1.11.1.1 +numba==0.58.0 +numcodecs==0.12.0 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 omnipose @ git+https://github.com/kevinjohncutler/omnipose.git@ce2e9aa -opencv-python-headless==4.8.0.76 +opencv-python-headless==4.8.1.78 opt-einsum==3.3.0 opt-einsum-fx==0.1.4 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 peakdetect==1.2 -pillow==10.0.0 -platformdirs==3.10.0 +pillow==10.0.1 +platformdirs==3.11.0 pluggy==1.3.0 -point-cloud-utils==0.29.6 +point-cloud-utils==0.30.0 pooch==1.7.0 -PrettyTable==3.8.0 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 -py3nj==0.2.1 +py3nj==0.1.2 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 +pydantic==2.4.2 +pydantic-core==2.10.1 pyerfa==2.0.0.3 pygments==2.16.1 pyjwt==2.8.0 -pymanopt==2.1.1 +pymanopt==2.2.0 pyntcloud==0.3.1 -pyparsing==3.0.9 +pyparsing==3.1.1 pyperclip==1.8.2 pyreadline3==3.4.1 pyrootutils==1.0.4 @@ -162,76 +149,66 @@ pytest==7.4.2 pytest-cov==4.1.0 python-dateutil==2.8.2 python-dotenv==1.0.0 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytorch-ranger==0.1.1 pytz==2023.3.post1 PyWavelets==1.4.1 pywin32==306 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 +rich==13.6.0 s3fs==2023.3.0 s3transfer==0.6.2 -safetensors==0.3.3 +safetensors==0.4.0 scikit-image==0.21.0 -scikit-learn==1.3.0 -scipy==1.10.1 -setuptools==68.2.0 +scikit-learn==1.3.1 +scipy==1.9.3 +scyjava==1.9.1 shellingham==1.5.3 -SimpleITK==2.2.1 +SimpleITK==2.3.0 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 sortedcontainers==2.4.0 -soupsieve==2.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 tblib==2.0.0 termcolor==2.3.0 -texttable==1.6.7 +texttable==1.7.0 threadpoolctl==3.2.0 tifffile==2023.7.10 timm==0.9.7 tomli==2.0.1 toolz==0.12.0 torch==2.0.1 -torch-geometric==2.3.1 +torch-geometric==2.4.0 torch-optimizer==0.3.0 torchio==0.19.1 -torchmetrics==1.1.1 -torchserve==0.8.2 +torchmetrics==1.2.0 +torchserve==0.9.0 torchvf==0.1.3 torchvision==0.15.2 tornado==6.3.3 tqdm==4.66.1 -traitlets==5.9.0 typer==0.9.0 -typing-extensions==4.7.1 +typing-extensions==4.8.0 universal-pathlib==0.1.3 -urllib3==1.26.16 -uvicorn==0.23.2 +urllib3==1.26.17 vtk==9.2.6 waitress==2.1.2 -wcwidth==0.2.6 -websocket-client==1.6.2 -websockets==11.0.3 -Werkzeug==2.3.7 +wcwidth==0.2.8 +websocket-client==1.6.4 +Werkzeug==3.0.0 wheel==0.41.2 wrapt==1.15.0 xarray==2023.1.0 -xmlschema==2.4.0 +xmlschema==2.5.0 xsdata==23.8 yarl==1.9.2 zarr==2.16.1 zict==3.0.0 -zipp==3.16.2 +zipp==3.17.0 diff --git a/requirements/windows/torchserve-requirements.txt b/requirements/windows/torchserve-requirements.txt index 2313564a5..8e0e738b3 100644 --- a/requirements/windows/torchserve-requirements.txt +++ b/requirements/windows/torchserve-requirements.txt @@ -3,28 +3,22 @@ aicsimageio==4.11.0 aiobotocore==2.4.2 -aiohttp==3.8.5 +aiohttp==3.8.6 aioitertools==0.11.0 aiosignal==1.3.1 alembic==1.12.0 anndata==0.9.2 -annotated-types==0.5.0 -ansicon==1.89.0 +annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 -anyio==3.7.1 -arrow==1.2.3 asciitree==0.3.3 async-timeout==4.0.3 attrs==23.1.0 autopage==0.5.1 -backoff==2.2.1 -beautifulsoup4==4.12.2 -bfio==2.3.0 -blessed==1.20.0 -blinker==1.6.2 +bfio==2.3.1 +blinker==1.6.3 botocore==1.27.59 certifi==2023.7.22 -charset-normalizer==3.2.0 +charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 @@ -32,118 +26,99 @@ cmaes==0.10.0 cmd2==2.4.3 colorama==0.4.6 colorlog==6.7.0 -contourpy==1.1.0 -croniter==1.4.1 -cycler==0.11.0 +contourpy==1.1.1 +cycler==0.12.1 dask==2023.5.0 -databricks-cli==0.17.7 -dateutils==0.6.12 -deepdiff==6.4.1 +databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 -einops==0.6.1 +einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 -exceptiongroup==1.1.3 -fastapi==0.103.1 -fasteners==0.18 -filelock==3.12.3 +fasteners==0.19 +filelock==3.12.4 fire==0.5.0 Flask==2.3.3 -fonttools==4.42.1 +fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 gitdb==4.0.10 -gitpython==3.1.35 +gitpython==3.1.37 gorilla==0.4.0 -greenlet==2.0.2 -h11==0.14.0 -h5py==3.9.0 +greenlet==3.0.0 +h5py==3.10.0 hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 imagecodecs==2023.3.16 -imageio==2.31.3 +imageio==2.31.5 importlib-metadata==6.8.0 -inquirer==3.1.3 itsdangerous==2.1.2 +jgo==1.0.5 Jinja2==3.1.2 -jinxed==1.2.0 jmespath==1.0.1 joblib==1.3.2 +jpype1==1.4.1 kiwisolver==1.4.5 lazy-loader==0.3 -lightning==2.0.8 -lightning-cloud==0.5.37 +lightning==2.1.0 lightning-utilities==0.9.0 locket==1.0.0 lxml==4.9.3 Mako==1.2.4 -markdown==3.4.4 -markdown-it-py==3.0.0 +markdown==3.5 MarkupSafe==2.1.3 -matplotlib==3.7.2 -mdurl==0.1.2 -mlflow==2.6.0 -monai-weekly==1.3.dev2336 +matplotlib==3.7.3 +mlflow==2.7.1 +monai-weekly==1.3.dev2341 mpmath==1.3.0 -msgpack==1.0.5 +msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.11.0 +numcodecs==0.12.0 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 -ome-zarr==0.8.0 +ome-zarr==0.8.2 omegaconf==2.3.0 optuna==2.10.1 -ordered-set==4.1.0 ostat==0.2 -packaging==23.1 +packaging==23.2 pandas==1.5.3 -partd==1.4.0 +partd==1.4.1 pbr==5.11.1 -pillow==10.0.0 -PrettyTable==3.8.0 +pillow==10.0.1 +PrettyTable==3.9.0 protobuf==3.20.1 psutil==5.9.5 pyarrow==10.0.1 -pydantic==2.1.1 -pydantic-core==2.4.0 -pygments==2.16.1 +pydantic==2.4.2 +pydantic-core==2.10.1 pyjwt==2.8.0 -pyparsing==3.0.9 +pyparsing==3.1.1 pyperclip==1.8.2 pyreadline3==3.4.1 python-dateutil==2.8.2 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.8 +pytorch-lightning==2.1.0 pytz==2023.3.post1 PyWavelets==1.4.1 pywin32==306 PyYAML==6.0.1 querystring-parser==1.2.4 -readchar==4.0.5 requests==2.31.0 resource-backed-dask-array==0.1.0 -rich==13.5.2 s3fs==2023.3.0 scikit-image==0.21.0 -scikit-learn==1.3.0 -scipy==1.10.1 -setuptools==68.2.0 +scikit-learn==1.3.1 +scipy==1.9.3 +scyjava==1.9.1 six==1.16.0 -smmap==5.0.0 -sniffio==1.3.0 +smmap==5.0.1 sortedcontainers==2.4.0 -soupsieve==2.5 -sqlalchemy==2.0.20 +sqlalchemy==2.0.22 sqlparse==0.4.4 -starlette==0.27.0 -starsessions==1.3.0 stevedore==5.1.0 sympy==1.12 tabulate==0.9.0 @@ -153,26 +128,23 @@ threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 torch==2.0.1 -torchmetrics==1.1.1 -torchserve==0.8.2 +torchmetrics==1.2.0 +torchserve==0.9.0 tornado==6.3.3 tqdm==4.66.1 -traitlets==5.9.0 -typing-extensions==4.7.1 +typing-extensions==4.8.0 universal-pathlib==0.1.3 -urllib3==1.26.16 -uvicorn==0.23.2 +urllib3==1.26.17 waitress==2.1.2 -wcwidth==0.2.6 -websocket-client==1.6.2 -websockets==11.0.3 -Werkzeug==2.3.7 +wcwidth==0.2.8 +websocket-client==1.6.4 +Werkzeug==3.0.0 wheel==0.41.2 wrapt==1.15.0 xarray==2023.1.0 -xmlschema==2.4.0 +xmlschema==2.5.0 xsdata==23.8 yarl==1.9.2 zarr==2.16.1 zict==3.0.0 -zipp==3.16.2 +zipp==3.17.0