diff --git a/requirements/linux/all-requirements.txt b/requirements/linux/all-requirements.txt index 74717b82c..69e0f1ea4 100644 --- a/requirements/linux/all-requirements.txt +++ b/requirements/linux/all-requirements.txt @@ -17,19 +17,17 @@ astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 autograd==1.6.2 -autopage==0.5.1 -bfio==2.3.1 +autopage==0.5.2 +bfio==2.3.2 blinker==1.6.3 boto3==1.24.4 botocore==1.27.59 -cellpose-omni==0.9.1 certifi==2023.7.22 charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 cmaes==0.10.0 -cmake==3.27.6 cmd2==2.4.3 colorama==0.4.6 colorlog==6.7.0 @@ -47,7 +45,6 @@ elementpath==4.1.5 entrypoints==0.4 escnn==1.0.11 fasteners==0.19 -fastremap==1.14.0 filelock==3.12.4 fire==0.5.0 Flask==2.3.3 @@ -57,7 +54,7 @@ fsspec==2023.3.0 future==0.18.3 geomloss==0.2.6 gitdb==4.0.10 -gitpython==3.1.37 +gitpython==3.1.40 gorilla==0.4.0 greenlet==3.0.0 gunicorn==21.2.0 @@ -68,7 +65,6 @@ hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 -igraph==0.11.2 imagecodecs==2023.3.16 imageio==2.31.5 importlib-metadata==6.8.0 @@ -83,48 +79,41 @@ lazy-loader==0.3 lie-learn @ git+https://github.com/colobas/lie_learn.git@d5be2ab lightning==2.1.0 lightning-utilities==0.9.0 -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==3.5 markdown-it-py==3.0.0 MarkupSafe==2.1.3 matplotlib==3.7.3 mdurl==0.1.2 -mgen==1.2.1 mlflow==2.7.1 -monai-weekly==1.3.dev2341 +monai-weekly==1.4.dev2342 mpmath==1.3.0 msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 -ncolor==1.2.1 networkx==3.1 nibabel==5.1.0 Ninja==1.11.1.1 -numba==0.58.0 -numcodecs==0.12.0 +numcodecs==0.12.1 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==12.3.52 +nvidia-nvtx-cu12==12.1.105 oauthlib==3.2.2 ome-types==0.4.2 ome-zarr==0.8.2 omegaconf==2.3.0 -omnipose @ git+https://github.com/kevinjohncutler/omnipose.git@ce2e9aa -opencv-python-headless==4.8.1.78 opt-einsum==3.3.0 opt-einsum-fx==0.1.4 optuna==2.10.1 @@ -133,14 +122,13 @@ packaging==23.2 pandas==1.5.3 partd==1.4.1 pbr==5.11.1 -peakdetect==1.2 -pillow==10.0.1 +pillow==10.1.0 platformdirs==3.11.0 point-cloud-utils==0.30.0 pooch==1.7.0 PrettyTable==3.9.0 protobuf==3.20.1 -psutil==5.9.5 +psutil==5.9.6 py3nj==0.1.2 pyarrow==10.0.1 pydantic==2.4.2 @@ -155,7 +143,6 @@ pyperclip==1.8.2 pyshtools==4.10.3 python-dateutil==2.8.2 pytorch-lightning==2.1.0 -pytorch-ranger==0.1.1 pytz==2023.3.post1 PyWavelets==1.4.1 PyYAML==6.0.1 @@ -170,7 +157,6 @@ 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 @@ -183,26 +169,23 @@ sympy==1.12 tabulate==0.9.0 tblib==2.0.0 termcolor==2.3.0 -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==2.1.0 torch-geometric==2.4.0 -torch-optimizer==0.3.0 torchio==0.19.1 torchmetrics==1.2.0 torchserve==0.9.0 -torchvf==0.1.3 -torchvision==0.15.2 +torchvision==0.16.0 tornado==6.3.3 tqdm==4.66.1 -triton==2.0.0 +triton==2.1.0 typer==0.9.0 typing-extensions==4.8.0 -universal-pathlib==0.1.3 -urllib3==1.26.17 +universal-pathlib==0.1.4 +urllib3==1.26.18 vtk==9.2.6 wcwidth==0.2.8 websocket-client==1.6.4 diff --git a/requirements/linux/docs-requirements.txt b/requirements/linux/docs-requirements.txt index 2d5db8a11..5b8924d51 100644 --- a/requirements/linux/docs-requirements.txt +++ b/requirements/linux/docs-requirements.txt @@ -18,21 +18,19 @@ astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 autograd==1.6.2 -autopage==0.5.1 +autopage==0.5.2 babel==2.13.0 beautifulsoup4==4.12.2 -bfio==2.3.1 +bfio==2.3.2 blinker==1.6.3 boto3==1.24.4 botocore==1.27.59 -cellpose-omni==0.9.1 certifi==2023.7.22 charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 cmaes==0.10.0 -cmake==3.27.6 cmd2==2.4.3 colorama==0.4.6 colorlog==6.7.0 @@ -51,7 +49,6 @@ elementpath==4.1.5 entrypoints==0.4 escnn==1.0.11 fasteners==0.19 -fastremap==1.14.0 filelock==3.12.4 fire==0.5.0 Flask==2.3.3 @@ -62,7 +59,7 @@ furo==2023.3.23 future==0.18.3 geomloss==0.2.6 gitdb==4.0.10 -gitpython==3.1.37 +gitpython==3.1.40 gorilla==0.4.0 greenlet==3.0.0 gunicorn==21.2.0 @@ -73,7 +70,6 @@ hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 -igraph==0.11.2 imagecodecs==2023.3.16 imageio==2.31.5 imagesize==1.4.1 @@ -89,50 +85,43 @@ lazy-loader==0.3 lie-learn @ git+https://github.com/colobas/lie_learn.git@d5be2ab lightning==2.1.0 lightning-utilities==0.9.0 -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==3.5 markdown-it-py==3.0.0 MarkupSafe==2.1.3 matplotlib==3.7.3 mdurl==0.1.2 -mgen==1.2.1 mistune==0.8.4 mlflow==2.7.1 -monai-weekly==1.3.dev2341 +monai-weekly==1.4.dev2342 mpmath==1.3.0 msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 -ncolor==1.2.1 networkx==3.1 nibabel==5.1.0 Ninja==1.11.1.1 -numba==0.58.0 -numcodecs==0.12.0 +numcodecs==0.12.1 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==12.3.52 +nvidia-nvtx-cu12==12.1.105 oauthlib==3.2.2 ome-types==0.4.2 ome-zarr==0.8.2 omegaconf==2.3.0 -omnipose @ git+https://github.com/kevinjohncutler/omnipose.git@ce2e9aa -opencv-python-headless==4.8.1.78 opt-einsum==3.3.0 opt-einsum-fx==0.1.4 optuna==2.10.1 @@ -141,14 +130,13 @@ packaging==23.2 pandas==1.5.3 partd==1.4.1 pbr==5.11.1 -peakdetect==1.2 -pillow==10.0.1 +pillow==10.1.0 platformdirs==3.11.0 point-cloud-utils==0.30.0 pooch==1.7.0 PrettyTable==3.9.0 protobuf==3.20.1 -psutil==5.9.5 +psutil==5.9.6 py3nj==0.1.2 pyarrow==10.0.1 pydantic==2.4.2 @@ -163,7 +151,6 @@ pyperclip==1.8.2 pyshtools==4.10.3 python-dateutil==2.8.2 pytorch-lightning==2.1.0 -pytorch-ranger==0.1.1 pytz==2023.3.post1 PyWavelets==1.4.1 PyYAML==6.0.1 @@ -178,7 +165,6 @@ 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 @@ -201,26 +187,23 @@ sympy==1.12 tabulate==0.9.0 tblib==2.0.0 termcolor==2.3.0 -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==2.1.0 torch-geometric==2.4.0 -torch-optimizer==0.3.0 torchio==0.19.1 torchmetrics==1.2.0 torchserve==0.9.0 -torchvf==0.1.3 -torchvision==0.15.2 +torchvision==0.16.0 tornado==6.3.3 tqdm==4.66.1 -triton==2.0.0 +triton==2.1.0 typer==0.9.0 typing-extensions==4.8.0 -universal-pathlib==0.1.3 -urllib3==1.26.17 +universal-pathlib==0.1.4 +urllib3==1.26.18 vtk==9.2.6 wcwidth==0.2.8 websocket-client==1.6.4 diff --git a/requirements/linux/equiv-requirements.txt b/requirements/linux/equiv-requirements.txt index 73db1eb2d..65321c7e2 100644 --- a/requirements/linux/equiv-requirements.txt +++ b/requirements/linux/equiv-requirements.txt @@ -11,11 +11,12 @@ anndata==0.9.2 annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 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 -bfio==2.3.1 +autopage==0.5.2 +bfio==2.3.2 blinker==1.6.3 botocore==1.27.59 certifi==2023.7.22 @@ -24,7 +25,6 @@ click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 cmaes==0.10.0 -cmake==3.27.6 cmd2==2.4.3 colorlog==6.7.0 contourpy==1.1.1 @@ -34,6 +34,7 @@ databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 e3nn==0.5.1 +edt==2.3.1 einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 @@ -47,7 +48,7 @@ frozenlist==1.4.0 fsspec==2023.3.0 future==0.18.3 gitdb==4.0.10 -gitpython==3.1.37 +gitpython==3.1.40 greenlet==3.0.0 gunicorn==21.2.0 h5py==3.10.0 @@ -69,7 +70,6 @@ lazy-loader==0.3 lie-learn @ git+https://github.com/colobas/lie_learn.git@d5be2ab lightning==2.1.0 lightning-utilities==0.9.0 -lit==17.0.2 locket==1.0.0 lxml==4.9.3 Mako==1.2.4 @@ -77,25 +77,26 @@ markdown==3.5 MarkupSafe==2.1.3 matplotlib==3.7.3 mlflow==2.7.1 -monai-weekly==1.3.dev2341 +monai-weekly==1.4.dev2342 mpmath==1.3.0 msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.12.0 +numcodecs==0.12.1 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==12.3.52 +nvidia-nvtx-cu12==12.1.105 oauthlib==3.2.2 ome-types==0.4.2 ome-zarr==0.8.2 @@ -108,14 +109,15 @@ packaging==23.2 pandas==1.5.3 partd==1.4.1 pbr==5.11.1 -pillow==10.0.1 +pillow==10.1.0 PrettyTable==3.9.0 protobuf==3.20.1 -psutil==5.9.5 +psutil==5.9.6 py3nj==0.1.2 pyarrow==10.0.1 pydantic==2.4.2 pydantic-core==2.10.1 +pyerfa==2.0.0.3 pyjwt==2.8.0 pymanopt==2.2.0 pyparsing==3.1.1 @@ -133,7 +135,6 @@ scikit-image==0.21.0 scikit-learn==1.3.1 scipy==1.9.3 scyjava==1.9.1 -setuptools==68.2.2 six==1.16.0 smmap==5.0.1 sortedcontainers==2.4.0 @@ -147,18 +148,17 @@ termcolor==2.3.0 threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 -torch==2.0.1 +torch==2.1.0 torchmetrics==1.2.0 tornado==6.3.3 tqdm==4.66.1 -triton==2.0.0 +triton==2.1.0 typing-extensions==4.8.0 -universal-pathlib==0.1.3 -urllib3==1.26.17 +universal-pathlib==0.1.4 +urllib3==1.26.18 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==2.5.0 diff --git a/requirements/linux/pdm.lock b/requirements/linux/pdm.lock index 9cc059da4..52a48521b 100644 --- a/requirements/linux/pdm.lock +++ b/requirements/linux/pdm.lock @@ -2,11 +2,11 @@ # It is not intended for manual editing. [metadata] -groups = ["default", "all", "docs", "equiv", "omnipose", "pcloud", "s3", "spharm", "test", "torchserve"] +groups = ["default", "all", "docs", "equiv", "pcloud", "s3", "spharm", "test", "torchserve"] cross_platform = false static_urls = false lock_version = "4.3" -content_hash = "sha256:e37073446848e15bbc0ccb7f651dad85c6d46e07816b4b1fe870c7ee6aa14abd" +content_hash = "sha256:41758e6f558cc07a12e3eded2035c39e2f4e7f36c7d9fa7b46043b1eaf1220e6" [[package]] name = "aicscytoparam" @@ -248,12 +248,12 @@ files = [ [[package]] name = "autopage" -version = "0.5.1" +version = "0.5.2" requires_python = ">=3.6" summary = "A library to provide automatic paging for console output" files = [ - {file = "autopage-0.5.1-py3-none-any.whl", hash = "sha256:0fbf5efbe78d466a26753e1dee3272423a3adc989d6a778c700e89a3f8ff0d88"}, - {file = "autopage-0.5.1.tar.gz", hash = "sha256:01be3ee61bb714e9090fcc5c10f4cf546c396331c620c6ae50a2321b28ed3199"}, + {file = "autopage-0.5.2-py3-none-any.whl", hash = "sha256:f5eae54dd20ccc8b1ff611263fc87bc46608a9cde749bbcfc93339713a429c55"}, + {file = "autopage-0.5.2.tar.gz", hash = "sha256:826996d74c5aa9f4b6916195547312ac6384bac3810b8517063f293248257b72"}, ] [[package]] @@ -281,8 +281,8 @@ files = [ [[package]] name = "bfio" -version = "2.3.1" -requires_python = ">=3.7" +version = "2.3.2" +requires_python = ">=3.8" summary = "Simple reading and writing classes for tiled tiffs using Bioformats." dependencies = [ "imagecodecs>=2021.2.26", @@ -290,12 +290,12 @@ dependencies = [ "numpy>=1.20.1", "ome-types>=0.4.2", "scyjava", - "tifffile", + "tifffile>=2022.8.12", "zarr>=2.6.1", ] files = [ - {file = "bfio-2.3.1-py2.py3-none-any.whl", hash = "sha256:9e2c19258956c34997dfdab7015819809093bda2f82fdb05a9f80b346cfe89b1"}, - {file = "bfio-2.3.1.tar.gz", hash = "sha256:4c96b7017866bfc9a07b98336fdea95d8dad90cc6c4c136ddbafcb460d8b78b0"}, + {file = "bfio-2.3.2-py2.py3-none-any.whl", hash = "sha256:26e52a0f5d7ad528013ed0945f66023b6a1acd0afd6ca23ac95ff747583223e8"}, + {file = "bfio-2.3.2.tar.gz", hash = "sha256:a53979da22b96f0cf21a97b55c1d005f9d6dcb80dffe52fddb3643bf47fda766"}, ] [[package]] @@ -338,45 +338,6 @@ files = [ {file = "botocore-1.27.59.tar.gz", hash = "sha256:eda4aed6ee719a745d1288eaf1beb12f6f6448ad1fa12f159405db14ba9c92cf"}, ] -[[package]] -name = "cellpose-omni" -version = "0.9.1" -summary = "cellpose fork developed for omnipose" -dependencies = [ - "fastremap", - "imagecodecs", - "natsort", - "numba", - "numpy>=1.22.4", - "opencv-python-headless", - "scipy", - "tifffile", - "torch>=1.6", - "tqdm", -] -files = [ - {file = "cellpose-omni-0.9.1.tar.gz", hash = "sha256:84f3199a751a74ddab643227bd0425ffafedcc2e739a57958f73a6d5f5348b6e"}, - {file = "cellpose_omni-0.9.1-py3-none-any.whl", hash = "sha256:7074f248656b5e29aae3e615ade4ce350dcc8a170cee94d5655a739fc454b6f8"}, -] - -[[package]] -name = "cellpose-omni" -version = "0.9.1" -extras = ["omni"] -summary = "cellpose fork developed for omnipose" -dependencies = [ - "cellpose-omni==0.9.1", - "edt", - "ncolor>=1.2.1", - "scikit-image", - "scikit-learn", - "torch-optimizer", -] -files = [ - {file = "cellpose-omni-0.9.1.tar.gz", hash = "sha256:84f3199a751a74ddab643227bd0425ffafedcc2e739a57958f73a6d5f5348b6e"}, - {file = "cellpose_omni-0.9.1-py3-none-any.whl", hash = "sha256:7074f248656b5e29aae3e615ade4ce350dcc8a170cee94d5655a739fc454b6f8"}, -] - [[package]] name = "certifi" version = "2023.7.22" @@ -449,16 +410,6 @@ files = [ {file = "cmaes-0.10.0.tar.gz", hash = "sha256:48afc70df027114739872b50489ae6b32461c307b92d084a63c7090a9742faf9"}, ] -[[package]] -name = "cmake" -version = "3.27.6" -summary = "CMake is an open-source, cross-platform family of tools designed to build, test and package software" -files = [ - {file = "cmake-3.27.6-py2.py3-none-manylinux2010_x86_64.manylinux_2_12_x86_64.whl", hash = "sha256:8ba53d322d5c84afd839138315d71ee9f892dcecb5e163e8d888f0d92cf43fe1"}, - {file = "cmake-3.27.6-py2.py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl", hash = "sha256:8c0ad28706b76d6b7c7643222d833af44bdd03da4371e3a6f0eac68e3a1d6366"}, - {file = "cmake-3.27.6.tar.gz", hash = "sha256:daaa867afeeafabb1544fb129e9fbc3c537a7261430b6f00605268530f75b948"}, -] - [[package]] name = "cmd2" version = "2.4.3" @@ -761,19 +712,6 @@ files = [ {file = "fasteners-0.19.tar.gz", hash = "sha256:b4f37c3ac52d8a445af3a66bce57b33b5e90b97c696b7b984f530cf8f0ded09c"}, ] -[[package]] -name = "fastremap" -version = "1.14.0" -requires_python = ">=3.7,<4.0" -summary = "Remap, mask, renumber, unique, and in-place transposition of 3D labeled images. 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!=3.3.*, !=3.4.*, !=3.5.*" summary = "HTTP library with thread-safe connection pooling, file post, and more." files = [ - {file = "urllib3-1.26.17-py2.py3-none-any.whl", hash = "sha256:94a757d178c9be92ef5539b8840d48dc9cf1b2709c9d6b588232a055c524458b"}, - {file = "urllib3-1.26.17.tar.gz", hash = "sha256:24d6a242c28d29af46c3fae832c36db3bbebcc533dd1bb549172cd739c82df21"}, + {file = "urllib3-1.26.18-py2.py3-none-any.whl", hash = "sha256:34b97092d7e0a3a8cf7cd10e386f401b3737364026c45e622aa02903dffe0f07"}, + {file = "urllib3-1.26.18.tar.gz", hash = "sha256:f8ecc1bba5667413457c529ab955bf8c67b45db799d159066261719e328580a0"}, ] [[package]] diff --git a/requirements/linux/requirements.txt b/requirements/linux/requirements.txt index 3eff70296..beb415087 100644 --- a/requirements/linux/requirements.txt +++ b/requirements/linux/requirements.txt @@ -11,10 +11,11 @@ anndata==0.9.2 annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 asciitree==0.3.3 +astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 -autopage==0.5.1 -bfio==2.3.1 +autopage==0.5.2 +bfio==2.3.2 blinker==1.6.3 botocore==1.31.17 certifi==2023.7.22 @@ -31,6 +32,7 @@ dask==2023.5.0 databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 +edt==2.3.1 einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 @@ -42,7 +44,7 @@ fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.9.2 gitdb==4.0.10 -gitpython==3.1.37 +gitpython==3.1.40 greenlet==3.0.0 gunicorn==21.2.0 h5py==3.10.0 @@ -70,13 +72,13 @@ markdown==3.5 MarkupSafe==2.1.3 matplotlib==3.7.3 mlflow==2.7.1 -monai-weekly==1.3.dev2341 +monai-weekly==1.4.dev2342 mpmath==1.3.0 msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.12.0 +numcodecs==0.12.1 numpy==1.24.4 nvidia-cublas-cu12==12.1.3.1 nvidia-cuda-cupti-cu12==12.1.105 @@ -88,7 +90,7 @@ 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-nvjitlink-cu12==12.3.52 nvidia-nvtx-cu12==12.1.105 oauthlib==3.2.2 ome-types==0.4.2 @@ -100,13 +102,14 @@ packaging==23.2 pandas==1.5.3 partd==1.4.1 pbr==5.11.1 -pillow==10.0.1 +pillow==10.1.0 PrettyTable==3.9.0 protobuf==3.20.1 -psutil==5.9.5 +psutil==5.9.6 pyarrow==10.0.1 pydantic==2.4.2 pydantic-core==2.10.1 +pyerfa==2.0.0.3 pyjwt==2.8.0 pyparsing==3.1.1 pyperclip==1.8.2 @@ -142,8 +145,8 @@ tornado==6.3.3 tqdm==4.66.1 triton==2.1.0 typing-extensions==4.8.0 -universal-pathlib==0.1.3 -urllib3==1.26.17 +universal-pathlib==0.1.4 +urllib3==1.26.18 wcwidth==0.2.8 websocket-client==1.6.4 Werkzeug==3.0.0 diff --git a/requirements/linux/spharm-requirements.txt b/requirements/linux/spharm-requirements.txt index 1d3331d66..24a966147 100644 --- a/requirements/linux/spharm-requirements.txt +++ b/requirements/linux/spharm-requirements.txt @@ -16,8 +16,8 @@ asciitree==0.3.3 astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 -autopage==0.5.1 -bfio==2.3.1 +autopage==0.5.2 +bfio==2.3.2 blinker==1.6.3 botocore==1.27.59 certifi==2023.7.22 @@ -26,7 +26,6 @@ click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 cmaes==0.10.0 -cmake==3.27.6 cmd2==2.4.3 colorlog==6.7.0 contourpy==1.1.1 @@ -35,6 +34,7 @@ dask==2023.5.0 databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 +edt==2.3.1 einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 @@ -46,7 +46,7 @@ fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 gitdb==4.0.10 -gitpython==3.1.37 +gitpython==3.1.40 greenlet==3.0.0 gunicorn==21.2.0 h5py==3.10.0 @@ -67,7 +67,6 @@ kiwisolver==1.4.5 lazy-loader==0.3 lightning==2.1.0 lightning-utilities==0.9.0 -lit==17.0.2 locket==1.0.0 lxml==4.9.3 Mako==1.2.4 @@ -75,25 +74,26 @@ markdown==3.5 MarkupSafe==2.1.3 matplotlib==3.7.3 mlflow==2.7.1 -monai-weekly==1.3.dev2341 +monai-weekly==1.4.dev2342 mpmath==1.3.0 msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.12.0 +numcodecs==0.12.1 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==12.3.52 +nvidia-nvtx-cu12==12.1.105 oauthlib==3.2.2 ome-types==0.4.2 ome-zarr==0.8.2 @@ -104,12 +104,12 @@ packaging==23.2 pandas==1.5.3 partd==1.4.1 pbr==5.11.1 -pillow==10.0.1 +pillow==10.1.0 platformdirs==3.11.0 pooch==1.7.0 PrettyTable==3.9.0 protobuf==3.20.1 -psutil==5.9.5 +psutil==5.9.6 pyarrow==10.0.1 pydantic==2.4.2 pydantic-core==2.10.1 @@ -131,7 +131,6 @@ scikit-image==0.21.0 scikit-learn==1.3.1 scipy==1.9.3 scyjava==1.9.1 -setuptools==68.2.2 six==1.16.0 smmap==5.0.1 sortedcontainers==2.4.0 @@ -145,19 +144,18 @@ termcolor==2.3.0 threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 -torch==2.0.1 +torch==2.1.0 torchmetrics==1.2.0 tornado==6.3.3 tqdm==4.66.1 -triton==2.0.0 +triton==2.1.0 typing-extensions==4.8.0 -universal-pathlib==0.1.3 -urllib3==1.26.17 +universal-pathlib==0.1.4 +urllib3==1.26.18 vtk==9.2.6 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==2.5.0 diff --git a/requirements/linux/test-requirements.txt b/requirements/linux/test-requirements.txt index b854fd7d8..9b2c83d08 100644 --- a/requirements/linux/test-requirements.txt +++ b/requirements/linux/test-requirements.txt @@ -17,19 +17,17 @@ astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 autograd==1.6.2 -autopage==0.5.1 -bfio==2.3.1 +autopage==0.5.2 +bfio==2.3.2 blinker==1.6.3 boto3==1.24.4 botocore==1.27.59 -cellpose-omni==0.9.1 certifi==2023.7.22 charset-normalizer==3.3.0 click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 cmaes==0.10.0 -cmake==3.27.6 cmd2==2.4.3 colorama==0.4.6 colorlog==6.7.0 @@ -49,7 +47,6 @@ entrypoints==0.4 escnn==1.0.11 exceptiongroup==1.1.3 fasteners==0.19 -fastremap==1.14.0 filelock==3.12.4 fire==0.5.0 Flask==2.3.3 @@ -59,7 +56,7 @@ fsspec==2023.3.0 future==0.18.3 geomloss==0.2.6 gitdb==4.0.10 -gitpython==3.1.37 +gitpython==3.1.40 gorilla==0.4.0 greenlet==3.0.0 gunicorn==21.2.0 @@ -70,7 +67,6 @@ hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 -igraph==0.11.2 imagecodecs==2023.3.16 imageio==2.31.5 importlib-metadata==6.8.0 @@ -86,48 +82,41 @@ lazy-loader==0.3 lie-learn @ git+https://github.com/colobas/lie_learn.git@d5be2ab lightning==2.1.0 lightning-utilities==0.9.0 -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==3.5 markdown-it-py==3.0.0 MarkupSafe==2.1.3 matplotlib==3.7.3 mdurl==0.1.2 -mgen==1.2.1 mlflow==2.7.1 -monai-weekly==1.3.dev2341 +monai-weekly==1.4.dev2342 mpmath==1.3.0 msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 -ncolor==1.2.1 networkx==3.1 nibabel==5.1.0 Ninja==1.11.1.1 -numba==0.58.0 -numcodecs==0.12.0 +numcodecs==0.12.1 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==12.3.52 +nvidia-nvtx-cu12==12.1.105 oauthlib==3.2.2 ome-types==0.4.2 ome-zarr==0.8.2 omegaconf==2.3.0 -omnipose @ git+https://github.com/kevinjohncutler/omnipose.git@ce2e9aa -opencv-python-headless==4.8.1.78 opt-einsum==3.3.0 opt-einsum-fx==0.1.4 optuna==2.10.1 @@ -136,15 +125,14 @@ packaging==23.2 pandas==1.5.3 partd==1.4.1 pbr==5.11.1 -peakdetect==1.2 -pillow==10.0.1 +pillow==10.1.0 platformdirs==3.11.0 pluggy==1.3.0 point-cloud-utils==0.30.0 pooch==1.7.0 PrettyTable==3.9.0 protobuf==3.20.1 -psutil==5.9.5 +psutil==5.9.6 py3nj==0.1.2 pyarrow==10.0.1 pydantic==2.4.2 @@ -163,7 +151,6 @@ pytest-cov==4.1.0 python-dateutil==2.8.2 python-dotenv==1.0.0 pytorch-lightning==2.1.0 -pytorch-ranger==0.1.1 pytz==2023.3.post1 PyWavelets==1.4.1 PyYAML==6.0.1 @@ -178,7 +165,6 @@ 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 @@ -191,27 +177,24 @@ sympy==1.12 tabulate==0.9.0 tblib==2.0.0 termcolor==2.3.0 -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==2.1.0 torch-geometric==2.4.0 -torch-optimizer==0.3.0 torchio==0.19.1 torchmetrics==1.2.0 torchserve==0.9.0 -torchvf==0.1.3 -torchvision==0.15.2 +torchvision==0.16.0 tornado==6.3.3 tqdm==4.66.1 -triton==2.0.0 +triton==2.1.0 typer==0.9.0 typing-extensions==4.8.0 -universal-pathlib==0.1.3 -urllib3==1.26.17 +universal-pathlib==0.1.4 +urllib3==1.26.18 vtk==9.2.6 wcwidth==0.2.8 websocket-client==1.6.4 diff --git a/requirements/linux/torchserve-requirements.txt b/requirements/linux/torchserve-requirements.txt index fde59e71a..7c484d57c 100644 --- a/requirements/linux/torchserve-requirements.txt +++ b/requirements/linux/torchserve-requirements.txt @@ -11,10 +11,11 @@ anndata==0.9.2 annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 asciitree==0.3.3 +astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 -autopage==0.5.1 -bfio==2.3.1 +autopage==0.5.2 +bfio==2.3.2 blinker==1.6.3 botocore==1.27.59 certifi==2023.7.22 @@ -23,7 +24,6 @@ click==8.1.7 cliff==4.3.0 cloudpickle==2.2.1 cmaes==0.10.0 -cmake==3.27.6 cmd2==2.4.3 colorlog==6.7.0 contourpy==1.1.1 @@ -32,6 +32,7 @@ dask==2023.5.0 databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 +edt==2.3.1 einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 @@ -43,7 +44,7 @@ fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 gitdb==4.0.10 -gitpython==3.1.37 +gitpython==3.1.40 gorilla==0.4.0 greenlet==3.0.0 gunicorn==21.2.0 @@ -65,7 +66,6 @@ kiwisolver==1.4.5 lazy-loader==0.3 lightning==2.1.0 lightning-utilities==0.9.0 -lit==17.0.2 locket==1.0.0 lxml==4.9.3 Mako==1.2.4 @@ -73,25 +73,26 @@ markdown==3.5 MarkupSafe==2.1.3 matplotlib==3.7.3 mlflow==2.7.1 -monai-weekly==1.3.dev2341 +monai-weekly==1.4.dev2342 mpmath==1.3.0 msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.12.0 +numcodecs==0.12.1 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==12.3.52 +nvidia-nvtx-cu12==12.1.105 oauthlib==3.2.2 ome-types==0.4.2 ome-zarr==0.8.2 @@ -102,13 +103,14 @@ packaging==23.2 pandas==1.5.3 partd==1.4.1 pbr==5.11.1 -pillow==10.0.1 +pillow==10.1.0 PrettyTable==3.9.0 protobuf==3.20.1 -psutil==5.9.5 +psutil==5.9.6 pyarrow==10.0.1 pydantic==2.4.2 pydantic-core==2.10.1 +pyerfa==2.0.0.3 pyjwt==2.8.0 pyparsing==3.1.1 pyperclip==1.8.2 @@ -125,7 +127,6 @@ scikit-image==0.21.0 scikit-learn==1.3.1 scipy==1.9.3 scyjava==1.9.1 -setuptools==68.2.2 six==1.16.0 smmap==5.0.1 sortedcontainers==2.4.0 @@ -139,15 +140,15 @@ termcolor==2.3.0 threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 -torch==2.0.1 +torch==2.1.0 torchmetrics==1.2.0 torchserve==0.9.0 tornado==6.3.3 tqdm==4.66.1 -triton==2.0.0 +triton==2.1.0 typing-extensions==4.8.0 -universal-pathlib==0.1.3 -urllib3==1.26.17 +universal-pathlib==0.1.4 +urllib3==1.26.18 wcwidth==0.2.8 websocket-client==1.6.4 Werkzeug==3.0.0 diff --git a/requirements/macos/all-requirements.txt b/requirements/macos/all-requirements.txt index 5b60d24a4..4a450f7d1 100644 --- a/requirements/macos/all-requirements.txt +++ b/requirements/macos/all-requirements.txt @@ -17,12 +17,11 @@ astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 autograd==1.6.2 -autopage==0.5.1 -bfio==2.3.1 +autopage==0.5.2 +bfio==2.3.2 blinker==1.6.3 boto3==1.24.4 botocore==1.27.59 -cellpose-omni==0.9.1 certifi==2023.7.22 charset-normalizer==3.3.0 click==8.1.7 @@ -46,7 +45,6 @@ elementpath==4.1.5 entrypoints==0.4 escnn==1.0.11 fasteners==0.19 -fastremap==1.14.0 filelock==3.12.4 fire==0.5.0 Flask==2.3.3 @@ -56,7 +54,7 @@ fsspec==2023.3.0 future==0.18.3 geomloss==0.2.6 gitdb==4.0.10 -gitpython==3.1.37 +gitpython==3.1.40 gorilla==0.4.0 greenlet==3.0.0 gunicorn==21.2.0 @@ -67,7 +65,6 @@ hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 -igraph==0.11.2 imagecodecs==2023.3.16 imageio==2.31.5 importlib-metadata==6.8.0 @@ -82,36 +79,29 @@ lazy-loader==0.3 lie-learn @ git+https://github.com/colobas/lie_learn.git@d5be2ab lightning==2.1.0 lightning-utilities==0.9.0 -llvmlite==0.41.0 locket==1.0.0 lxml==4.9.3 -mahotas==1.4.13 Mako==1.2.4 markdown==3.5 markdown-it-py==3.0.0 MarkupSafe==2.1.3 matplotlib==3.7.3 mdurl==0.1.2 -mgen==1.2.1 mlflow==2.7.1 -monai-weekly==1.3.dev2341 +monai-weekly==1.4.dev2342 mpmath==1.3.0 msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 -ncolor==1.2.1 networkx==3.1 nibabel==5.1.0 Ninja==1.11.1.1 -numba==0.58.0 -numcodecs==0.12.0 +numcodecs==0.12.1 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 ome-zarr==0.8.2 omegaconf==2.3.0 -omnipose @ git+https://github.com/kevinjohncutler/omnipose.git@ce2e9aa -opencv-python-headless==4.8.1.78 opt-einsum==3.3.0 opt-einsum-fx==0.1.4 optuna==2.10.1 @@ -120,14 +110,13 @@ packaging==23.2 pandas==1.5.3 partd==1.4.1 pbr==5.11.1 -peakdetect==1.2 -pillow==10.0.1 +pillow==10.1.0 platformdirs==3.11.0 point-cloud-utils==0.30.0 pooch==1.7.0 PrettyTable==3.9.0 protobuf==3.20.1 -psutil==5.9.5 +psutil==5.9.6 py3nj==0.1.2 pyarrow==10.0.1 pydantic==2.4.2 @@ -142,7 +131,6 @@ pyperclip==1.8.2 pyshtools==4.10.3 python-dateutil==2.8.2 pytorch-lightning==2.1.0 -pytorch-ranger==0.1.1 pytz==2023.3.post1 PyWavelets==1.4.1 PyYAML==6.0.1 @@ -169,25 +157,22 @@ sympy==1.12 tabulate==0.9.0 tblib==2.0.0 termcolor==2.3.0 -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==2.1.0 torch-geometric==2.4.0 -torch-optimizer==0.3.0 torchio==0.19.1 torchmetrics==1.2.0 torchserve==0.9.0 -torchvf==0.1.3 -torchvision==0.15.2 +torchvision==0.16.0 tornado==6.3.3 tqdm==4.66.1 typer==0.9.0 typing-extensions==4.8.0 -universal-pathlib==0.1.3 -urllib3==1.26.17 +universal-pathlib==0.1.4 +urllib3==1.26.18 vtk==9.2.6 wcwidth==0.2.8 websocket-client==1.6.4 diff --git a/requirements/macos/docs-requirements.txt b/requirements/macos/docs-requirements.txt index 79140e07c..38b6d8a99 100644 --- a/requirements/macos/docs-requirements.txt +++ b/requirements/macos/docs-requirements.txt @@ -18,14 +18,13 @@ astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 autograd==1.6.2 -autopage==0.5.1 +autopage==0.5.2 babel==2.13.0 beautifulsoup4==4.12.2 -bfio==2.3.1 +bfio==2.3.2 blinker==1.6.3 boto3==1.24.4 botocore==1.27.59 -cellpose-omni==0.9.1 certifi==2023.7.22 charset-normalizer==3.3.0 click==8.1.7 @@ -50,7 +49,6 @@ elementpath==4.1.5 entrypoints==0.4 escnn==1.0.11 fasteners==0.19 -fastremap==1.14.0 filelock==3.12.4 fire==0.5.0 Flask==2.3.3 @@ -61,7 +59,7 @@ furo==2023.3.23 future==0.18.3 geomloss==0.2.6 gitdb==4.0.10 -gitpython==3.1.37 +gitpython==3.1.40 gorilla==0.4.0 greenlet==3.0.0 gunicorn==21.2.0 @@ -72,7 +70,6 @@ hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 -igraph==0.11.2 imagecodecs==2023.3.16 imageio==2.31.5 imagesize==1.4.1 @@ -88,38 +85,31 @@ lazy-loader==0.3 lie-learn @ git+https://github.com/colobas/lie_learn.git@d5be2ab lightning==2.1.0 lightning-utilities==0.9.0 -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==3.5 markdown-it-py==3.0.0 MarkupSafe==2.1.3 matplotlib==3.7.3 mdurl==0.1.2 -mgen==1.2.1 mistune==0.8.4 mlflow==2.7.1 -monai-weekly==1.3.dev2341 +monai-weekly==1.4.dev2342 mpmath==1.3.0 msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 -ncolor==1.2.1 networkx==3.1 nibabel==5.1.0 Ninja==1.11.1.1 -numba==0.58.0 -numcodecs==0.12.0 +numcodecs==0.12.1 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 ome-zarr==0.8.2 omegaconf==2.3.0 -omnipose @ git+https://github.com/kevinjohncutler/omnipose.git@ce2e9aa -opencv-python-headless==4.8.1.78 opt-einsum==3.3.0 opt-einsum-fx==0.1.4 optuna==2.10.1 @@ -128,14 +118,13 @@ packaging==23.2 pandas==1.5.3 partd==1.4.1 pbr==5.11.1 -peakdetect==1.2 -pillow==10.0.1 +pillow==10.1.0 platformdirs==3.11.0 point-cloud-utils==0.30.0 pooch==1.7.0 PrettyTable==3.9.0 protobuf==3.20.1 -psutil==5.9.5 +psutil==5.9.6 py3nj==0.1.2 pyarrow==10.0.1 pydantic==2.4.2 @@ -150,7 +139,6 @@ pyperclip==1.8.2 pyshtools==4.10.3 python-dateutil==2.8.2 pytorch-lightning==2.1.0 -pytorch-ranger==0.1.1 pytz==2023.3.post1 PyWavelets==1.4.1 PyYAML==6.0.1 @@ -187,25 +175,22 @@ sympy==1.12 tabulate==0.9.0 tblib==2.0.0 termcolor==2.3.0 -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==2.1.0 torch-geometric==2.4.0 -torch-optimizer==0.3.0 torchio==0.19.1 torchmetrics==1.2.0 torchserve==0.9.0 -torchvf==0.1.3 -torchvision==0.15.2 +torchvision==0.16.0 tornado==6.3.3 tqdm==4.66.1 typer==0.9.0 typing-extensions==4.8.0 -universal-pathlib==0.1.3 -urllib3==1.26.17 +universal-pathlib==0.1.4 +urllib3==1.26.18 vtk==9.2.6 wcwidth==0.2.8 websocket-client==1.6.4 diff --git a/requirements/macos/equiv-requirements.txt b/requirements/macos/equiv-requirements.txt index c1d701be0..47bc6830d 100644 --- a/requirements/macos/equiv-requirements.txt +++ b/requirements/macos/equiv-requirements.txt @@ -11,11 +11,12 @@ anndata==0.9.2 annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 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 -bfio==2.3.1 +autopage==0.5.2 +bfio==2.3.2 blinker==1.6.3 botocore==1.27.59 certifi==2023.7.22 @@ -33,6 +34,7 @@ databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 e3nn==0.5.1 +edt==2.3.1 einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 @@ -46,7 +48,7 @@ frozenlist==1.4.0 fsspec==2023.3.0 future==0.18.3 gitdb==4.0.10 -gitpython==3.1.37 +gitpython==3.1.40 greenlet==3.0.0 gunicorn==21.2.0 h5py==3.10.0 @@ -75,13 +77,13 @@ markdown==3.5 MarkupSafe==2.1.3 matplotlib==3.7.3 mlflow==2.7.1 -monai-weekly==1.3.dev2341 +monai-weekly==1.4.dev2342 mpmath==1.3.0 msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.12.0 +numcodecs==0.12.1 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 @@ -95,14 +97,15 @@ packaging==23.2 pandas==1.5.3 partd==1.4.1 pbr==5.11.1 -pillow==10.0.1 +pillow==10.1.0 PrettyTable==3.9.0 protobuf==3.20.1 -psutil==5.9.5 +psutil==5.9.6 py3nj==0.1.2 pyarrow==10.0.1 pydantic==2.4.2 pydantic-core==2.10.1 +pyerfa==2.0.0.3 pyjwt==2.8.0 pymanopt==2.2.0 pyparsing==3.1.1 @@ -133,13 +136,13 @@ termcolor==2.3.0 threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 -torch==2.0.1 +torch==2.1.0 torchmetrics==1.2.0 tornado==6.3.3 tqdm==4.66.1 typing-extensions==4.8.0 -universal-pathlib==0.1.3 -urllib3==1.26.17 +universal-pathlib==0.1.4 +urllib3==1.26.18 wcwidth==0.2.8 websocket-client==1.6.4 Werkzeug==3.0.0 diff --git a/requirements/macos/pdm.lock b/requirements/macos/pdm.lock index efab9c2ce..d6b5c83f4 100644 --- a/requirements/macos/pdm.lock +++ b/requirements/macos/pdm.lock @@ -2,11 +2,11 @@ # It is not intended for manual editing. [metadata] -groups = ["default", "all", "docs", "equiv", "omnipose", "pcloud", "s3", "spharm", "test", "torchserve"] +groups = ["default", "all", "docs", "equiv", "pcloud", "s3", "spharm", "test", "torchserve"] cross_platform = false static_urls = false lock_version = "4.3" -content_hash = "sha256:e37073446848e15bbc0ccb7f651dad85c6d46e07816b4b1fe870c7ee6aa14abd" +content_hash = "sha256:41758e6f558cc07a12e3eded2035c39e2f4e7f36c7d9fa7b46043b1eaf1220e6" [[package]] name = "aicscytoparam" @@ -249,12 +249,12 @@ files = [ [[package]] name = "autopage" -version = "0.5.1" +version = "0.5.2" requires_python = ">=3.6" summary = "A library to provide automatic paging for console output" files = [ - {file = "autopage-0.5.1-py3-none-any.whl", hash = "sha256:0fbf5efbe78d466a26753e1dee3272423a3adc989d6a778c700e89a3f8ff0d88"}, - {file = "autopage-0.5.1.tar.gz", hash = "sha256:01be3ee61bb714e9090fcc5c10f4cf546c396331c620c6ae50a2321b28ed3199"}, + {file = "autopage-0.5.2-py3-none-any.whl", hash = "sha256:f5eae54dd20ccc8b1ff611263fc87bc46608a9cde749bbcfc93339713a429c55"}, + {file = "autopage-0.5.2.tar.gz", hash = "sha256:826996d74c5aa9f4b6916195547312ac6384bac3810b8517063f293248257b72"}, ] [[package]] @@ -282,8 +282,8 @@ files = [ [[package]] name = "bfio" -version = "2.3.1" -requires_python = ">=3.7" +version = "2.3.2" +requires_python = ">=3.8" summary = "Simple reading and writing classes for tiled tiffs using Bioformats." dependencies = [ "imagecodecs>=2021.2.26", @@ -291,12 +291,12 @@ dependencies = [ "numpy>=1.20.1", "ome-types>=0.4.2", "scyjava", - "tifffile", + "tifffile>=2022.8.12", "zarr>=2.6.1", ] files = [ - {file = "bfio-2.3.1-py2.py3-none-any.whl", hash = "sha256:9e2c19258956c34997dfdab7015819809093bda2f82fdb05a9f80b346cfe89b1"}, - {file = "bfio-2.3.1.tar.gz", hash = "sha256:4c96b7017866bfc9a07b98336fdea95d8dad90cc6c4c136ddbafcb460d8b78b0"}, + {file = "bfio-2.3.2-py2.py3-none-any.whl", hash = "sha256:26e52a0f5d7ad528013ed0945f66023b6a1acd0afd6ca23ac95ff747583223e8"}, + {file = "bfio-2.3.2.tar.gz", hash = "sha256:a53979da22b96f0cf21a97b55c1d005f9d6dcb80dffe52fddb3643bf47fda766"}, ] [[package]] @@ -339,45 +339,6 @@ files = [ {file = "botocore-1.27.59.tar.gz", hash = "sha256:eda4aed6ee719a745d1288eaf1beb12f6f6448ad1fa12f159405db14ba9c92cf"}, ] -[[package]] -name = "cellpose-omni" -version = "0.9.1" -summary = "cellpose fork developed for omnipose" -dependencies = [ - "fastremap", - "imagecodecs", - "natsort", - "numba", - "numpy>=1.22.4", - "opencv-python-headless", - "scipy", - "tifffile", - "torch>=1.6", - "tqdm", -] -files = [ - {file = "cellpose-omni-0.9.1.tar.gz", hash = "sha256:84f3199a751a74ddab643227bd0425ffafedcc2e739a57958f73a6d5f5348b6e"}, - {file = "cellpose_omni-0.9.1-py3-none-any.whl", hash = "sha256:7074f248656b5e29aae3e615ade4ce350dcc8a170cee94d5655a739fc454b6f8"}, -] - -[[package]] -name = "cellpose-omni" -version = "0.9.1" -extras = ["omni"] -summary = "cellpose fork developed for omnipose" -dependencies = [ - "cellpose-omni==0.9.1", - "edt", - "ncolor>=1.2.1", - "scikit-image", - "scikit-learn", - "torch-optimizer", -] -files = [ - {file = "cellpose-omni-0.9.1.tar.gz", hash = "sha256:84f3199a751a74ddab643227bd0425ffafedcc2e739a57958f73a6d5f5348b6e"}, - {file = "cellpose_omni-0.9.1-py3-none-any.whl", hash = "sha256:7074f248656b5e29aae3e615ade4ce350dcc8a170cee94d5655a739fc454b6f8"}, -] - [[package]] name = "certifi" version = "2023.7.22" @@ -754,20 +715,6 @@ files = [ {file = "fasteners-0.19.tar.gz", hash = "sha256:b4f37c3ac52d8a445af3a66bce57b33b5e90b97c696b7b984f530cf8f0ded09c"}, ] -[[package]] -name = "fastremap" -version = "1.14.0" -requires_python = ">=3.7,<4.0" -summary = "Remap, mask, renumber, unique, and in-place transposition of 3D labeled images. Point cloud too." -dependencies = [ - "numpy", -] -files = [ - {file = "fastremap-1.14.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:80b4a751e0c353dcea1a4b0fa9540dfd1f03e7af6d5e2e1acf9dff23fefebe6a"}, - {file = "fastremap-1.14.