Merge remote-tracking branch 'upstream/dev' into dev

Author: YanxuanLiu

.github/dco.yml

@@ -0,0 +1,2 @@
+allowRemediationCommits:
+  individual: true

.github/pull_request_template.md

@@ -1,10 +1,8 @@
 Fixes # .
 
 ### Description
-A few sentences describing the changes proposed in this pull request.
 
-### Status
-**Ready/Work in progress/Hold**
+A few sentences describing the changes proposed in this pull request.
 
 ### Types of changes
 <!--- Put an `x` in all the boxes that apply, and remove the not applicable items -->

.github/workflows/blossom-ci.yml

@@ -59,7 +59,7 @@ jobs:
       #- name: Setup java
       #  uses: actions/setup-java@v1
       #  with:
-      #    java-version: 1.8
+      #    java-version: '1.8'
 
       # add blackduck properties https://synopsys.atlassian.net/wiki/spaces/INTDOCS/pages/631308372/Methods+for+Configuring+Analysis#Using-a-configuration-file
       #- name: Setup blackduck properties

.github/workflows/chatops.yml

@@ -1,3 +1,4 @@
+# triggering the workflows by commenting `/black` and `/integration-test`
 name: chatops
 
 # currently dispatches /black command to project-monai/monai-code-formatter

.github/workflows/conda.yml

@@ -1,4 +1,5 @@
-name: conda
+# daily tests for different OS with conda
+name: cron-conda
 
 on:
   schedule:
@@ -18,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [windows-latest, macOS-latest, ubuntu-latest]
-        python-version: ["3.7"]
+        python-version: ["3.8"]
     runs-on: ${{ matrix.os }}
     env:
       QUICKTEST: True

.github/workflows/cron-mmar.yml

@@ -1,3 +1,4 @@
+# daily tests for clara mmar models
 name: cron-mmar
 
 on:
@@ -18,12 +19,12 @@ jobs:
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python 3.8
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.8'
     - name: cache weekly timestamp
       id: pip-cache
-      run: echo "::set-output name=datew::$(date '+%Y-%V')"
+      run: echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
     - name: cache for pip
       uses: actions/cache@v3
       id: cache

.github/workflows/cron.yml

@@ -1,4 +1,5 @@
-name: crons
+# nightly: Jenkinsfile.monai-pytorch-versions, monai-latest-image, monai-pip, monai-latest-docker, monai-notebooks
+name: nightly-crons
 
 on:
   # schedule:
@@ -9,31 +10,86 @@ on:
 jobs:
   cron-gpu:
     if: github.repository == 'Project-MONAI/MONAI'
+    strategy:
+      matrix:
+        environment:
+          - "PT182+CUDA102"
+          - "PT191+CUDA113"
+          - "PT110+CUDA113"
+          - "PT112+CUDA113"
+          - "PTLATEST+CUDA117"
+        include:
+          # https://docs.nvidia.com/deeplearning/frameworks/pytorch-release-notes
+          - environment: PT182+CUDA102
+            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: PT191+CUDA113
+            pytorch: "torch==1.9.1 torchvision==0.10.1 --extra-index-url https://download.pytorch.org/whl/cu113"
+            base: "nvcr.io/nvidia/pytorch:21.06-py3"  # CUDA 11.3
+          - environment: PT110+CUDA113
+            pytorch: "torch==1.10.2 torchvision==0.11.3 --extra-index-url https://download.pytorch.org/whl/cu113"
+            base: "nvcr.io/nvidia/pytorch:21.06-py3"  # CUDA 11.3
+          - environment: PT112+CUDA113
+            pytorch: "torch==1.12.1 torchvision==0.13.1 --extra-index-url https://download.pytorch.org/whl/cu113"
+            base: "nvcr.io/nvidia/pytorch:21.06-py3"  # CUDA 11.3
+          - environment: PTLATEST+CUDA117
+            pytorch: "-U torch torchvision --extra-index-url https://download.pytorch.org/whl/cu117"
+            base: "nvcr.io/nvidia/pytorch:22.08-py3"  # CUDA 11.7
     container:
-      image: nvcr.io/nvidia/pytorch:21.06-py3  # CUDA 11.3
+      image: ${{ matrix.base }}
       options: "--gpus all"
     runs-on: [self-hosted, linux, x64, common]
-    strategy:
-      matrix:
-        pytorch-version: [1.7.1, 1.8.1, 1.9.1, 1.10.2, latest]
     steps:
     - uses: actions/checkout@v3
+    - name: apt install
+      run: |
+        # FIXME: 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 [ ${{ matrix.environment }} = "PT182+CUDA102" ]
+        then
+        PYVER=3.7 PYSFX=3 DISTUTILS=python3-distutils && \
+        apt-get update && apt-get install -y --no-install-recommends \
+          curl \
+          pkg-config \
+          python$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 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 --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 --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 --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 --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 ${{ matrix.pytorch }}
         python -m pip install -r requirements-dev.txt
         python -m pip list
     - name: Run tests report coverage
@@ -42,31 +98,32 @@ jobs:
         echo "Sleep $LAUNCH_DELAY"
         sleep $LAUNCH_DELAY
         nvidia-smi
-        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils | tail -n 1)
         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")))'
         BUILD_MONAI=1 ./runtests.sh --build --coverage --unittests --disttests  # unit tests with coverage report
         BUILD_MONAI=1 ./runtests.sh --build --coverage --net  # integration tests with coverage report
-        coverage xml
+        coverage xml --ignore-errors
         if pgrep python; then pkill python; fi
+      shell: bash
     - name: Upload coverage
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
         fail_ci_if_error: false
-        file: ./coverage.xml
+        files: ./coverage.xml
 
