merge master

.deepsource.toml

@@ -24,4 +24,4 @@ enabled = true
 
 [[analyzers]]
 name = "shell"
-enabled = true
+enabled = true

.dockerignore

@@ -11,4 +11,3 @@ coverage.xml
 *.toml
 
 !README.md
-

.github/ISSUE_TEMPLATE/question.md

@@ -9,4 +9,4 @@ assignees: ''
 **Please use MONAI's Discussions tab**
 For questions relating to MONAI usage, please do not create an issue.
 
-Instead, use [MONAI's GitHub Discussions tab](https://github.com/Project-MONAI/MONAI/discussions). This can be found next to Issues and Pull Requests along the top of our repository.
+Instead, use [MONAI's GitHub Discussions tab](https://github.com/Project-MONAI/MONAI/discussions). This can be found next to Issues and Pull Requests along the top of our repository.

.github/workflows/cron.yml

@@ -1,8 +1,8 @@
 name: crons
 
 on:
-  schedule:
-    - cron: "0 2 * * *"  # at 02:00 UTC
+  # schedule:
+  #   - cron: "0 2 * * *"  # at 02:00 UTC
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
@@ -62,7 +62,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:21.02", "pytorch:21.06"]  # 21.02 for backward comp.
+        container: ["pytorch:21.02", "pytorch:21.08"]  # 21.02 for backward comp.
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
@@ -106,7 +106,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:21.02", "pytorch:21.06"]  # 21.02 for backward comp.
+        container: ["pytorch:21.02", "pytorch:21.08"]  # 21.02 for backward comp.
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
@@ -204,7 +204,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     needs: cron-gpu  # so that monai itself is verified first
     container:
-      image: nvcr.io/nvidia/pytorch:21.06-py3  # testing with the latest pytorch base image
+      image: nvcr.io/nvidia/pytorch:21.08-py3  # testing with the latest pytorch base image
       options: "--gpus all --ipc=host"
     runs-on: [self-hosted, linux, x64, common]
     steps:

.github/workflows/pythonapp-gpu.yml

@@ -0,0 +1,134 @@
+name: build-gpu
+
+on:
+  # quick tests for pull requests and the releasing branches
+  push:
+    branches:
+      - main
+      - releasing/*
+  pull_request:
+
+concurrency:
+  # automatically cancel the previously triggered workflows when there's a newer version
+  group: build-gpu-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  GPU-quick-py3:  # GPU with full dependencies
+    if: github.repository == 'Project-MONAI/MONAI'
+    strategy:
+      matrix:
+        environment:
+          - "PT16+CUDA110"
+          - "PT17+CUDA102"
+          - "PT17+CUDA110"
+          - "PT18+CUDA102"
+          - "PT19+CUDA114"
+          - "PT19+CUDA102"
+        include:
+          - environment: PT16+CUDA110
+            # we explicitly set pytorch to -h to avoid pip install error
+            pytorch: "-h"
+            base: "nvcr.io/nvidia/pytorch:20.07-py3"
+          - environment: PT17+CUDA102
+            pytorch: "torch==1.7.1 torchvision==0.8.2"
+            base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
+          - environment: PT17+CUDA110
+            # we explicitly set pytorch to -h to avoid pip install error
+            pytorch: "-h"
+            base: "nvcr.io/nvidia/pytorch:20.09-py3"
+          - environment: PT18+CUDA102
+            pytorch: "torch==1.8.1 torchvision==0.9.1"
+            base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
+          - environment: PT19+CUDA114
+            # we explicitly set pytorch to -h to avoid pip install error
+            # https://docs.nvidia.com/deeplearning/frameworks/pytorch-release-notes
+            # 21.08: 1.10.0a0+3fd9dcf
+            pytorch: "-h"
+            base: "nvcr.io/nvidia/pytorch:21.08-py3"
+          - environment: PT19+CUDA102
+            pytorch: "torch==1.9.0 torchvision==0.10.0"
+            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
+    - name: apt install
+      run: |
+        if [ ${{ matrix.environment }} = "PT17+CUDA102" ] || \
+          [ ${{ matrix.environment }} = "PT18+CUDA102" ] || \
+          [ ${{ matrix.environment }} = "PT19+CUDA102" ]
+        then
+        PYVER=3.6 PYSFX=3 DISTUTILS=python3-distutils && \
+        apt-get update && apt-get install -y --no-install-recommends \
+          curl \
+          pkg-config \
+          python$PYVER \
+          python$PYVER-dev \
+          python$PYSFX-pip \
+          $DISTUTILS \
+          rsync \
+          swig \
+          unzip \
+          zip \
+          zlib1g-dev \
+          libboost-locale-dev \
+          libboost-program-options-dev \
+          libboost-system-dev \
+          libboost-thread-dev \
+          libboost-test-dev \
+          libgoogle-glog-dev \
+          libjsoncpp-dev \
+          cmake \
+          git && \
+        rm -rf /var/lib/apt/lists/* && \
+        export PYTHONIOENCODING=utf-8 LC_ALL=C.UTF-8 && \
+        rm -f /usr/bin/python && \
+        rm -f /usr/bin/python`echo $PYVER | cut -c1-1` && \
+        ln -s /usr/bin/python$PYVER /usr/bin/python && \
+        ln -s /usr/bin/python$PYVER /usr/bin/python`echo $PYVER | cut -c1-1` &&
+        curl -O https://bootstrap.pypa.io/get-pip.py && \
+        python get-pip.py && \
+        rm get-pip.py;
+        fi
+    - if: matrix.environment == 'PT19+CUDA114'
+      name: Optional Cupy dependency (cuda114)
+      run: echo "cupy-cuda114" >> requirements-dev.txt
+    - name: Install dependencies
+      run: |
+        which python
+        python -m pip install --upgrade pip wheel
+        python -m pip install ${{ matrix.pytorch }}
+        python -m pip install -r requirements-dev.txt
+        python -m pip list
+    - name: Run quick tests (GPU)
+      run: |
+        git clone --depth 1 \
+          https://github.com/Project-MONAI/MONAI-extra-test-data.git /MONAI-extra-test-data
+        export MONAI_EXTRA_TEST_DATA="/MONAI-extra-test-data"
+        nvidia-smi
+        export LAUNCH_DELAY=$(python -c "import numpy; print(numpy.random.randint(30) * 10)")
+        echo "Sleep $LAUNCH_DELAY"
+        sleep $LAUNCH_DELAY
+        export CUDA_VISIBLE_DEVICES=$(coverage run -m tests.utils)
+        echo $CUDA_VISIBLE_DEVICES
+        trap 'if pgrep python; then pkill python; fi;' ERR
+        python -c $'import torch\na,b=torch.zeros(1,device="cuda:0"),torch.zeros(1,device="cuda:1");\nwhile True:print(a,b)' > /dev/null &
+        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
+        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
+        python -c "import monai; monai.config.print_config()"
+        # build for the current self-hosted CI Tesla V100
+        BUILD_MONAI=1 TORCH_CUDA_ARCH_LIST="7.0" ./runtests.sh --quick --unittests
+        if [ ${{ matrix.environment }} = "PT19+CUDA102" ]; then
+          # test the clang-format tool downloading once
+          coverage run -m tests.clang_format_utils
+        fi
+        coverage xml
+        if pgrep python; then pkill python; fi
+      shell: bash
+    - name: Upload coverage
+      uses: codecov/codecov-action@v1
+      with:
+        file: ./coverage.xml

