Updating lock files and requirements (#338)

Co-authored-by: benjijamorris <[email protected]>
AllenCellModeling · Feb 22, 2024 · 2b89383 · 2b89383
1 parent 47b98ae
commit 2b89383
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Showing 24 changed files with 602 additions and 591 deletions.
diff --git a/requirements/linux/all-requirements.txt b/requirements/linux/all-requirements.txt
@@ -12,7 +12,7 @@ alembic==1.13.1
 anndata==0.9.2
 annotated-types==0.6.0
 antlr4-python3-runtime==4.9.3
-anyio==4.2.0
+anyio==4.3.0
 arrow==1.3.0
 asciitree==0.3.3
 astropy==5.2.2
@@ -30,7 +30,7 @@ botocore==1.27.59
 certifi==2024.2.2
 charset-normalizer==3.3.2
 click==8.1.7
-cliff==4.5.0
+cliff==4.6.0
 cloudpickle==3.0.0
 cmaes==0.10.0
 cmake==3.28.3
@@ -47,9 +47,9 @@ Deprecated==1.2.14
 distributed==2023.5.0
 docker==7.0.0
 e3nn==0.5.1
-edt==2.3.2
+edt==2.4.0
 einops==0.7.0
-elementpath==4.2.1
+elementpath==4.3.0
 entrypoints==0.4
 escnn==1.0.11
 exceptiongroup==1.2.0
@@ -58,13 +58,13 @@ fasteners==0.19
 filelock==3.13.1
 fire==0.5.0
 Flask==3.0.2
-fonttools==4.48.1
+fonttools==4.49.0
 frozenlist==1.4.1
 fsspec==2023.3.0
-future==0.18.3
+future==1.0.0
 geomloss==0.2.6
 gitdb==4.0.11
-gitpython==3.1.41
+gitpython==3.1.42
 gorilla==0.4.0
 greenlet==3.0.3
 gunicorn==21.2.0
@@ -97,10 +97,10 @@ Mako==1.3.2
 markdown==3.5.2
 markdown-it-py==3.0.0
 MarkupSafe==2.1.5
-matplotlib==3.7.4
+matplotlib==3.7.5
 mdurl==0.1.2
 mlflow==2.10.2
-monai-weekly==1.4.dev2406
+monai-weekly==1.4.dev2407
 mpmath==1.3.0
 msgpack==1.0.7
 multidict==6.0.5
@@ -121,7 +121,7 @@ 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
-ome-types==0.4.5
+ome-types==0.5.0
 ome-zarr==0.8.3
 omegaconf==2.3.0
 opt-einsum==3.3.0
@@ -136,8 +136,8 @@ pbr==6.0.0
 pillow==10.2.0
 platformdirs==4.2.0
 point-cloud-utils==0.30.4
-pooch==1.8.0
-PrettyTable==3.9.0
+pooch==1.8.1
+PrettyTable==3.10.0
 protobuf==3.20.1
 psutil==5.9.8
 py3nj==0.1.2
@@ -153,7 +153,7 @@ pyntcloud==0.3.1
 pyparsing==3.1.1
 pyperclip==1.8.2
 pyrootutils==1.0.4
-pyshtools==4.11.10
+pyshtools==4.10.3
 python-dateutil==2.8.2
 python-dotenv==1.0.1
 python-editor==1.0.4
@@ -185,17 +185,17 @@ sqlalchemy==2.0.27
 sqlparse==0.4.4
 starlette==0.36.3
 starsessions==1.3.0
-stevedore==5.1.0
+stevedore==5.2.0
 sympy==1.12
 tblib==3.0.0
 termcolor==2.4.0
 threadpoolctl==3.3.0
 tifffile==2023.7.10
-timm==0.9.12
+timm==0.9.16
 toolz==0.12.1
 torch==2.0.1
-torch-geometric==2.4.0
-torchio==0.19.5
+torch-geometric==2.5.0
+torchio==0.19.6
 torchmetrics==1.3.1
 torchserve==0.9.0
 torchvision==0.15.2
@@ -206,7 +206,7 @@ triton==2.0.0
 typer==0.9.0
 types-python-dateutil==2.8.19.20240106
