ENH: Upgrade DICOM-RT Version to 1.1.0 (#807)

Upgrading DICOM-RT to incorporate fixes to various DICOM issues.
microsoft · Oct 14, 2022 · 02e7d9a · 02e7d9a
1 parent 78b7de2
commit 02e7d9a
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Showing 3 changed files with 51 additions and 53 deletions.
diff --git a/TestSubmodule/environment.yml b/TestSubmodule/environment.yml
@@ -11,7 +11,7 @@ dependencies:
  - blosc=1.21.0=h4ff587b_1
  - bzip2=1.0.8=h7b6447c_0
  - ca-certificates=2022.07.19=h06a4308_0
- - certifi=2022.9.14=py38h06a4308_0
+ - certifi=2022.9.24=py38h06a4308_0
  - cudatoolkit=11.3.1=h2bc3f7f_2
  - ffmpeg=4.2.2=h20bf706_0
  - freetype=2.11.0=h70c0345_0
@@ -37,8 +37,8 @@ dependencies:
  - libunistring=0.9.10=h27cfd23_0
  - libuv=1.40.0=h7b6447c_0
  - libvpx=1.7.0=h439df22_0
- - libwebp=1.2.2=h55f646e_0
- - libwebp-base=1.2.2=h7f8727e_0
+ - libwebp=1.2.4=h11a3e52_0
+ - libwebp-base=1.2.4=h5eee18b_0
  - lz4-c=1.9.3=h295c915_1
  - mkl=2021.4.0=h06a4308_640
  - mkl-service=2.4.0=py38h7f8727e_0
@@ -55,13 +55,13 @@ dependencies:
  - pytorch-mutex=1.0=cuda
  - readline=8.1.2=h7f8727e_1
  - setuptools=63.4.1=py38h06a4308_0
- - sqlite=3.39.2=h5082296_0
+ - sqlite=3.39.3=h5082296_0
  - tk=8.6.12=h1ccaba5_0
  - torchvision=0.11.1=py38_cu113
  - typing_extensions=4.3.0=py38h06a4308_0
  - wheel=0.37.1=pyhd3eb1b0_0
  - x264=1!157.20191217=h7b6447c_0
- - xz=5.2.5=h7f8727e_1
+ - xz=5.2.6=h5eee18b_0
  - zlib=1.2.12=h5eee18b_3
  - zstd=1.5.2=ha4553b6_0
  - pip:
@@ -78,7 +78,7 @@ dependencies:
  - async-timeout==4.0.2
  - attrs==22.1.0
  - azure-common==1.1.28
- - azure-core==1.25.1
+ - azure-core==1.26.0
  - azure-graphrbac==0.61.1
  - azure-identity==1.7.0
  - azure-mgmt-authorization==0.61.0
@@ -109,7 +109,7 @@ dependencies:
  - backports-tempfile==1.0
  - backports-weakref==1.0.post1
  - beautifulsoup4==4.11.1
- - black==22.8.0
+ - black==22.10.0
  - bleach==5.0.1
  - cachetools==4.2.4
  - cffi==1.15.1
@@ -120,15 +120,15 @@ dependencies:
  - commonmark==0.9.1
  - conda-merge==0.1.5
  - contextlib2==21.6.0
- - coverage==6.4.4
+ - coverage==6.5.0
  - cryptography==3.3.2
  - cycler==0.11.0
  - databricks-cli==0.17.3
  - dataclasses-json==0.5.2
  - debugpy==1.6.3
  - defusedxml==0.7.1
  - deprecated==1.2.13
- - distro==1.7.0
+ - distro==1.8.0
  - docker==4.3.1
  - docutils==0.18.1
  - dotnetcore2==2.1.23
@@ -147,7 +147,7 @@ dependencies:
  - google-auth==1.35.0
  - google-auth-oauthlib==0.4.6
  - gputil==1.4.0
- - greenlet==1.1.3
+ - greenlet==1.1.3.post0
  - grpcio==1.49.1
  - gunicorn==20.1.0
  - h5py==2.10.0
@@ -157,10 +157,10 @@ dependencies:
  - idna==3.4
  - imageio==2.15.0
  - imagesize==1.4.1
- - importlib-metadata==4.12.0
- - importlib-resources==5.9.0
+ - importlib-metadata==5.0.0
+ - importlib-resources==5.10.0
  - iniconfig==1.1.1
- - innereye-dicom-rt==1.0.3
+ - innereye-dicom-rt==1.1.0
  - ipykernel==6.16.0
  - ipython==7.31.1
  - ipython-genutils==0.2.0
@@ -182,7 +182,6 @@ dependencies:
  - kiwisolver==1.4.4
  - lightning-bolts==0.4.0
  - llvmlite==0.34.0
- - lxml==4.9.1
  - mako==1.2.3
  - markdown==3.4.1
  - markdown-it-py==2.1.0
@@ -198,20 +197,20 @@ dependencies:
  - mlflow-skinny==1.29.0
  - monai==0.6.0
  - more-itertools==8.14.0
- - msal==1.19.0
+ - msal==1.20.0
  - msal-extensions==0.3.1
  - msrest==0.7.1
  - msrestazure==0.6.4
  - multidict==6.0.2
  - mypy==0.910
  - mypy-extensions==0.4.3
  - myst-parser==0.18.0
- - nbclient==0.6.8
- - nbconvert==7.0.0
- - nbformat==5.6.1
+ - nbclient==0.7.0
+ - nbconvert==7.2.1
+ - nbformat==5.7.0
  - ndg-httpsclient==0.5.1
- - nest-asyncio==1.5.5
- - networkx==2.8.6
+ - nest-asyncio==1.5.6
+ - networkx==2.8.7
  - nibabel==4.0.2
  - notebook==6.4.12
  - numba==0.51.2
@@ -256,12 +255,12 @@ dependencies:
  - pytest-xdist==1.34.0
  - python-dateutil==2.8.2
  - pytorch-lightning==1.6.5
- - pytz==2022.2.1
+ - pytz==2022.4
  - pywavelets==1.4.1
  - pyyaml==6.0
  - pyzmq==24.0.1
  - qtconsole==5.3.2
- - qtpy==2.2.0
+ - qtpy==2.2.1
  - querystring-parser==1.2.4
  - requests==2.28.1
  - requests-oauthlib==1.3.1
@@ -284,7 +283,7 @@ dependencies:
  - soupsieve==2.3.2.post1
  - sphinx==5.0.2
  - sphinx-argparse==0.3.1
- - sphinx-basic-ng==0.0.1a12
+ - sphinx-basic-ng==1.0.0b1
  - sphinx-rtd-theme==1.0.0
  - sphinxcontrib-applehelp==1.0.2
  - sphinxcontrib-devhelp==1.0.2
@@ -301,10 +300,10 @@ dependencies:
  - tensorboard==2.3.0
  - tensorboard-plugin-wit==1.8.1
  - tensorboardx==2.1
- - terminado==0.15.0
+ - terminado==0.16.0
  - textwrap3==0.9.2
  - threadpoolctl==3.1.0
- - tifffile==2022.8.12
+ - tifffile==2022.10.10
  - tinycss2==1.1.1
  - toml==0.10.2
  - tomli==2.0.1
@@ -322,4 +321,4 @@ dependencies:
  - wrapt==1.14.1
  - yacs==0.1.8
  - yarl==1.8.1
- - zipp==3.8.1
+ - zipp==3.9.0
diff --git a/environment.yml b/environment.yml
@@ -11,7 +11,7 @@ dependencies:
  - blosc=1.21.0=h4ff587b_1
  - bzip2=1.0.8=h7b6447c_0
  - ca-certificates=2022.07.19=h06a4308_0
- - certifi=2022.9.14=py38h06a4308_0
+ - certifi=2022.9.24=py38h06a4308_0
  - cudatoolkit=11.3.1=h2bc3f7f_2
  - ffmpeg=4.2.2=h20bf706_0
  - freetype=2.11.0=h70c0345_0
@@ -37,8 +37,8 @@ dependencies:
  - libunistring=0.9.10=h27cfd23_0
  - libuv=1.40.0=h7b6447c_0
  - libvpx=1.7.0=h439df22_0
- - libwebp=1.2.2=h55f646e_0
- - libwebp-base=1.2.2=h7f8727e_0
+ - libwebp=1.2.4=h11a3e52_0
+ - libwebp-base=1.2.4=h5eee18b_0
  - lz4-c=1.9.3=h295c915_1
  - mkl=2021.4.0=h06a4308_640
  - mkl-service=2.4.0=py38h7f8727e_0
@@ -55,13 +55,13 @@ dependencies:
  - pytorch-mutex=1.0=cuda
  - readline=8.1.2=h7f8727e_1
  - setuptools=63.4.1=py38h06a4308_0
- - sqlite=3.39.2=h5082296_0
+ - sqlite=3.39.3=h5082296_0
  - tk=8.6.12=h1ccaba5_0
  - torchvision=0.11.1=py38_cu113
  - typing_extensions=4.3.0=py38h06a4308_0
  - wheel=0.37.1=pyhd3eb1b0_0
  - x264=1!157.20191217=h7b6447c_0
- - xz=5.2.5=h7f8727e_1
+ - xz=5.2.6=h5eee18b_0
  - zlib=1.2.12=h5eee18b_3
  - zstd=1.5.2=ha4553b6_0
  - pip:
@@ -78,7 +78,7 @@ dependencies:
  - async-timeout==4.0.2
  - attrs==22.1.0
  - azure-common==1.1.28
- - azure-core==1.25.1
+ - azure-core==1.26.0
  - azure-graphrbac==0.61.1
  - azure-identity==1.7.0
  - azure-mgmt-authorization==0.61.0
@@ -109,7 +109,7 @@ dependencies:
  - backports-tempfile==1.0
  - backports-weakref==1.0.post1
  - beautifulsoup4==4.11.1
- - black==22.8.0