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:c68a1a69d0c7f01459f64ec2aba1ba62a879520afb1a20960debab295aed2ab0"}, - {file = "fastremap-1.14.0.tar.gz", hash = "sha256:189d329a60d741fcef8945ad79068e3165e80bc5aa69b8d8897c2d33e701e95c"}, -] - [[package]] name = "filelock" version = "3.12.4" @@ -924,15 +871,15 @@ files = [ [[package]] name = "gitpython" -version = "3.1.37" +version = "3.1.40" requires_python = ">=3.7" summary = "GitPython is a Python library used to interact with Git repositories" dependencies = [ "gitdb<5,>=4.0.1", ] files = [ - {file = "GitPython-3.1.37-py3-none-any.whl", hash = "sha256:5f4c4187de49616d710a77e98ddf17b4782060a1788df441846bddefbb89ab33"}, - {file = "GitPython-3.1.37.tar.gz", hash = "sha256:f9b9ddc0761c125d5780eab2d64be4873fc6817c2899cbcb34b02344bdc7bc54"}, + {file = "GitPython-3.1.40-py3-none-any.whl", hash = "sha256:cf14627d5a8049ffbf49915732e5eddbe8134c3bdb9d476e6182b676fc573f8a"}, + {file = "GitPython-3.1.40.tar.gz", hash = "sha256:22b126e9ffb671fdd0c129796343a02bf67bf2994b35449ffc9321aa755e18a4"}, ] [[package]] @@ -1059,19 +1006,6 @@ files = [ {file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"}, ] -[[package]] -name = "igraph" -version = "0.11.2" -requires_python = ">=3.8" -summary = "High performance graph data structures and algorithms" -dependencies = [ - "texttable>=1.6.2", -] -files = [ - {file = "igraph-0.11.2-cp39-abi3-macosx_10_9_x86_64.whl", hash = "sha256:3617a7b71b2e6c8b69a1b0756863334d9ac5a4d82ae8f1937447f53daa0f23a3"}, - {file = "igraph-0.11.2.tar.gz", hash = "sha256:c4053e47156d7685ad48bd72e6ff400d46b09deeebc746b96b5cf9737939fa2d"}, -] - [[package]] name = "imagecodecs" version = "2023.3.16" @@ -1272,16 +1206,6 @@ files = [ {file = "lightning_utilities-0.9.0-py3-none-any.whl", hash = "sha256:918dd90c775719e3855631db6282ad75c14da4c5727c4cebdd1589d865fad03d"}, ] -[[package]] -name = "llvmlite" -version = "0.41.0" -requires_python = ">=3.8" -summary = "lightweight wrapper around basic LLVM functionality" -files = [ - {file = "llvmlite-0.41.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:acc81c1279f858e5eab460844cc381e30d6666bc8eea04724b54d4eeb1fd1e54"}, - {file = "llvmlite-0.41.0.tar.gz", hash = "sha256:7d41db345d76d2dfa31871178ce0d8e9fd8aa015aa1b7d4dab84b5cb393901e0"}, -] - [[package]] name = "locket" version = "1.0.0" @@ -1316,18 +1240,6 @@ files = [ {file = "m2r2-0.3.3.post2.tar.gz", hash = "sha256:e62bcb0e74b3ce19cda0737a0556b04cf4a43b785072fcef474558f2c1482ca8"}, ] -[[package]] -name = "mahotas" -version = "1.4.13" -summary = "Mahotas: Computer Vision Library" -dependencies = [ - "numpy", -] -files = [ - {file = 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networks in Python with strong GPU acceleration" dependencies = [ "filelock", + "fsspec", "jinja2", "networkx", "sympy", "typing-extensions", ] files = [ - {file = "torch-2.0.1-cp310-none-macosx_10_9_x86_64.whl", hash = "sha256:567f84d657edc5582d716900543e6e62353dbe275e61cdc36eda4929e46df9e7"}, + {file = "torch-2.1.0-cp310-none-macosx_10_9_x86_64.whl", hash = "sha256:101c139152959cb20ab370fc192672c50093747906ee4ceace44d8dd703f29af"}, ] [[package]] @@ -2730,20 +2522,6 @@ files = [ {file = "torch_geometric-2.4.0.tar.gz", hash = "sha256:343c6906d0678f16553c2d02b7267d0ec77eafb5b44324070ebcf7da8a934557"}, ] -[[package]] -name = "torch-optimizer" -version = "0.3.0" -requires_python = ">=3.6.0" -summary = "pytorch-optimizer" -dependencies = [ - "pytorch-ranger>=0.1.1", - "torch>=1.5.0", -] -files = [ - {file = "torch-optimizer-0.3.0.tar.gz", hash = "sha256:b2180629df9d6cd7a2aeabe71fa4a872bba938e8e275965092568cd9931b924c"}, - {file = "torch_optimizer-0.3.0-py3-none-any.whl", hash = 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datasets and models for torch deep learning" dependencies = [ "numpy", "pillow!=8.3.*,>=5.3.0", "requests", - "torch==2.0.1", + "torch==2.1.0", ] files = [ - {file = "torchvision-0.15.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:7754088774e810c5672b142a45dcf20b1bd986a5a7da90f8660c43dc43fb850c"}, + {file = "torchvision-0.16.0-cp310-cp310-macosx_10_13_x86_64.whl", hash = "sha256:16c300fdbbe91469f5e9feef8d24c6acabd8849db502a06160dd76ba68e897a0"}, ] [[package]] @@ -2894,25 +2651,25 @@ files = [ [[package]] name = "universal-pathlib" -version = "0.1.3" +version = "0.1.4" requires_python = ">=3.8" summary = "pathlib api extended to use fsspec backends" dependencies = [ - "fsspec", + "fsspec>=2022.1.0", ] files = [ - {file = "universal_pathlib-0.1.3-py3-none-any.whl", hash = "sha256:9c6a78cd75dad2988eb1d5db52f4e85a8a3092cbe5eb2cf18882c1ef06470d43"}, - {file = "universal_pathlib-0.1.3.tar.gz", hash = "sha256:1a052ab5e0517301df66be6517e9fe63cd9fc00813e5ce71a73701441ac2b5c8"}, + {file = 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"sha256:f8ecc1bba5667413457c529ab955bf8c67b45db799d159066261719e328580a0"}, ] [[package]] diff --git a/requirements/macos/requirements.txt b/requirements/macos/requirements.txt index adeaf1652..83ffcc2e6 100644 --- a/requirements/macos/requirements.txt +++ b/requirements/macos/requirements.txt @@ -11,10 +11,11 @@ anndata==0.9.2 annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 asciitree==0.3.3 +astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 -autopage==0.5.1 -bfio==2.3.1 +autopage==0.5.2 +bfio==2.3.2 blinker==1.6.3 botocore==1.31.17 certifi==2023.7.22 @@ -31,6 +32,7 @@ dask==2023.5.0 databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 +edt==2.3.1 einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 @@ -42,7 +44,7 @@ fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.9.2 gitdb==4.0.10 -gitpython==3.1.37 +gitpython==3.1.40 greenlet==3.0.0 gunicorn==21.2.0 h5py==3.10.0 @@ -70,13 +72,13 @@ markdown==3.5 MarkupSafe==2.1.3 matplotlib==3.7.3 mlflow==2.7.1 -monai-weekly==1.3.dev2341 +monai-weekly==1.4.dev2342 mpmath==1.3.0 msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.12.0 +numcodecs==0.12.1 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 @@ -88,13 +90,14 @@ packaging==23.2 pandas==1.5.3 partd==1.4.1 pbr==5.11.1 -pillow==10.0.1 +pillow==10.1.0 PrettyTable==3.9.0 protobuf==3.20.1 -psutil==5.9.5 +psutil==5.9.6 pyarrow==10.0.1 pydantic==2.4.2 pydantic-core==2.10.1 +pyerfa==2.0.0.3 pyjwt==2.8.0 pyparsing==3.1.1 pyperclip==1.8.2 @@ -129,8 +132,8 @@ torchmetrics==1.2.0 tornado==6.3.3 tqdm==4.66.1 typing-extensions==4.8.0 -universal-pathlib==0.1.3 -urllib3==1.26.17 +universal-pathlib==0.1.4 +urllib3==1.26.18 wcwidth==0.2.8 websocket-client==1.6.4 Werkzeug==3.0.0 diff --git a/requirements/macos/spharm-requirements.txt b/requirements/macos/spharm-requirements.txt index 5e3de1915..1781dc414 100644 --- a/requirements/macos/spharm-requirements.txt +++ b/requirements/macos/spharm-requirements.txt @@ -16,8 +16,8 @@ asciitree==0.3.3 astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 -autopage==0.5.1 -bfio==2.3.1 +autopage==0.5.2 +bfio==2.3.2 blinker==1.6.3 botocore==1.27.59 certifi==2023.7.22 @@ -34,6 +34,7 @@ dask==2023.5.0 databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 +edt==2.3.1 einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 @@ -45,7 +46,7 @@ fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 gitdb==4.0.10 -gitpython==3.1.37 +gitpython==3.1.40 greenlet==3.0.0 gunicorn==21.2.0 h5py==3.10.0 @@ -73,13 +74,13 @@ markdown==3.5 MarkupSafe==2.1.3 matplotlib==3.7.3 mlflow==2.7.1 -monai-weekly==1.3.dev2341 +monai-weekly==1.4.dev2342 mpmath==1.3.0 msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.12.0 +numcodecs==0.12.1 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 @@ -91,12 +92,12 @@ packaging==23.2 pandas==1.5.3 partd==1.4.1 pbr==5.11.1 -pillow==10.0.1 +pillow==10.1.0 platformdirs==3.11.0 pooch==1.7.0 PrettyTable==3.9.0 protobuf==3.20.1 -psutil==5.9.5 +psutil==5.9.6 pyarrow==10.0.1 pydantic==2.4.2 pydantic-core==2.10.1 @@ -131,13 +132,13 @@ termcolor==2.3.0 threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 -torch==2.0.1 +torch==2.1.0 torchmetrics==1.2.0 tornado==6.3.3 tqdm==4.66.1 typing-extensions==4.8.0 -universal-pathlib==0.1.3 -urllib3==1.26.17 +universal-pathlib==0.1.4 +urllib3==1.26.18 vtk==9.2.6 wcwidth==0.2.8 websocket-client==1.6.4 diff --git a/requirements/macos/test-requirements.txt b/requirements/macos/test-requirements.txt index d68b0f324..a014ab025 100644 --- a/requirements/macos/test-requirements.txt +++ b/requirements/macos/test-requirements.txt @@ -17,12 +17,11 @@ astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 autograd==1.6.2 -autopage==0.5.1 -bfio==2.3.1 +autopage==0.5.2 +bfio==2.3.2 blinker==1.6.3 boto3==1.24.4 botocore==1.27.59 -cellpose-omni==0.9.1 certifi==2023.7.22 charset-normalizer==3.3.0 click==8.1.7 @@ -48,7 +47,6 @@ entrypoints==0.4 escnn==1.0.11 exceptiongroup==1.1.3 fasteners==0.19 -fastremap==1.14.0 filelock==3.12.4 fire==0.5.0 Flask==2.3.3 @@ -58,7 +56,7 @@ fsspec==2023.3.0 future==0.18.3 geomloss==0.2.6 gitdb==4.0.10 -gitpython==3.1.37 +gitpython==3.1.40 gorilla==0.4.0 greenlet==3.0.0 gunicorn==21.2.0 @@ -69,7 +67,6 @@ hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 -igraph==0.11.2 imagecodecs==2023.3.16 imageio==2.31.5 importlib-metadata==6.8.0 @@ -85,36 +82,29 @@ lazy-loader==0.3 lie-learn @ git+https://github.com/colobas/lie_learn.git@d5be2ab lightning==2.1.0 lightning-utilities==0.9.0 -llvmlite==0.41.0 locket==1.0.0 lxml==4.9.3 -mahotas==1.4.13 Mako==1.2.4 markdown==3.5 markdown-it-py==3.0.0 MarkupSafe==2.1.3 matplotlib==3.7.3 mdurl==0.1.2 -mgen==1.2.1 mlflow==2.7.1 -monai-weekly==1.3.dev2341 +monai-weekly==1.4.dev2342 mpmath==1.3.0 msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 -ncolor==1.2.1 networkx==3.1 nibabel==5.1.0 Ninja==1.11.1.1 -numba==0.58.0 -numcodecs==0.12.0 +numcodecs==0.12.1 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 ome-zarr==0.8.2 omegaconf==2.3.0 -omnipose @ git+https://github.com/kevinjohncutler/omnipose.git@ce2e9aa -opencv-python-headless==4.8.1.78 opt-einsum==3.3.0 opt-einsum-fx==0.1.4 optuna==2.10.1 @@ -123,15 +113,14 @@ packaging==23.2 pandas==1.5.3 partd==1.4.1 pbr==5.11.1 -peakdetect==1.2 -pillow==10.0.1 +pillow==10.1.0 platformdirs==3.11.0 pluggy==1.3.0 point-cloud-utils==0.30.0 pooch==1.7.0 PrettyTable==3.9.0 protobuf==3.20.1 -psutil==5.9.5 +psutil==5.9.6 py3nj==0.1.2 pyarrow==10.0.1 pydantic==2.4.2 @@ -150,7 +139,6 @@ pytest-cov==4.1.0 python-dateutil==2.8.2 python-dotenv==1.0.0 pytorch-lightning==2.1.0 -pytorch-ranger==0.1.1 pytz==2023.3.post1 PyWavelets==1.4.1 PyYAML==6.0.1 @@ -177,26 +165,23 @@ sympy==1.12 tabulate==0.9.0 tblib==2.0.0 termcolor==2.3.0 -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==2.1.0 torch-geometric==2.4.0 -torch-optimizer==0.3.0 torchio==0.19.1 torchmetrics==1.2.0 torchserve==0.9.0 -torchvf==0.1.3 -torchvision==0.15.2 +torchvision==0.16.0 tornado==6.3.3 tqdm==4.66.1 typer==0.9.0 typing-extensions==4.8.0 -universal-pathlib==0.1.3 -urllib3==1.26.17 +universal-pathlib==0.1.4 +urllib3==1.26.18 vtk==9.2.6 wcwidth==0.2.8 websocket-client==1.6.4 diff --git a/requirements/macos/torchserve-requirements.txt b/requirements/macos/torchserve-requirements.txt index beb5bd4f3..92b9ef4b8 100644 --- a/requirements/macos/torchserve-requirements.txt +++ b/requirements/macos/torchserve-requirements.txt @@ -11,10 +11,11 @@ anndata==0.9.2 annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 asciitree==0.3.3 +astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 -autopage==0.5.1 -bfio==2.3.1 +autopage==0.5.2 +bfio==2.3.2 blinker==1.6.3 botocore==1.27.59 certifi==2023.7.22 @@ -31,6 +32,7 @@ dask==2023.5.0 databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 +edt==2.3.1 einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 @@ -42,7 +44,7 @@ fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 gitdb==4.0.10 -gitpython==3.1.37 +gitpython==3.1.40 gorilla==0.4.0 greenlet==3.0.0 gunicorn==21.2.0 @@ -71,13 +73,13 @@ markdown==3.5 MarkupSafe==2.1.3 matplotlib==3.7.3 mlflow==2.7.1 -monai-weekly==1.3.dev2341 +monai-weekly==1.4.dev2342 mpmath==1.3.0 msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.12.0 +numcodecs==0.12.1 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 @@ -89,13 +91,14 @@ packaging==23.2 pandas==1.5.3 partd==1.4.1 pbr==5.11.1 -pillow==10.0.1 +pillow==10.1.0 PrettyTable==3.9.0 protobuf==3.20.1 -psutil==5.9.5 +psutil==5.9.6 pyarrow==10.0.1 pydantic==2.4.2 pydantic-core==2.10.1 +pyerfa==2.0.0.3 pyjwt==2.8.0 pyparsing==3.1.1 pyperclip==1.8.2 @@ -125,14 +128,14 @@ termcolor==2.3.0 threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 -torch==2.0.1 +torch==2.1.0 torchmetrics==1.2.0 torchserve==0.9.0 tornado==6.3.3 tqdm==4.66.1 typing-extensions==4.8.0 -universal-pathlib==0.1.3 -urllib3==1.26.17 +universal-pathlib==0.1.4 +urllib3==1.26.18 wcwidth==0.2.8 websocket-client==1.6.4 Werkzeug==3.0.0 diff --git a/requirements/windows/all-requirements.txt b/requirements/windows/all-requirements.txt index 13c24483f..fa647c08d 100644 --- a/requirements/windows/all-requirements.txt +++ b/requirements/windows/all-requirements.txt @@ -17,12 +17,11 @@ astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 autograd==1.6.2 -autopage==0.5.1 -bfio==2.3.1 +autopage==0.5.2 +bfio==2.3.2 blinker==1.6.3 boto3==1.24.4 botocore==1.27.59 -cellpose-omni==0.9.1 certifi==2023.7.22 charset-normalizer==3.3.0 click==8.1.7 @@ -46,7 +45,6 @@ elementpath==4.1.5 entrypoints==0.4 escnn==1.0.11 fasteners==0.19 -fastremap==1.14.0 filelock==3.12.4 fire==0.5.0 Flask==2.3.3 @@ -56,7 +54,7 @@ fsspec==2023.3.0 future==0.18.3 geomloss==0.2.6 gitdb==4.0.10 -gitpython==3.1.37 +gitpython==3.1.40 gorilla==0.4.0 greenlet==3.0.0 h5py==3.10.0 @@ -66,7 +64,6 @@ hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 -igraph==0.11.2 imagecodecs==2023.3.16 imageio==2.31.5 importlib-metadata==6.8.0 @@ -81,36 +78,29 @@ lazy-loader==0.3 lie-learn @ git+https://github.com/colobas/lie_learn.git@d5be2ab lightning==2.1.0 lightning-utilities==0.9.0 -llvmlite==0.41.0 locket==1.0.0 lxml==4.9.3 -mahotas==1.4.13 Mako==1.2.4 markdown==3.5 markdown-it-py==3.0.0 MarkupSafe==2.1.3 matplotlib==3.7.3 mdurl==0.1.2 -mgen==1.2.1 mlflow==2.7.1 -monai-weekly==1.3.dev2341 +monai-weekly==1.4.dev2342 mpmath==1.3.0 msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 -ncolor==1.2.1 networkx==3.1 nibabel==5.1.0 Ninja==1.11.1.1 -numba==0.58.0 -numcodecs==0.12.0 +numcodecs==0.12.1 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 ome-zarr==0.8.2 omegaconf==2.3.0 -omnipose @ git+https://github.com/kevinjohncutler/omnipose.git@ce2e9aa -opencv-python-headless==4.8.1.78 opt-einsum==3.3.0 opt-einsum-fx==0.1.4 optuna==2.10.1 @@ -119,14 +109,13 @@ packaging==23.2 pandas==1.5.3 partd==1.4.1 pbr==5.11.1 -peakdetect==1.2 -pillow==10.0.1 +pillow==10.1.0 platformdirs==3.11.0 point-cloud-utils==0.30.0 pooch==1.7.0 PrettyTable==3.9.0 protobuf==3.20.1 -psutil==5.9.5 +psutil==5.9.6 py3nj==0.1.2 pyarrow==10.0.1 pydantic==2.4.2 @@ -142,7 +131,6 @@ pyreadline3==3.4.1 pyshtools==4.10.3 python-dateutil==2.8.2 pytorch-lightning==2.1.0 -pytorch-ranger==0.1.1 pytz==2023.3.post1 PyWavelets==1.4.1 pywin32==306 @@ -170,25 +158,22 @@ sympy==1.12 tabulate==0.9.0 tblib==2.0.0 termcolor==2.3.0 -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==2.1.0 torch-geometric==2.4.0 -torch-optimizer==0.3.0 torchio==0.19.1 torchmetrics==1.2.0 torchserve==0.9.0 -torchvf==0.1.3 -torchvision==0.15.2 +torchvision==0.16.0 tornado==6.3.3 tqdm==4.66.1 typer==0.9.0 typing-extensions==4.8.0 -universal-pathlib==0.1.3 -urllib3==1.26.17 +universal-pathlib==0.1.4 +urllib3==1.26.18 vtk==9.2.6 waitress==2.1.2 wcwidth==0.2.8 diff --git a/requirements/windows/docs-requirements.txt b/requirements/windows/docs-requirements.txt index 0a419b3f5..e467114e0 100644 --- a/requirements/windows/docs-requirements.txt +++ b/requirements/windows/docs-requirements.txt @@ -18,14 +18,13 @@ astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 autograd==1.6.2 -autopage==0.5.1 +autopage==0.5.2 babel==2.13.0 beautifulsoup4==4.12.2 -bfio==2.3.1 +bfio==2.3.2 blinker==1.6.3 boto3==1.24.4 botocore==1.27.59 -cellpose-omni==0.9.1 certifi==2023.7.22 charset-normalizer==3.3.0 click==8.1.7 @@ -50,7 +49,6 @@ elementpath==4.1.5 entrypoints==0.4 escnn==1.0.11 fasteners==0.19 -fastremap==1.14.0 filelock==3.12.4 fire==0.5.0 Flask==2.3.3 @@ -61,7 +59,7 @@ furo==2023.3.23 future==0.18.3 geomloss==0.2.6 gitdb==4.0.10 -gitpython==3.1.37 +gitpython==3.1.40 gorilla==0.4.0 greenlet==3.0.0 h5py==3.10.0 @@ -71,7 +69,6 @@ hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 -igraph==0.11.2 imagecodecs==2023.3.16 imageio==2.31.5 imagesize==1.4.1 @@ -87,38 +84,31 @@ lazy-loader==0.3 lie-learn @ git+https://github.com/colobas/lie_learn.git@d5be2ab lightning==2.1.0 lightning-utilities==0.9.0 -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==3.5 markdown-it-py==3.0.0 MarkupSafe==2.1.3 matplotlib==3.7.3 mdurl==0.1.2 -mgen==1.2.1 mistune==0.8.4 mlflow==2.7.1 -monai-weekly==1.3.dev2341 +monai-weekly==1.4.dev2342 mpmath==1.3.0 msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 -ncolor==1.2.1 networkx==3.1 nibabel==5.1.0 Ninja==1.11.1.1 -numba==0.58.0 -numcodecs==0.12.0 +numcodecs==0.12.1 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 ome-zarr==0.8.2 omegaconf==2.3.0 -omnipose @ git+https://github.com/kevinjohncutler/omnipose.git@ce2e9aa -opencv-python-headless==4.8.1.78 opt-einsum==3.3.0 opt-einsum-fx==0.1.4 optuna==2.10.1 @@ -127,14 +117,13 @@ packaging==23.2 pandas==1.5.3 partd==1.4.1 pbr==5.11.1 -peakdetect==1.2 -pillow==10.0.1 +pillow==10.1.0 platformdirs==3.11.0 point-cloud-utils==0.30.0 pooch==1.7.0 PrettyTable==3.9.0 protobuf==3.20.1 -psutil==5.9.5 +psutil==5.9.6 py3nj==0.1.2 pyarrow==10.0.1 pydantic==2.4.2 @@ -150,7 +139,6 @@ pyreadline3==3.4.1 pyshtools==4.10.3 python-dateutil==2.8.2 pytorch-lightning==2.1.0 -pytorch-ranger==0.1.1 pytz==2023.3.post1 PyWavelets==1.4.1 pywin32==306 @@ -188,25 +176,22 @@ sympy==1.12 tabulate==0.9.0 tblib==2.0.0 termcolor==2.3.0 -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==2.1.0 torch-geometric==2.4.0 -torch-optimizer==0.3.0 torchio==0.19.1 torchmetrics==1.2.0 torchserve==0.9.0 -torchvf==0.1.3 -torchvision==0.15.2 +torchvision==0.16.0 