 typing-extensions==4.9.0
-universal-pathlib==0.2.0
+universal-pathlib==0.2.1
 urllib3==1.26.18
 uvicorn==0.27.1
 vtk==9.3.0
@@ -217,8 +217,8 @@ Werkzeug==3.0.1
 wheel==0.42.0
 wrapt==1.16.0
 xarray==2023.1.0
-xmlschema==3.0.1
-xsdata==24.1
+xmlschema==3.0.2
+xsdata==24.2.1
 yarl==1.9.4
 zarr==2.16.1
 zict==3.0.0

diff --git a/requirements/linux/docs-requirements.txt b/requirements/linux/docs-requirements.txt
@@ -13,7 +13,7 @@ alembic==1.13.1
 anndata==0.9.2
 annotated-types==0.6.0
 antlr4-python3-runtime==4.9.3
-anyio==4.2.0
+anyio==4.3.0
 arrow==1.3.0
 asciitree==0.3.3
 astropy==5.2.2
@@ -32,7 +32,7 @@ botocore==1.27.59
 certifi==2024.2.2
 charset-normalizer==3.3.2
 click==8.1.7
-cliff==4.5.0
+cliff==4.6.0
 cloudpickle==3.0.0
 cmaes==0.10.0
 cmake==3.28.3
@@ -50,9 +50,9 @@ distributed==2023.5.0
 docker==7.0.0
 docutils==0.19
 e3nn==0.5.1
-edt==2.3.2
+edt==2.4.0
 einops==0.7.0
-elementpath==4.2.1
+elementpath==4.3.0
 entrypoints==0.4
 escnn==1.0.11
 exceptiongroup==1.2.0
@@ -61,14 +61,14 @@ fasteners==0.19
 filelock==3.13.1
 fire==0.5.0
 Flask==3.0.2
-fonttools==4.48.1
+fonttools==4.49.0
 frozenlist==1.4.1
 fsspec==2023.3.0
 furo==2023.3.23
-future==0.18.3
+future==1.0.0
 geomloss==0.2.6
 gitdb==4.0.11
-gitpython==3.1.41
+gitpython==3.1.42
 gorilla==0.4.0
 greenlet==3.0.3
 gunicorn==21.2.0
@@ -103,11 +103,11 @@ Mako==1.3.2
 markdown==3.5.2
 markdown-it-py==3.0.0
 MarkupSafe==2.1.5
-matplotlib==3.7.4
+matplotlib==3.7.5
 mdurl==0.1.2
 mistune==0.8.4
 mlflow==2.10.2
-monai-weekly==1.4.dev2406
+monai-weekly==1.4.dev2407
 mpmath==1.3.0
 msgpack==1.0.7
 multidict==6.0.5
@@ -128,7 +128,7 @@ 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
-ome-types==0.4.5
+ome-types==0.5.0
 ome-zarr==0.8.3
 omegaconf==2.3.0
 opt-einsum==3.3.0
@@ -143,8 +143,8 @@ pbr==6.0.0
 pillow==10.2.0
 platformdirs==4.2.0
 point-cloud-utils==0.30.4
-pooch==1.8.0
-PrettyTable==3.9.0
+pooch==1.8.1
+PrettyTable==3.10.0
 protobuf==3.20.1
 psutil==5.9.8
 py3nj==0.1.2
@@ -160,7 +160,7 @@ pyntcloud==0.3.1
 pyparsing==3.1.1
 pyperclip==1.8.2
 pyrootutils==1.0.4
-pyshtools==4.11.10
+pyshtools==4.10.3
 python-dateutil==2.8.2
 python-dotenv==1.0.1
 python-editor==1.0.4
@@ -201,17 +201,17 @@ sqlalchemy==2.0.27
 sqlparse==0.4.4
 starlette==0.36.3
 starsessions==1.3.0
-stevedore==5.1.0
+stevedore==5.2.0
 sympy==1.12
 tblib==3.0.0
 termcolor==2.4.0
 threadpoolctl==3.3.0
 tifffile==2023.7.10
-timm==0.9.12
+timm==0.9.16
 toolz==0.12.1
 torch==2.0.1
-torch-geometric==2.4.0
-torchio==0.19.5
+torch-geometric==2.5.0
+torchio==0.19.6
 torchmetrics==1.3.1
 torchserve==0.9.0
 torchvision==0.15.2
@@ -222,7 +222,7 @@ triton==2.0.0