.github/workflows/pythonapp.yml

@@ -200,122 +200,11 @@ jobs:
       env:
         QUICKTEST: True
 
-  GPU-quick-py3:  # GPU with full dependencies
-    if: github.repository == 'Project-MONAI/MONAI'
-    strategy:
-      matrix:
-        environment:
-          - "PT16+CUDA110"
-          - "PT17+CUDA102"
-          - "PT17+CUDA110"
-          - "PT18+CUDA102"
-          - "PT19+CUDA113"
-          - "PT19+CUDA102"
-        include:
-          - environment: PT16+CUDA110
-            # we explicitly set pytorch to -h to avoid pip install error
-            pytorch: "-h"
-            base: "nvcr.io/nvidia/pytorch:20.07-py3"
-          - environment: PT17+CUDA102
-            pytorch: "torch==1.7.1 torchvision==0.8.2"
-            base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
-          - environment: PT17+CUDA110
-            # we explicitly set pytorch to -h to avoid pip install error
-            pytorch: "-h"
-            base: "nvcr.io/nvidia/pytorch:20.09-py3"
-          - environment: PT18+CUDA102
-            pytorch: "torch==1.8.1 torchvision==0.9.1"
-            base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
-          - environment: PT19+CUDA113
-            # we explicitly set pytorch to -h to avoid pip install error
-            pytorch: "-h"
-            base: "nvcr.io/nvidia/pytorch:21.06-py3"
-          - environment: PT19+CUDA102
-            pytorch: "torch==1.9.0 torchvision==0.10.0"
-            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
-    - name: apt install
-      run: |
-        if [ ${{ matrix.environment }} = "PT17+CUDA102" ] || \
-           [ ${{ matrix.environment }} = "PT18+CUDA102" ] || \
-           [ ${{ matrix.environment }} = "PT19+CUDA102" ]
-        then
-        PYVER=3.6 PYSFX=3 DISTUTILS=python3-distutils && \
-        apt-get update && apt-get install -y --no-install-recommends \
-          curl \
-          pkg-config \
-          python$PYVER \
-          python$PYVER-dev \
-          python$PYSFX-pip \
-          $DISTUTILS \
-          rsync \
-          swig \
-          unzip \
-          zip \
-          zlib1g-dev \
-          libboost-locale-dev \
-          libboost-program-options-dev \
-          libboost-system-dev \
-          libboost-thread-dev \
-          libboost-test-dev \
-          libgoogle-glog-dev \
-          libjsoncpp-dev \
-          cmake \
-          git && \
-        rm -rf /var/lib/apt/lists/* && \
-        export PYTHONIOENCODING=utf-8 LC_ALL=C.UTF-8 && \
-        rm -f /usr/bin/python && \
-        rm -f /usr/bin/python`echo $PYVER | cut -c1-1` && \
-        ln -s /usr/bin/python$PYVER /usr/bin/python && \
-        ln -s /usr/bin/python$PYVER /usr/bin/python`echo $PYVER | cut -c1-1` &&
-        curl -O https://bootstrap.pypa.io/get-pip.py && \
-        python get-pip.py && \
-        rm get-pip.py;
-        fi
-    - name: Install dependencies
-      run: |
-        which python
-        python -m pip install --upgrade pip wheel
-        python -m pip install ${{ matrix.pytorch }}
-        python -m pip install -r requirements-dev.txt
-        python -m pip list
-    - name: Run quick tests (GPU)
-      run: |
-        git clone --depth 1 \
-          https://github.com/Project-MONAI/MONAI-extra-test-data.git /MONAI-extra-test-data
-        export MONAI_EXTRA_TEST_DATA="/MONAI-extra-test-data"
-        nvidia-smi
-        export LAUNCH_DELAY=$(python -c "import numpy; print(numpy.random.randint(30) * 10)")
-        echo "Sleep $LAUNCH_DELAY"
-        sleep $LAUNCH_DELAY
-        export CUDA_VISIBLE_DEVICES=$(coverage run -m tests.utils)
-        echo $CUDA_VISIBLE_DEVICES
-        trap 'if pgrep python; then pkill python; fi;' ERR