+ - black==22.10.0
  - bleach==5.0.1
  - cachetools==4.2.4
  - cffi==1.15.1
@@ -120,15 +120,15 @@ dependencies:
  - commonmark==0.9.1
  - conda-merge==0.1.5
  - contextlib2==21.6.0
- - coverage==6.4.4
+ - coverage==6.5.0
  - cryptography==3.3.2
  - cycler==0.11.0
  - databricks-cli==0.17.3
  - dataclasses-json==0.5.2
  - debugpy==1.6.3
  - defusedxml==0.7.1
  - deprecated==1.2.13
- - distro==1.7.0
+ - distro==1.8.0
  - docker==4.3.1
  - docutils==0.18.1
  - dotnetcore2==2.1.23
@@ -147,7 +147,7 @@ dependencies:
  - google-auth==1.35.0
  - google-auth-oauthlib==0.4.6
  - gputil==1.4.0
- - greenlet==1.1.3
+ - greenlet==1.1.3.post0
  - grpcio==1.49.1
  - gunicorn==20.1.0
  - h5py==2.10.0
@@ -157,10 +157,10 @@ dependencies:
  - idna==3.4
  - imageio==2.15.0
  - imagesize==1.4.1
- - importlib-metadata==4.12.0
- - importlib-resources==5.9.0
+ - importlib-metadata==5.0.0
+ - importlib-resources==5.10.0
  - iniconfig==1.1.1
- - innereye-dicom-rt==1.0.3
+ - innereye-dicom-rt==1.1.0
  - ipykernel==6.16.0
  - ipython==7.31.1
  - ipython-genutils==0.2.0
@@ -182,7 +182,6 @@ dependencies:
  - kiwisolver==1.4.4
  - lightning-bolts==0.4.0
  - llvmlite==0.34.0
- - lxml==4.9.1
  - mako==1.2.3
  - markdown==3.4.1
  - markdown-it-py==2.1.0
@@ -198,20 +197,20 @@ dependencies:
  - mlflow-skinny==1.29.0
  - monai==0.6.0
  - more-itertools==8.14.0
- - msal==1.19.0
+ - msal==1.20.0
  - msal-extensions==0.3.1
  - msrest==0.7.1
  - msrestazure==0.6.4
  - multidict==6.0.2
  - mypy==0.910
  - mypy-extensions==0.4.3
  - myst-parser==0.18.0
- - nbclient==0.6.8
- - nbconvert==7.0.0
- - nbformat==5.6.1
+ - nbclient==0.7.0
+ - nbconvert==7.2.1
+ - nbformat==5.7.0
  - ndg-httpsclient==0.5.1
- - nest-asyncio==1.5.5
- - networkx==2.8.6
+ - nest-asyncio==1.5.6
+ - networkx==2.8.7
  - nibabel==4.0.2
  - notebook==6.4.12
  - numba==0.51.2
@@ -256,12 +255,12 @@ dependencies:
  - pytest-xdist==1.34.0
  - python-dateutil==2.8.2
  - pytorch-lightning==1.6.5
- - pytz==2022.2.1
+ - pytz==2022.4
  - pywavelets==1.4.1
  - pyyaml==6.0
  - pyzmq==24.0.1
  - qtconsole==5.3.2
- - qtpy==2.2.0
+ - qtpy==2.2.1
  - querystring-parser==1.2.4
  - requests==2.28.1
  - requests-oauthlib==1.3.1
@@ -284,7 +283,7 @@ dependencies:
  - soupsieve==2.3.2.post1
  - sphinx==5.0.2
  - sphinx-argparse==0.3.1
- - sphinx-basic-ng==0.0.1a12
+ - sphinx-basic-ng==1.0.0b1
  - sphinx-rtd-theme==1.0.0
  - sphinxcontrib-applehelp==1.0.2
  - sphinxcontrib-devhelp==1.0.2
@@ -301,10 +300,10 @@ dependencies:
  - tensorboard==2.3.0
  - tensorboard-plugin-wit==1.8.1
  - tensorboardx==2.1
- - terminado==0.15.0
+ - terminado==0.16.0
  - textwrap3==0.9.2
  - threadpoolctl==3.1.0
- - tifffile==2022.8.12
+ - tifffile==2022.10.10
  - tinycss2==1.1.1
  - toml==0.10.2
  - tomli==2.0.1
@@ -322,4 +321,4 @@ dependencies:
  - wrapt==1.14.1
  - yacs==0.1.8
  - yarl==1.8.1
- - zipp==3.8.1
+ - zipp==3.9.0
diff --git a/primary_deps.yml b/primary_deps.yml
@@ -31,7 +31,7 @@ dependencies:
  - hi-ml==0.2.5
  - hi-ml-azure==0.2.5
  - imageio==2.15.0
- - InnerEye-DICOM-RT==1.0.3
+ - InnerEye-DICOM-RT==1.1.0
  - ipython==7.31.1
  - joblib==0.16.0
  - jupyter-client==6.1.5