Merge pull request #429 from Project-MONAI/dev

merge master
Project-MONAI · Jul 8, 2022 · ca62306 · ca62306
2 parents ec463d6 + e270741
commit ca62306
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diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
@@ -38,11 +38,11 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v1
+      uses: github/codeql-action/init@v2
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -53,7 +53,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     # - name: Autobuild
-    #   uses: github/codeql-action/autobuild@v1
+    #   uses: github/codeql-action/autobuild@v2
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 https://git.io/JvXDl
@@ -68,4 +68,4 @@ jobs:
         BUILD_MONAI=1 ./runtests.sh --build
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v1
+      uses: github/codeql-action/analyze@v2
diff --git a/.github/workflows/conda.yml b/.github/workflows/conda.yml
@@ -30,7 +30,7 @@ jobs:
         minimum-size: 8
         maximum-size: 16
         disk-root: "D:"
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - uses: conda-incubator/setup-miniconda@v2
       with:
         auto-update-conda: true

diff --git a/.github/workflows/cron-mmar.yml b/.github/workflows/cron-mmar.yml
@@ -16,16 +16,16 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version: 3.8
     - name: cache weekly timestamp
       id: pip-cache
       run: echo "::set-output name=datew::$(date '+%Y-%V')"
     - name: cache for pip
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache
       with:
         path: ~/.cache/pip

diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml
@@ -15,24 +15,24 @@ jobs:
     runs-on: [self-hosted, linux, x64, common]
     strategy:
       matrix:
-        pytorch-version: [1.6.0, 1.7.1, 1.8.1, 1.9.1, latest]
+        pytorch-version: [1.7.1, 1.8.1, 1.9.1, 1.10.2, latest]
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Install the dependencies
       run: |
         which python
         python -m pip install --upgrade pip wheel
         python -m pip uninstall -y torch torchvision
         if [ ${{ matrix.pytorch-version }} == "latest" ]; then
-          python -m pip install torch torchvision
-        elif [ ${{ matrix.pytorch-version }} == "1.6.0" ]; then
-          python -m pip install torch==1.6.0 torchvision==0.7.0
+          python -m pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cu113
         elif [ ${{ matrix.pytorch-version }} == "1.7.1" ]; then
-          python -m pip install torch==1.7.1 torchvision==0.8.2
+          python -m pip install torch==1.7.1 torchvision==0.8.2 --extra-index-url https://download.pytorch.org/whl/cu113
         elif [ ${{ matrix.pytorch-version }} == "1.8.1" ]; then
-          python -m pip install torch==1.8.1 torchvision==0.9.1
+          python -m pip install torch==1.8.1 torchvision==0.9.1 --extra-index-url https://download.pytorch.org/whl/cu113
         elif [ ${{ matrix.pytorch-version }} == "1.9.1" ]; then
-          python -m pip install torch==1.9.1 torchvision==0.10.1
+          python -m pip install torch==1.9.1 torchvision==0.10.1 --extra-index-url https://download.pytorch.org/whl/cu113
+        elif [ ${{ matrix.pytorch-version }} == "1.10.2" ]; then
+          python -m pip install torch==1.10.2 torchvision==0.11.3 --extra-index-url https://download.pytorch.org/whl/cu113
         fi
         python -m pip install -r requirements-dev.txt
         python -m pip list
@@ -62,13 +62,13 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:21.02", "pytorch:21.10", "pytorch:22.03"]  # 21.02, 21.10 for backward comp.
+        container: ["pytorch:21.02", "pytorch:21.10", "pytorch:22.06"]  # 21.02, 21.10 for backward comp.
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
     runs-on: [self-hosted, linux, x64, common]
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Install APT dependencies
       run: |
         apt-get update
@@ -106,13 +106,13 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:21.02", "pytorch:21.10", "pytorch:22.03"]  # 21.02, 21.10 for backward comp.
+        container: ["pytorch:21.02", "pytorch:21.10", "pytorch:22.06"]  # 21.02, 21.10 for backward comp.
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
     runs-on: [self-hosted, linux, x64, common]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - name: Install the dependencies
@@ -204,11 +204,11 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     needs: cron-gpu  # so that monai itself is verified first
     container:
-      image: nvcr.io/nvidia/pytorch:22.03-py3  # testing with the latest pytorch base image
+      image: nvcr.io/nvidia/pytorch:22.06-py3  # testing with the latest pytorch base image
       options: "--gpus all --ipc=host"
     runs-on: [self-hosted, linux, x64, common]
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Install MONAI
       id: monai-install
       run: |
@@ -223,7 +223,7 @@ jobs:
     - name: Checkout tutorials and install their requirements
       run: |
         cd /opt
-        git clone --depth 1 --branch master --single-branch https://github.com/Project-MONAI/tutorials.git  # latest commit of master branch
+        git clone --depth 1 --branch main --single-branch https://github.com/Project-MONAI/tutorials.git  # latest commit of main branch
         cd tutorials
         python -m pip install -r requirements.txt
     - name: Run tutorial notebooks

