Updating lock files and requirements (#303)

Co-authored-by: benjijamorris <[email protected]>

requirements/linux/all-requirements.txt

@@ -12,13 +12,18 @@ alembic==1.12.0
 anndata==0.9.2
 annotated-types==0.6.0
 antlr4-python3-runtime==4.9.3
+anyio==3.7.1
+arrow==1.3.0
 asciitree==0.3.3
 astropy==5.2.2
 async-timeout==4.0.3
 attrs==23.1.0
 autograd==1.6.2
 autopage==0.5.2
-bfio==2.3.2
+backoff==2.2.1
+beautifulsoup4==4.12.2
+bfio==2.3.0
+blessed==1.20.0
 blinker==1.6.3
 boto3==1.24.4
 botocore==1.27.59
@@ -28,13 +33,17 @@ click==8.1.7
 cliff==4.3.0
 cloudpickle==2.2.1
 cmaes==0.10.0
+cmake==3.27.7
 cmd2==2.4.3
 colorama==0.4.6
 colorlog==6.7.0
 contourpy==1.1.1
+croniter==1.4.1
 cycler==0.12.1
 dask==2023.5.0
 databricks-cli==0.18.0
+dateutils==0.6.12
+deepdiff==6.6.1
 Deprecated==1.2.14
 distributed==2023.5.0
 docker==6.1.3
@@ -44,6 +53,8 @@ einops==0.7.0
 elementpath==4.1.5
 entrypoints==0.4
 escnn==1.0.11
+exceptiongroup==1.1.3
+fastapi==0.104.0
 fasteners==0.19
 filelock==3.12.4
 fire==0.5.0
@@ -53,11 +64,12 @@ frozenlist==1.4.0
 fsspec==2023.3.0
 future==0.18.3
 geomloss==0.2.6
-gitdb==4.0.10
+gitdb==4.0.11
 gitpython==3.1.40
 gorilla==0.4.0
 greenlet==3.0.0
 gunicorn==21.2.0
+h11==0.14.0
 h5py==3.10.0
 huggingface-hub==0.17.3
 humanize==4.8.0
@@ -68,17 +80,18 @@ idna==3.4
 imagecodecs==2023.3.16
 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==2.1.0
+lightning==2.0.9.post0
+lightning-cloud==0.5.43
 lightning-utilities==0.9.0
+lit==17.0.3
 locket==1.0.0
 lxml==4.9.3
 Mako==1.2.4
@@ -98,25 +111,25 @@ nibabel==5.1.0
 Ninja==1.11.1.1
 numcodecs==0.12.1
 numpy==1.24.4
-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==12.3.52
-nvidia-nvtx-cu12==12.1.105
+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
 oauthlib==3.2.2
 ome-types==0.4.2
 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==23.2
 pandas==1.5.3
@@ -131,8 +144,8 @@ protobuf==3.20.1
 psutil==5.9.6
 py3nj==0.1.2
 pyarrow==10.0.1
-pydantic==2.4.2
-pydantic-core==2.10.1
+pydantic==2.1.1
+pydantic-core==2.4.0
 pyerfa==2.0.0.3
 pygments==2.16.1
 pyjwt==2.8.0
@@ -142,11 +155,14 @@ 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==2.1.0
 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==13.6.0
@@ -156,14 +172,18 @@ safetensors==0.4.0
 scikit-image==0.21.0
 scikit-learn==1.3.1
 scipy==1.9.3
-scyjava==1.9.1
+setuptools==68.2.2
 shellingham==1.5.3
 SimpleITK==2.3.0
 six==1.16.0
 smmap==5.0.1
+sniffio==1.3.0
 sortedcontainers==2.4.0
+soupsieve==2.5
 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
@@ -173,22 +193,26 @@ threadpoolctl==3.2.0
 tifffile==2023.7.10
 timm==0.9.7
 toolz==0.12.0
-torch==2.1.0
+torch==2.0.1
 torch-geometric==2.4.0
 torchio==0.19.1
 torchmetrics==1.2.0
 torchserve==0.9.0
-torchvision==0.16.0
+torchvision==0.15.2
 tornado==6.3.3
 tqdm==4.66.1
-triton==2.1.0
+traitlets==5.11.2
+triton==2.0.0
 typer==0.9.0
+types-python-dateutil==2.8.19.14
 typing-extensions==4.8.0
 universal-pathlib==0.1.4
 urllib3==1.26.18
+uvicorn==0.23.2
 vtk==9.2.6
 wcwidth==0.2.8
 websocket-client==1.6.4
+websockets==11.0.3
 Werkzeug==3.0.0
 wheel==0.41.2
 wrapt==1.15.0

