Merge pull request #296 from AllenCellModeling/admin/requirements-upd…

…ate_2023-10-13_00-44

admin/requirements-update_2023-10-13_00-44

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