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -19,13 +19,13 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         # full history so that we can git describe
         with:
           ref: dev
           fetch-depth: 0
       - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: 3.8
       - shell: bash
@@ -50,7 +50,7 @@ jobs:
     needs: versioning_dev
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         ref: dev
     - name: Download version

diff --git a/.github/workflows/integration.yml b/.github/workflows/integration.yml
@@ -7,12 +7,12 @@ on:
 jobs:
   integration-py3:
     container:
-      image: nvcr.io/nvidia/pytorch:21.12-py3  # CUDA 11.5
-      options: --gpus all
+      image: nvcr.io/nvidia/pytorch:22.04-py3  # CUDA 11.6
+      options: --gpus all  # shm-size 4g works fine
     runs-on: [self-hosted, linux, x64, common]
     steps:
     # checkout the pull request branch
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         token: ${{ secrets.PR_MAINTAIN }}
         repository: ${{ github.event.client_payload.pull_request.head.repo.full_name }}
@@ -22,7 +22,7 @@ jobs:
       run: |
         echo "::set-output name=datew::$(date '+%Y-%V')"
     - name: cache for pip
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache
       with:
         path: |
@@ -34,7 +34,7 @@ jobs:
         which python
         python -m pip install --upgrade pip wheel
         python -m pip uninstall -y torch torchvision
-        python -m pip install torch==1.11.0+cu115 torchvision==0.12.0+cu115 -f https://download.pytorch.org/whl/torch_stable.html
+        python -m pip install torch==1.12.0+cu116 torchvision==0.13.0+cu116 -f https://download.pytorch.org/whl/torch_stable.html
         python -m pip install -r requirements-dev.txt
         rm -rf /github/home/.cache/torch/hub/mmars/
     - name: Run integration tests

diff --git a/.github/workflows/pythonapp-gpu.yml b/.github/workflows/pythonapp-gpu.yml
@@ -23,16 +23,17 @@ jobs:
           - "PT17+CUDA102"
           - "PT18+CUDA102"
           - "PT18+CUDA112"
-          - "PT111+CUDA116"
+          - "PT112+CUDA116"
           - "PT110+CUDA102"
-          - "PT111+CUDA102"
+          - "PT112+CUDA102"
         include:
           # https://docs.nvidia.com/deeplearning/frameworks/pytorch-release-notes
           - environment: PT17+CUDA102
             pytorch: "torch==1.7.1 torchvision==0.8.2"
             base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
           - environment: PT18+CUDA102
-            pytorch: "torch==1.8.1 torchvision==0.9.1"
+            # pytorch 1.8.2 LTS
+            pytorch: "torch==1.8.2 torchvision==0.9.2 --extra-index-url https://download.pytorch.org/whl/lts/1.8/cu102"
             base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
           - environment: PT18+CUDA112
             # we explicitly set pytorch to -h to avoid pip install error
@@ -44,29 +45,36 @@ jobs:
             # 21.10: 1.10.0a0+0aef44c
             pytorch: "-h"
             base: "nvcr.io/nvidia/pytorch:21.10-py3"
-          - environment: PT111+CUDA116
+          - environment: PT112+CUDA116
             # we explicitly set pytorch to -h to avoid pip install error
-            # 22.03: 1.12.0a0+2c916ef
+            # 22.06: 1.13.0a0+340c412
             pytorch: "-h"
-            base: "nvcr.io/nvidia/pytorch:22.03-py3"
+            base: "nvcr.io/nvidia/pytorch:22.06-py3"
           - environment: PT110+CUDA102
-            pytorch: "torch==1.10.1 torchvision==0.11.2"
+            pytorch: "torch==1.10.2 torchvision==0.11.3"
             base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
-          - environment: PT111+CUDA102
-            pytorch: "torch==1.11.0 torchvision==0.12.0"
+          - environment: PT112+CUDA102
+            pytorch: "torch==1.12.0 torchvision==0.13.0"
             base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
     container:
       image: ${{ matrix.base }}
       options: --gpus all
     runs-on: [self-hosted, linux, x64, common]
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: apt install
       run: |
+        # workaround for https://github.com/Project-MONAI/MONAI/issues/4200
+        apt-key del 7fa2af80 && rm -rf /etc/apt/sources.list.d/nvidia-ml.list /etc/apt/sources.list.d/cuda.list
+        apt-get update
+        apt-get install -y wget
+        wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-keyring_1.0-1_all.deb
+        dpkg -i cuda-keyring_1.0-1_all.deb
+
         if [ ${{ matrix.environment }} = "PT17+CUDA102" ] || \
           [ ${{ matrix.environment }} = "PT18+CUDA102" ] || \
           [ ${{ matrix.environment }} = "PT110+CUDA102" ] || \
-          [ ${{ matrix.environment }} = "PT111+CUDA102" ]
+          [ ${{ matrix.environment }} = "PT112+CUDA102" ]
         then
         PYVER=3.7 PYSFX=3 DISTUTILS=python3-distutils && \
         apt-get update && apt-get install -y --no-install-recommends \