requirements/linux/docs-requirements.txt

@@ -13,15 +13,19 @@ alembic==1.12.0
 anndata==0.9.2
 annotated-types==0.6.0
 antlr4-python3-runtime==4.9.3
+anyio==3.7.1
+arrow==1.3.0
 asciitree==0.3.3
 astropy==5.2.2
 async-timeout==4.0.3
 attrs==23.1.0
 autograd==1.6.2
 autopage==0.5.2
 babel==2.13.0
+backoff==2.2.1
 beautifulsoup4==4.12.2
-bfio==2.3.2
+bfio==2.3.0
+blessed==1.20.0
 blinker==1.6.3
 boto3==1.24.4
 botocore==1.27.59
@@ -31,13 +35,17 @@ click==8.1.7
 cliff==4.3.0
 cloudpickle==2.2.1
 cmaes==0.10.0
+cmake==3.27.7
 cmd2==2.4.3
 colorama==0.4.6
 colorlog==6.7.0
 contourpy==1.1.1
+croniter==1.4.1
 cycler==0.12.1
 dask==2023.5.0
 databricks-cli==0.18.0
+dateutils==0.6.12
+deepdiff==6.6.1
 Deprecated==1.2.14
 distributed==2023.5.0
 docker==6.1.3
@@ -48,6 +56,8 @@ einops==0.7.0
 elementpath==4.1.5
 entrypoints==0.4
 escnn==1.0.11
+exceptiongroup==1.1.3
+fastapi==0.104.0
 fasteners==0.19
 filelock==3.12.4
 fire==0.5.0
@@ -58,11 +68,12 @@ fsspec==2023.3.0
 furo==2023.3.23
 future==0.18.3
 geomloss==0.2.6
-gitdb==4.0.10
+gitdb==4.0.11
 gitpython==3.1.40
 gorilla==0.4.0
 greenlet==3.0.0
 gunicorn==21.2.0
+h11==0.14.0
 h5py==3.10.0
 huggingface-hub==0.17.3
 humanize==4.8.0
@@ -74,17 +85,18 @@ imagecodecs==2023.3.16
 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==2.1.0
+lightning==2.0.9.post0
+lightning-cloud==0.5.43
 lightning-utilities==0.9.0
+lit==17.0.3
 locket==1.0.0
 lxml==4.9.3
 m2r2==0.3.3.post2
@@ -106,25 +118,25 @@ nibabel==5.1.0
 Ninja==1.11.1.1
 numcodecs==0.12.1
 numpy==1.24.4
-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==12.3.52
-nvidia-nvtx-cu12==12.1.105
+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
 oauthlib==3.2.2
 ome-types==0.4.2
 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==23.2
 pandas==1.5.3
@@ -139,8 +151,8 @@ protobuf==3.20.1
 psutil==5.9.6
 py3nj==0.1.2
 pyarrow==10.0.1
-pydantic==2.4.2
-pydantic-core==2.10.1
+pydantic==2.1.1
+pydantic-core==2.4.0
 pyerfa==2.0.0.3
 pygments==2.16.1
 pyjwt==2.8.0
@@ -150,11 +162,14 @@ 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==2.1.0
 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==13.6.0
@@ -164,11 +179,12 @@ safetensors==0.4.0
 scikit-image==0.21.0
 scikit-learn==1.3.1
 scipy==1.9.3
-scyjava==1.9.1
+setuptools==68.2.2
 shellingham==1.5.3
 SimpleITK==2.3.0
 six==1.16.0
 smmap==5.0.1
+sniffio==1.3.0
 snowballstemmer==2.2.0
 sortedcontainers==2.4.0
 soupsieve==2.5
@@ -182,6 +198,8 @@ sphinxcontrib-qthelp==1.0.3
 sphinxcontrib-serializinghtml==1.1.5
 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
@@ -191,22 +209,26 @@ threadpoolctl==3.2.0
 tifffile==2023.7.10
 timm==0.9.7
 toolz==0.12.0
-torch==2.1.0
+torch==2.0.1
 torch-geometric==2.4.0
 torchio==0.19.1
 torchmetrics==1.2.0
 torchserve==0.9.0
-torchvision==0.16.0
+torchvision==0.15.2
 tornado==6.3.3
 tqdm==4.66.1
-triton==2.1.0
+traitlets==5.11.2
+triton==2.0.0
 typer==0.9.0
+types-python-dateutil==2.8.19.14
 typing-extensions==4.8.0
 universal-pathlib==0.1.4
 urllib3==1.26.18
+uvicorn==0.23.2
 vtk==9.2.6
 wcwidth==0.2.8
 websocket-client==1.6.4
+websockets==11.0.3
 Werkzeug==3.0.0
 wheel==0.41.2
 wrapt==1.15.0