tornado==6.3.3 tqdm==4.66.1 typer==0.9.0 typing-extensions==4.8.0 -universal-pathlib==0.1.3 -urllib3==1.26.17 +universal-pathlib==0.1.4 +urllib3==1.26.18 vtk==9.2.6 waitress==2.1.2 wcwidth==0.2.8 diff --git a/requirements/windows/equiv-requirements.txt b/requirements/windows/equiv-requirements.txt index 354d23938..579631eae 100644 --- a/requirements/windows/equiv-requirements.txt +++ b/requirements/windows/equiv-requirements.txt @@ -11,11 +11,12 @@ anndata==0.9.2 annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 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 -bfio==2.3.1 +autopage==0.5.2 +bfio==2.3.2 blinker==1.6.3 botocore==1.27.59 certifi==2023.7.22 @@ -34,6 +35,7 @@ databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 e3nn==0.5.1 +edt==2.3.1 einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 @@ -47,7 +49,7 @@ frozenlist==1.4.0 fsspec==2023.3.0 future==0.18.3 gitdb==4.0.10 -gitpython==3.1.37 +gitpython==3.1.40 greenlet==3.0.0 h5py==3.10.0 hydra-colorlog==1.2.0 @@ -75,13 +77,13 @@ markdown==3.5 MarkupSafe==2.1.3 matplotlib==3.7.3 mlflow==2.7.1 -monai-weekly==1.3.dev2341 +monai-weekly==1.4.dev2342 mpmath==1.3.0 msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.12.0 +numcodecs==0.12.1 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 @@ -95,14 +97,15 @@ packaging==23.2 pandas==1.5.3 partd==1.4.1 pbr==5.11.1 -pillow==10.0.1 +pillow==10.1.0 PrettyTable==3.9.0 protobuf==3.20.1 -psutil==5.9.5 +psutil==5.9.6 py3nj==0.1.2 pyarrow==10.0.1 pydantic==2.4.2 pydantic-core==2.10.1 +pyerfa==2.0.0.3 pyjwt==2.8.0 pymanopt==2.2.0 pyparsing==3.1.1 @@ -135,13 +138,13 @@ termcolor==2.3.0 threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 -torch==2.0.1 +torch==2.1.0 torchmetrics==1.2.0 tornado==6.3.3 tqdm==4.66.1 typing-extensions==4.8.0 -universal-pathlib==0.1.3 -urllib3==1.26.17 +universal-pathlib==0.1.4 +urllib3==1.26.18 waitress==2.1.2 wcwidth==0.2.8 websocket-client==1.6.4 diff --git a/requirements/windows/pdm.lock b/requirements/windows/pdm.lock index 2addbd625..d1b4e0feb 100644 --- a/requirements/windows/pdm.lock +++ b/requirements/windows/pdm.lock @@ -2,11 +2,11 @@ # It is not intended for manual editing. [metadata] -groups = ["default", "all", "docs", "equiv", "omnipose", "pcloud", "s3", "spharm", "test", "torchserve"] +groups = ["default", "all", "docs", "equiv", "pcloud", "s3", "spharm", "test", "torchserve"] cross_platform = false static_urls = false lock_version = "4.3" -content_hash = "sha256:e37073446848e15bbc0ccb7f651dad85c6d46e07816b4b1fe870c7ee6aa14abd" +content_hash = "sha256:41758e6f558cc07a12e3eded2035c39e2f4e7f36c7d9fa7b46043b1eaf1220e6" [[package]] name = "aicscytoparam" @@ -248,12 +248,12 @@ files = [ [[package]] name = "autopage" -version = "0.5.1" +version = "0.5.2" requires_python = ">=3.6" summary = "A library to provide automatic paging for console output" files = [ - {file = "autopage-0.5.1-py3-none-any.whl", hash = "sha256:0fbf5efbe78d466a26753e1dee3272423a3adc989d6a778c700e89a3f8ff0d88"}, - {file = "autopage-0.5.1.tar.gz", hash = "sha256:01be3ee61bb714e9090fcc5c10f4cf546c396331c620c6ae50a2321b28ed3199"}, + {file = "autopage-0.5.2-py3-none-any.whl", hash = "sha256:f5eae54dd20ccc8b1ff611263fc87bc46608a9cde749bbcfc93339713a429c55"}, + {file = "autopage-0.5.2.tar.gz", hash = "sha256:826996d74c5aa9f4b6916195547312ac6384bac3810b8517063f293248257b72"}, ] [[package]] @@ -281,8 +281,8 @@ files = [ [[package]] name = "bfio" -version = "2.3.1" -requires_python = ">=3.7" +version = "2.3.2" +requires_python = ">=3.8" summary = "Simple reading and writing classes for tiled tiffs using Bioformats." dependencies = [ "imagecodecs>=2021.2.26", @@ -290,12 +290,12 @@ dependencies = [ "numpy>=1.20.1", "ome-types>=0.4.2", "scyjava", - "tifffile", + "tifffile>=2022.8.12", "zarr>=2.6.1", ] files = [ - {file = "bfio-2.3.1-py2.py3-none-any.whl", hash = "sha256:9e2c19258956c34997dfdab7015819809093bda2f82fdb05a9f80b346cfe89b1"}, - {file = "bfio-2.3.1.tar.gz", hash = "sha256:4c96b7017866bfc9a07b98336fdea95d8dad90cc6c4c136ddbafcb460d8b78b0"}, + {file = "bfio-2.3.2-py2.py3-none-any.whl", hash = "sha256:26e52a0f5d7ad528013ed0945f66023b6a1acd0afd6ca23ac95ff747583223e8"}, + {file = "bfio-2.3.2.tar.gz", hash = "sha256:a53979da22b96f0cf21a97b55c1d005f9d6dcb80dffe52fddb3643bf47fda766"}, ] [[package]] @@ -338,45 +338,6 @@ files = [ {file = "botocore-1.27.59.tar.gz", hash = "sha256:eda4aed6ee719a745d1288eaf1beb12f6f6448ad1fa12f159405db14ba9c92cf"}, ] -[[package]] -name = "cellpose-omni" -version = "0.9.1" -summary = "cellpose fork developed for omnipose" -dependencies = [ - "fastremap", - "imagecodecs", - "natsort", - "numba", - "numpy>=1.22.4", - "opencv-python-headless", - "scipy", - "tifffile", - "torch>=1.6", - "tqdm", -] -files = [ - {file = "cellpose-omni-0.9.1.tar.gz", hash = "sha256:84f3199a751a74ddab643227bd0425ffafedcc2e739a57958f73a6d5f5348b6e"}, - {file = "cellpose_omni-0.9.1-py3-none-any.whl", hash = "sha256:7074f248656b5e29aae3e615ade4ce350dcc8a170cee94d5655a739fc454b6f8"}, -] - -[[package]] -name = "cellpose-omni" -version = "0.9.1" -extras = ["omni"] -summary = "cellpose fork developed for omnipose" -dependencies = [ - "cellpose-omni==0.9.1", - "edt", - "ncolor>=1.2.1", - "scikit-image", - "scikit-learn", - "torch-optimizer", -] -files = [ - {file = "cellpose-omni-0.9.1.tar.gz", hash = "sha256:84f3199a751a74ddab643227bd0425ffafedcc2e739a57958f73a6d5f5348b6e"}, - {file = "cellpose_omni-0.9.1-py3-none-any.whl", hash = "sha256:7074f248656b5e29aae3e615ade4ce350dcc8a170cee94d5655a739fc454b6f8"}, -] - [[package]] name = "certifi" version = "2023.7.22" @@ -759,19 +720,6 @@ files = [ {file = "fasteners-0.19.tar.gz", hash = "sha256:b4f37c3ac52d8a445af3a66bce57b33b5e90b97c696b7b984f530cf8f0ded09c"}, ] -[[package]] -name = "fastremap" -version = "1.14.0" -requires_python = ">=3.7,<4.0" -summary = "Remap, mask, renumber, unique, and in-place transposition of 3D labeled images. 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"sha256:cf14627d5a8049ffbf49915732e5eddbe8134c3bdb9d476e6182b676fc573f8a"}, + {file = "GitPython-3.1.40.tar.gz", hash = "sha256:22b126e9ffb671fdd0c129796343a02bf67bf2994b35449ffc9321aa755e18a4"}, ] [[package]] @@ -1048,19 +996,6 @@ files = [ {file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"}, ] -[[package]] -name = "igraph" -version = "0.11.2" -requires_python = ">=3.8" -summary = "High performance graph data structures and algorithms" -dependencies = [ - "texttable>=1.6.2", -] -files = [ - {file = "igraph-0.11.2-cp39-abi3-win_amd64.whl", hash = "sha256:76f0b8aa232e836e5bcdf8993360e8fec186c2bdbd02d6219607331329b3cf0e"}, - {file = "igraph-0.11.2.tar.gz", hash = "sha256:c4053e47156d7685ad48bd72e6ff400d46b09deeebc746b96b5cf9737939fa2d"}, -] - [[package]] name = "imagecodecs" version = "2023.3.16" @@ -1260,16 +1195,6 @@ files = [ {file = "lightning_utilities-0.9.0-py3-none-any.whl", hash = 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"torch>=1.9", ] files = [ - {file = "monai-weekly-1.3.dev2341.tar.gz", hash = "sha256:976ece4b5412447697efaa3ca87827d8bdb43d2683d6838e9ad70ed9f6cf694b"}, - {file = "monai_weekly-1.3.dev2341-py3-none-any.whl", hash = "sha256:c61a3d2bc270c43ec5946d7d039e5c9659ef86c7759bbe1b100fe65a65cd88d8"}, + {file = "monai-weekly-1.4.dev2342.tar.gz", hash = "sha256:173176225b6606408077e89fcd8a1f727bab5c385872f9d50b01201eecb87bfe"}, + {file = "monai_weekly-1.4.dev2342-py3-none-any.whl", hash = "sha256:213bf1e627d206d5c4052c944f7f5dc71f4129a134fb8d02fcd5989b28419fa9"}, ] [[package]] @@ -1506,23 +1406,6 @@ files = [ {file = "natsort-8.4.0.tar.gz", hash = "sha256:45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581"}, ] -[[package]] -name = "ncolor" -version = "1.2.1" -summary = "label matrix coloring algorithm" -dependencies = [ - "fastremap", - "mahotas>=1.4.13", - "numba", - "numpy>=1.22.4", - "scikit-image", - "scipy", -] -files = [ - {file = "ncolor-1.2.1-py3-none-any.whl", hash = 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buffer compression and transformation codecs for use in data storage and communication applications." dependencies = [ "numpy>=1.7", ] files = [ - {file = "numcodecs-0.12.0-cp310-cp310-win_amd64.whl", hash = "sha256:3b5a0be940093d81eb49b0adba62615d3b973174d8167dbd63cc6d392e157bf6"}, - {file = "numcodecs-0.12.0.tar.gz", hash = "sha256:6388e5f4e94d18a7165fbd1c9d3637673b74157cff8bc644005f9e2a4c717d6e"}, + {file = "numcodecs-0.12.1-cp310-cp310-win_amd64.whl", hash = "sha256:82d7107f80f9307235cb7e74719292d101c7ea1e393fe628817f0d635b7384f5"}, + {file = "numcodecs-0.12.1.tar.gz", hash = "sha256:05d91a433733e7eef268d7e80ec226a0232da244289614a8f3826901aec1098e"}, ] [[package]] @@ -1652,47 +1521,6 @@ files = [ {file = "omegaconf-2.3.0.tar.gz", hash = "sha256:d5d4b6d29955cc50ad50c46dc269bcd92c6e00f5f90d23ab5fee7bfca4ba4cc7"}, ] -[[package]] -name = "omnipose" -version = "0.4.1.dev5+gce2e9aa" -git = "https://github.com/kevinjohncutler/omnipose.git" -ref = "ce2e9aa" -revision = 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"sha256:b5b08f68937f138fe92f6c089b99f1e2da0ae56c52b78bf7075fd95420fd9a5a"}, ] -[[package]] -name = "texttable" -version = "1.7.0" -summary = "module to create simple ASCII tables" -files = [ - {file = "texttable-1.7.0-py2.py3-none-any.whl", hash = "sha256:72227d592c82b3d7f672731ae73e4d1f88cd8e2ef5b075a7a7f01a23a3743917"}, - {file = "texttable-1.7.0.tar.gz", hash = "sha256:2d2068fb55115807d3ac77a4ca68fa48803e84ebb0ee2340f858107a36522638"}, -] - [[package]] name = "threadpoolctl" version = "3.2.0" @@ -2696,18 +2489,19 @@ files = [ [[package]] name = "torch" -version = "2.0.1" +version = "2.1.0" requires_python = ">=3.8.0" summary = "Tensors and Dynamic neural networks in Python with strong GPU acceleration" dependencies = [ "filelock", + "fsspec", "jinja2", "networkx", "sympy", "typing-extensions", ] files = [ - {file = "torch-2.0.1-cp310-cp310-win_amd64.whl", hash = "sha256:7c84e44d9002182edd859f3400deaa7410f5ec948a519cc7ef512c2f9b34d2c4"}, + {file = 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antlr4-python3-runtime==4.9.3 asciitree==0.3.3 +astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 -autopage==0.5.1 -bfio==2.3.1 +autopage==0.5.2 +bfio==2.3.2 blinker==1.6.3 botocore==1.31.17 certifi==2023.7.22 @@ -32,6 +33,7 @@ dask==2023.5.0 databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 +edt==2.3.1 einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 @@ -43,7 +45,7 @@ fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.9.2 gitdb==4.0.10 -gitpython==3.1.37 +gitpython==3.1.40 greenlet==3.0.0 h5py==3.10.0 hydra-colorlog==1.2.0 @@ -70,13 +72,13 @@ markdown==3.5 MarkupSafe==2.1.3 matplotlib==3.7.3 mlflow==2.7.1 -monai-weekly==1.3.dev2341 +monai-weekly==1.4.dev2342 mpmath==1.3.0 msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.12.0 +numcodecs==0.12.1 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 @@ -88,13 +90,14 @@ packaging==23.2 pandas==1.5.3 partd==1.4.1 pbr==5.11.1 -pillow==10.0.1 +pillow==10.1.0 PrettyTable==3.9.0 protobuf==3.20.1 -psutil==5.9.5 +psutil==5.9.6 pyarrow==10.0.1 pydantic==2.4.2 pydantic-core==2.10.1 +pyerfa==2.0.0.3 pyjwt==2.8.0 pyparsing==3.1.1 pyperclip==1.8.2 @@ -131,8 +134,8 @@ torchmetrics==1.2.0 tornado==6.3.3 tqdm==4.66.1 typing-extensions==4.8.0 -universal-pathlib==0.1.3 -urllib3==1.26.17 +universal-pathlib==0.1.4 +urllib3==1.26.18 waitress==2.1.2 wcwidth==0.2.8 websocket-client==1.6.4 diff --git a/requirements/windows/spharm-requirements.txt b/requirements/windows/spharm-requirements.txt index 708ade3b9..4d89f3959 100644 --- a/requirements/windows/spharm-requirements.txt +++ b/requirements/windows/spharm-requirements.txt @@ -16,8 +16,8 @@ asciitree==0.3.3 astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 -autopage==0.5.1 -bfio==2.3.1 +autopage==0.5.2 +bfio==2.3.2 blinker==1.6.3 botocore==1.27.59 certifi==2023.7.22 @@ -35,6 +35,7 @@ dask==2023.5.0 databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 +edt==2.3.1 einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 @@ -46,7 +47,7 @@ fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 gitdb==4.0.10 -gitpython==3.1.37 +gitpython==3.1.40 greenlet==3.0.0 h5py==3.10.0 hydra-colorlog==1.2.0 @@ -73,13 +74,13 @@ markdown==3.5 MarkupSafe==2.1.3 matplotlib==3.7.3 mlflow==2.7.1 -monai-weekly==1.3.dev2341 +monai-weekly==1.4.dev2342 mpmath==1.3.0 msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.12.0 +numcodecs==0.12.1 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 @@ -91,12 +92,12 @@ packaging==23.2 pandas==1.5.3 partd==1.4.1 pbr==5.11.1 -pillow==10.0.1 +pillow==10.1.0 platformdirs==3.11.0 pooch==1.7.0 PrettyTable==3.9.0 protobuf==3.20.1 -psutil==5.9.5 +psutil==5.9.6 pyarrow==10.0.1 pydantic==2.4.2 pydantic-core==2.10.1 @@ -133,13 +134,13 @@ termcolor==2.3.0 threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 -torch==2.0.1 +torch==2.1.0 torchmetrics==1.2.0 tornado==6.3.3 tqdm==4.66.1 typing-extensions==4.8.0 -universal-pathlib==0.1.3 -urllib3==1.26.17 +universal-pathlib==0.1.4 +urllib3==1.26.18 vtk==9.2.6 waitress==2.1.2 wcwidth==0.2.8 diff --git a/requirements/windows/test-requirements.txt b/requirements/windows/test-requirements.txt index 950ed3b19..ab1b9fccb 100644 --- a/requirements/windows/test-requirements.txt +++ b/requirements/windows/test-requirements.txt @@ -17,12 +17,11 @@ astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 autograd==1.6.2 -autopage==0.5.1 -bfio==2.3.1 +autopage==0.5.2 +bfio==2.3.2 blinker==1.6.3 boto3==1.24.4 botocore==1.27.59 -cellpose-omni==0.9.1 certifi==2023.7.22 charset-normalizer==3.3.0 click==8.1.7 @@ -48,7 +47,6 @@ entrypoints==0.4 escnn==1.0.11 exceptiongroup==1.1.3 fasteners==0.19 -fastremap==1.14.0 filelock==3.12.4 fire==0.5.0 Flask==2.3.3 @@ -58,7 +56,7 @@ fsspec==2023.3.0 future==0.18.3 geomloss==0.2.6 gitdb==4.0.10 -gitpython==3.1.37 +gitpython==3.1.40 gorilla==0.4.0 greenlet==3.0.0 h5py==3.10.0 @@ -68,7 +66,6 @@ hydra-colorlog==1.2.0 hydra-core==1.3.2 hydra-optuna-sweeper==1.2.0 idna==3.4 -igraph==0.11.2 imagecodecs==2023.3.16 imageio==2.31.5 importlib-metadata==6.8.0 @@ -84,36 +81,29 @@ lazy-loader==0.3 lie-learn @ git+https://github.com/colobas/lie_learn.git@d5be2ab lightning==2.1.0 lightning-utilities==0.9.0 -llvmlite==0.41.0 locket==1.0.0 lxml==4.9.3 -mahotas==1.4.13 Mako==1.2.4 markdown==3.5 markdown-it-py==3.0.0 MarkupSafe==2.1.3 matplotlib==3.7.3 mdurl==0.1.2 -mgen==1.2.1 mlflow==2.7.1 -monai-weekly==1.3.dev2341 +monai-weekly==1.4.dev2342 mpmath==1.3.0 msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 -ncolor==1.2.1 networkx==3.1 nibabel==5.1.0 Ninja==1.11.1.1 -numba==0.58.0 -numcodecs==0.12.0 +numcodecs==0.12.1 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 ome-zarr==0.8.2 omegaconf==2.3.0 -omnipose @ git+https://github.com/kevinjohncutler/omnipose.git@ce2e9aa -opencv-python-headless==4.8.1.78 opt-einsum==3.3.0 opt-einsum-fx==0.1.4 optuna==2.10.1 @@ -122,15 +112,14 @@ packaging==23.2 pandas==1.5.3 partd==1.4.1 pbr==5.11.1 -peakdetect==1.2 -pillow==10.0.1 +pillow==10.1.0 platformdirs==3.11.0 pluggy==1.3.0 point-cloud-utils==0.30.0 pooch==1.7.0 PrettyTable==3.9.0 protobuf==3.20.1 -psutil==5.9.5 +psutil==5.9.6 py3nj==0.1.2 pyarrow==10.0.1 pydantic==2.4.2 @@ -150,7 +139,6 @@ pytest-cov==4.1.0 python-dateutil==2.8.2 python-dotenv==1.0.0 pytorch-lightning==2.1.0 -pytorch-ranger==0.1.1 pytz==2023.3.post1 PyWavelets==1.4.1 pywin32==306 @@ -178,26 +166,23 @@ sympy==1.12 tabulate==0.9.0 tblib==2.0.0 termcolor==2.3.0 -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==2.1.0 torch-geometric==2.4.0 -torch-optimizer==0.3.0 torchio==0.19.1 torchmetrics==1.2.0 torchserve==0.9.0 -torchvf==0.1.3 -torchvision==0.15.2 +torchvision==0.16.0 tornado==6.3.3 tqdm==4.66.1 typer==0.9.0 typing-extensions==4.8.0 -universal-pathlib==0.1.3 -urllib3==1.26.17 +universal-pathlib==0.1.4 +urllib3==1.26.18 vtk==9.2.6 waitress==2.1.2 wcwidth==0.2.8 diff --git a/requirements/windows/torchserve-requirements.txt b/requirements/windows/torchserve-requirements.txt index 8e0e738b3..630224004 100644 --- a/requirements/windows/torchserve-requirements.txt +++ b/requirements/windows/torchserve-requirements.txt @@ -11,10 +11,11 @@ anndata==0.9.2 annotated-types==0.6.0 antlr4-python3-runtime==4.9.3 asciitree==0.3.3 +astropy==5.2.2 async-timeout==4.0.3 attrs==23.1.0 -autopage==0.5.1 -bfio==2.3.1 +autopage==0.5.2 +bfio==2.3.2 blinker==1.6.3 botocore==1.27.59 certifi==2023.7.22 @@ -32,6 +33,7 @@ dask==2023.5.0 databricks-cli==0.18.0 distributed==2023.5.0 docker==6.1.3 +edt==2.3.1 einops==0.7.0 elementpath==4.1.5 entrypoints==0.4 @@ -43,7 +45,7 @@ fonttools==4.43.1 frozenlist==1.4.0 fsspec==2023.3.0 gitdb==4.0.10 -gitpython==3.1.37 +gitpython==3.1.40 gorilla==0.4.0 greenlet==3.0.0 h5py==3.10.0 @@ -71,13 +73,13 @@ markdown==3.5 MarkupSafe==2.1.3 matplotlib==3.7.3 mlflow==2.7.1 -monai-weekly==1.3.dev2341 +monai-weekly==1.4.dev2342 mpmath==1.3.0 msgpack==1.0.7 multidict==6.0.4 natsort==8.4.0 networkx==3.1 -numcodecs==0.12.0 +numcodecs==0.12.1 numpy==1.24.4 oauthlib==3.2.2 ome-types==0.4.2 @@ -89,13 +91,14 @@ packaging==23.2 pandas==1.5.3 partd==1.4.1 pbr==5.11.1 -pillow==10.0.1 +pillow==10.1.0 PrettyTable==3.9.0 protobuf==3.20.1 -psutil==5.9.5 +psutil==5.9.6 pyarrow==10.0.1 pydantic==2.4.2 pydantic-core==2.10.1 +pyerfa==2.0.0.3 pyjwt==2.8.0 pyparsing==3.1.1 pyperclip==1.8.2 @@ -127,14 +130,14 @@ termcolor==2.3.0 threadpoolctl==3.2.0 tifffile==2023.7.10 toolz==0.12.0 -torch==2.0.1 +torch==2.1.0 torchmetrics==1.2.0 torchserve==0.9.0 tornado==6.3.3 tqdm==4.66.1 typing-extensions==4.8.0 -universal-pathlib==0.1.3 -urllib3==1.26.17 +universal-pathlib==0.1.4 +urllib3==1.26.18 waitress==2.1.2 wcwidth==0.2.8 websocket-client==1.6.4