diff --git a/.github/workflows/pythonapp-min.yml b/.github/workflows/pythonapp-min.yml
@@ -27,9 +27,9 @@ jobs:
         os: [windows-latest, macOS-latest, ubuntu-latest]
     timeout-minutes: 40
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version: 3.8
     - name: Prepare pip wheel
@@ -43,19 +43,19 @@ jobs:
         echo "::set-output name=dir::$(pip cache dir)"
       shell: bash
     - name: cache for pip
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache
       with:
         path: ${{ steps.pip-cache.outputs.dir }}
         key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
     - if: runner.os == 'windows'
       name: Install torch cpu from pytorch.org (Windows only)
       run: |
-        python -m pip install torch==1.11.0+cpu -f https://download.pytorch.org/whl/torch_stable.html
+        python -m pip install torch==1.12.0+cpu -f https://download.pytorch.org/whl/torch_stable.html
     - name: Install the dependencies
       run: |
         # min. requirements
-        python -m pip install torch==1.11.0
+        python -m pip install torch==1.12.0
         python -m pip install -r requirements-min.txt
         python -m pip list
         BUILD_MONAI=0 python setup.py develop  # no compile of extensions
@@ -77,9 +77,9 @@ jobs:
         python-version: [3.7, 3.8, 3.9]
     timeout-minutes: 40
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
     - name: Prepare pip wheel
@@ -93,15 +93,15 @@ jobs:
         echo "::set-output name=dir::$(pip cache dir)"
       shell: bash
     - name: cache for pip
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache
       with:
         path: ${{ steps.pip-cache.outputs.dir }}
         key: ubuntu-latest-latest-pip-${{ steps.pip-cache.outputs.datew }}
     - name: Install the dependencies
       run: |
         # min. requirements
-        python -m pip install torch==1.11.0
+        python -m pip install torch==1.12.0
         python -m pip install -r requirements-min.txt
         python -m pip list
         BUILD_MONAI=0 python setup.py develop  # no compile of extensions
@@ -119,12 +119,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        pytorch-version: [1.6.0, 1.7.1, 1.8.1, 1.9.1, 1.10.1, latest]
+        pytorch-version: [1.7.1, 1.8.2, 1.9.1, 1.10.2, 1.11.0, latest]
     timeout-minutes: 40
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version: 3.8
     - name: Prepare pip wheel
@@ -138,7 +138,7 @@ jobs:
         echo "::set-output name=dir::$(pip cache dir)"
       shell: bash
     - name: cache for pip
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache
       with:
         path: ${{ steps.pip-cache.outputs.dir }}
@@ -148,16 +148,16 @@ jobs:
         # min. requirements
         if [ ${{ matrix.pytorch-version }} == "latest" ]; then
           python -m pip install torch
-        elif [ ${{ matrix.pytorch-version }} == "1.6.0" ]; then
-          python -m pip install torch==1.6.0
         elif [ ${{ matrix.pytorch-version }} == "1.7.1" ]; then
           python -m pip install torch==1.7.1
-        elif [ ${{ matrix.pytorch-version }} == "1.8.1" ]; then
-          python -m pip install torch==1.8.1
+        elif [ ${{ matrix.pytorch-version }} == "1.8.2" ]; then
+          python -m pip install torch==1.8.2 --extra-index-url https://download.pytorch.org/whl/lts/1.8/cpu
         elif [ ${{ matrix.pytorch-version }} == "1.9.1" ]; then
           python -m pip install torch==1.9.1
-        elif [ ${{ matrix.pytorch-version }} == "1.10.1" ]; then
-          python -m pip install torch==1.10.1
+        elif [ ${{ matrix.pytorch-version }} == "1.10.2" ]; then
+          python -m pip install torch==1.10.2
+        elif [ ${{ matrix.pytorch-version }} == "1.11.0" ]; then
+          python -m pip install torch==1.11.0
         fi
         python -m pip install -r requirements-min.txt
         python -m pip list