   cron-pt-image:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:21.02", "pytorch:21.10", "pytorch:22.07"]  # 21.02, 21.10 for backward comp.
+        container: ["pytorch:21.02", "pytorch:21.10", "pytorch:22.10"]  # 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]
+    runs-on: [self-hosted, linux, x64, integration]
     steps:
     - uses: actions/checkout@v3
     - name: Install APT dependencies
@@ -85,32 +142,33 @@ jobs:
         echo "Sleep $LAUNCH_DELAY"
         sleep $LAUNCH_DELAY
         nvidia-smi
-        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils | tail -n 1)
         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")))'
         BUILD_MONAI=1 ./runtests.sh --build --coverage --unittests --disttests  # unit tests with coverage report
         BUILD_MONAI=1 ./runtests.sh --build --coverage --net  # integration tests with coverage report
-        coverage xml
+        coverage xml --ignore-errors
         if pgrep python; then pkill python; fi
+      shell: bash
     - name: Upload coverage
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
         fail_ci_if_error: false
-        file: ./coverage.xml
+        files: ./coverage.xml
 
   cron-pip:
     # pip install monai[all] and use it to run unit tests
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:21.02", "pytorch:21.10", "pytorch:22.07"]  # 21.02, 21.10 for backward comp.
+        container: ["pytorch:21.02", "pytorch:21.10", "pytorch:22.10"]  # 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]
+    runs-on: [self-hosted, linux, x64, integration]
     steps:
       - uses: actions/checkout@v3
         with:
@@ -121,6 +179,7 @@ jobs:
           python -m pip install --upgrade pip wheel twine
           python -m pip list
       - name: Run tests report coverage
+        shell: bash
         run: |
           pip uninstall monai
           pip list | grep -iv monai
@@ -160,7 +219,7 @@ jobs:
           echo "Sleep $LAUNCH_DELAY"
           sleep $LAUNCH_DELAY
           nvidia-smi
-          export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+          export CUDA_VISIBLE_DEVICES=$(python -m tests.utils | tail -n 1)
           echo $CUDA_VISIBLE_DEVICES
           trap 'if pgrep python; then pkill python; fi;' ERR
           python -c $'import torch\na,b=torch.zeros(1,device="cuda:0"),torch.zeros(1,device="cuda:1");\nwhile True:print(a,b)' > /dev/null &
@@ -175,15 +234,15 @@ jobs:
     container:
       image: docker://projectmonai/monai:latest  # this might be slow and has the pull count limitations
       options: "--gpus all"
-    runs-on: [self-hosted, linux, x64, common]
+    runs-on: [self-hosted, linux, x64, integration]
     steps:
     - name: Run tests report coverage
       # The docker image process has done the compilation.
       # BUILD_MONAI=1 is necessary for triggering the USE_COMPILED flag.
       run: |
         cd /opt/monai
         nvidia-smi
-        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils | tail -n 1)
         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 &
@@ -192,21 +251,22 @@ jobs:
         ngc --version
         BUILD_MONAI=1 ./runtests.sh --build --coverage --pytype --unittests --disttests  # unit tests with pytype checks, coverage report
         BUILD_MONAI=1 ./runtests.sh --build --coverage --net  # integration tests with coverage report
-        coverage xml
+        coverage xml --ignore-errors
         if pgrep python; then pkill python; fi
+      shell: bash
     - name: Upload coverage
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
         fail_ci_if_error: false
-        file: ./coverage.xml
+        files: ./coverage.xml
 
   cron-tutorial-notebooks:
     if: github.repository == 'Project-MONAI/MONAI'
     needs: cron-gpu  # so that monai itself is verified first
     container:
-      image: nvcr.io/nvidia/pytorch:22.07-py3  # testing with the latest pytorch base image
+      image: nvcr.io/nvidia/pytorch:22.10-py3  # testing with the latest pytorch base image
       options: "--gpus all --ipc=host"
-    runs-on: [self-hosted, linux, x64, common]
+    runs-on: [self-hosted, linux, x64, integration]
     steps:
     - uses: actions/checkout@v3
     - name: Install MONAI
@@ -217,9 +277,9 @@ jobs:
         python -m pip install -r requirements-dev.txt
         BUILD_MONAI=1 python setup.py develop  # install monai
         nvidia-smi
-        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils | tail -n 1)
         echo $CUDA_VISIBLE_DEVICES
-        echo "::set-output name=devices::$CUDA_VISIBLE_DEVICES"
+        echo "devices=$CUDA_VISIBLE_DEVICES" >> $GITHUB_OUTPUT
     - name: Checkout tutorials and install their requirements
       run: |
         cd /opt
@@ -238,3 +298,4 @@ jobs:
         $(pwd)/runner.sh
         python -c 'import monai; monai.config.print_debug_info()'
         if pgrep python; then pkill python; fi
+      shell: bash

.github/workflows/docker.yml

@@ -1,3 +1,4 @@
+# this is the docker image releasing pipeline, pushing to https://hub.docker.com/r/projectmonai/monai
 name: docker
 # versioning: compute a static version file
 # local_docker: use the version file to build docker images
@@ -25,9 +26,9 @@ jobs:
           ref: dev
           fetch-depth: 0
       - name: Set up Python 3.8
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: '3.8'
       - shell: bash
         run: |
           git describe
@@ -91,7 +92,7 @@ jobs:
     steps:
     - name: Import
       run: |
-        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils | tail -n 1)
         echo $CUDA_VISIBLE_DEVICES
         python -c 'import monai; monai.config.print_debug_info()'
         cd /opt/monai