-        python -c $'import torch\na,b=torch.zeros(1,device="cuda:0"),torch.zeros(1,device="cuda:1");\nwhile True:print(a,b)' > /dev/null &
-        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
-        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
-        python -c "import monai; monai.config.print_config()"
-        # build for the current self-hosted CI Tesla V100
-        BUILD_MONAI=1 TORCH_CUDA_ARCH_LIST="7.0" ./runtests.sh --quick --unittests
-        if [ ${{ matrix.environment }} = "PT19+CUDA102" ]; then
-          # test the clang-format tool downloading once
-          coverage run -m tests.clang_format_utils
-        fi
-        coverage xml
-        if pgrep python; then pkill python; fi
-      shell: bash
-    - name: Upload coverage
-      uses: codecov/codecov-action@v1
-      with:
-        file: ./coverage.xml
-
   packaging:
     runs-on: ubuntu-latest
+    env:
+      QUICKTEST: True
+      shell: bash
     steps:
     - uses: actions/checkout@v2
       with:
@@ -343,51 +232,57 @@ jobs:
         # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
         # fresh torch installation according to pyproject.toml
         python -m pip install torch>=1.5 torchvision
-    - name: Test source archive and wheel file
+    - name: Check packages
       run: |
         pip uninstall monai
         pip list | grep -iv monai
         git fetch --depth=1 origin +refs/tags/*:refs/tags/*
-        root_dir=$PWD
-        echo "$root_dir"
         set -e
 
         # build tar.gz and wheel
         python setup.py check -m -s
         python setup.py sdist bdist_wheel
         python -m twine check dist/*
-
+    - run: echo "::set-output name=pwd::$PWD"
+      id: root
+    - run: echo "::set-output name=tmp_dir::$(mktemp -d)"
+      id: mktemp
+    - name: Move packages
+      run: |
+        printf ${{ steps.root.outputs.pwd }}
+        printf ${{ steps.mktemp.outputs.tmp_dir }}
         # move packages to a temp dir
-        tmp_dir=$(mktemp -d)
-        cp dist/monai* "$tmp_dir"
+        cp dist/monai* "${{ steps.mktemp.outputs.tmp_dir }}"
         rm -r build dist monai.egg-info
-        cd "$tmp_dir"
+        cd "${{ steps.mktemp.outputs.tmp_dir }}"
         ls -al
-
+    - name: Install wheel file
+      working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
+      run: |
         # install from wheel
         python -m pip install monai*.whl
         python -c 'import monai; monai.config.print_config()' 2>&1 | grep -iv "unknown"
         python -c 'import monai; print(monai.__file__)'
         python -m pip uninstall -y monai
         rm monai*.whl
-
+    - name: Install source archive
+      working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
+      run: |
         # install from tar.gz
         name=$(ls *.tar.gz | head -n1)
         echo $name
         python -m pip install $name[all]
         python -c 'import monai; monai.config.print_config()' 2>&1 | grep -iv "unknown"
         python -c 'import monai; print(monai.__file__)'
-
+    - name: Quick test
+      working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
+      run: |
         # run min tests
-        cp $root_dir/requirements*.txt "$tmp_dir"
-        cp -r $root_dir/tests "$tmp_dir"
-        pwd
+        cp ${{ steps.root.outputs.pwd }}/requirements*.txt .
+        cp -r ${{ steps.root.outputs.pwd }}/tests .
         ls -al
         python -m pip install -r requirements-dev.txt
         python -m unittest -v
-      env:
-        QUICKTEST: True
-        shell: bash
 
   build-docs:
     runs-on: ubuntu-latest

.github/workflows/setupapp.yml

@@ -4,7 +4,6 @@ on:
   # full tests for all the important branches
   push:
     branches:
-      - dev
       - main
       - releasing/*
       - feature/*