 typer==0.9.0
 types-python-dateutil==2.8.19.20240106
 typing-extensions==4.9.0
-universal-pathlib==0.2.0
+universal-pathlib==0.2.1
 urllib3==1.26.18
 uvicorn==0.27.1
 vtk==9.3.0
@@ -233,8 +233,8 @@ Werkzeug==3.0.1
 wheel==0.42.0
 wrapt==1.16.0
 xarray==2023.1.0
-xmlschema==3.0.1
-xsdata==24.1
+xmlschema==3.0.2
+xsdata==24.2.1
 yarl==1.9.4
 zarr==2.16.1
 zict==3.0.0

diff --git a/requirements/linux/equiv-requirements.txt b/requirements/linux/equiv-requirements.txt
@@ -10,7 +10,7 @@ alembic==1.13.1
 anndata==0.9.2
 annotated-types==0.6.0
 antlr4-python3-runtime==4.9.3
-anyio==4.2.0
+anyio==4.3.0
 arrow==1.3.0
 asciitree==0.3.3
 astropy==5.2.2
@@ -28,7 +28,7 @@ botocore==1.27.59
 certifi==2024.2.2
 charset-normalizer==3.3.2
 click==8.1.7
-cliff==4.5.0
+cliff==4.6.0
 cloudpickle==3.0.0
 cmaes==0.10.0
 cmake==3.28.3
@@ -43,9 +43,9 @@ deepdiff==6.7.1
 distributed==2023.5.0
 docker==7.0.0
 e3nn==0.5.1
-edt==2.3.2
+edt==2.4.0
 einops==0.7.0
-elementpath==4.2.1
+elementpath==4.3.0
 entrypoints==0.4
 escnn==1.0.11
 exceptiongroup==1.2.0
@@ -54,12 +54,12 @@ fasteners==0.19
 filelock==3.13.1
 fire==0.5.0
 Flask==3.0.2
-fonttools==4.48.1
+fonttools==4.49.0
 frozenlist==1.4.1
 fsspec==2023.3.0
-future==0.18.3
+future==1.0.0
 gitdb==4.0.11
-gitpython==3.1.41
+gitpython==3.1.42
 greenlet==3.0.3
 gunicorn==21.2.0
 h11==0.14.0
@@ -90,10 +90,10 @@ Mako==1.3.2
 markdown==3.5.2
 markdown-it-py==3.0.0
 MarkupSafe==2.1.5
-matplotlib==3.7.4
+matplotlib==3.7.5
 mdurl==0.1.2
 mlflow==2.10.2
-monai-weekly==1.4.dev2406
+monai-weekly==1.4.dev2407
 mpmath==1.3.0
 msgpack==1.0.7
 multidict==6.0.5
@@ -112,7 +112,7 @@ 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
-ome-types==0.4.5
+ome-types==0.5.0
 ome-zarr==0.8.3
 omegaconf==2.3.0
 opt-einsum==3.3.0
@@ -125,7 +125,7 @@ pandas==1.5.3
 partd==1.4.1
 pbr==6.0.0
 pillow==10.2.0
-PrettyTable==3.9.0
+PrettyTable==3.10.0
 protobuf==3.20.1
 psutil==5.9.8
 py3nj==0.1.2
@@ -169,13 +169,13 @@ sqlalchemy==2.0.27
 sqlparse==0.4.4
 starlette==0.36.3
 starsessions==1.3.0
-stevedore==5.1.0
+stevedore==5.2.0
 sympy==1.12
 tblib==3.0.0
 termcolor==2.4.0
 threadpoolctl==3.3.0
 tifffile==2023.7.10
-timm==0.9.12
+timm==0.9.16
 toolz==0.12.1
 torch==2.0.1
 torchmetrics==1.3.1
@@ -186,7 +186,7 @@ traitlets==5.14.1
 triton==2.0.0
 types-python-dateutil==2.8.19.20240106
 typing-extensions==4.9.0
-universal-pathlib==0.2.0
+universal-pathlib==0.2.1
 urllib3==1.26.18
 uvicorn==0.27.1
 wcwidth==0.2.13
@@ -196,8 +196,8 @@ Werkzeug==3.0.1
 wheel==0.42.0
 wrapt==1.16.0
 xarray==2023.1.0
-xmlschema==3.0.1
-xsdata==24.1
+xmlschema==3.0.2
+xsdata==24.2.1
 yarl==1.9.4
 zarr==2.16.1
 zict==3.0.0