merge master

.github/workflows/cron-mmar.yml

@@ -0,0 +1,42 @@
+name: cron-mmar
+
+on:
+  schedule:
+    - cron: "0 2 * * *"  # at 02:00 UTC
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+concurrency:
+  # automatically cancel the previously triggered workflows when there's a newer version
+  group: mmar-tests-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  cron-load:
+    if: github.repository == 'Project-MONAI/MONAI'
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: cache weekly timestamp
+      id: pip-cache
+      run: echo "::set-output name=datew::$(date '+%Y-%V')"
+    - name: cache for pip
+      uses: actions/cache@v2
+      id: cache
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip wheel
+        python -m pip install -r requirements-dev.txt
+    - name: Loading MMARs
+      run: |
+        # clean up temporary files
+        $(pwd)/runtests.sh --clean
+        # run tests
+        python -m tests.ngc_mmar_loading

.github/workflows/cron.yml

@@ -62,7 +62,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:21.02", "pytorch:21.08"]  # 21.02 for backward comp.
+        container: ["pytorch:21.02", "pytorch:21.09"]  # 21.02 for backward comp.
     container:
       image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
@@ -106,7 +106,7 @@ jobs:
     if: github.repository == 'Project-MONAI/MONAI'
     strategy:
       matrix:
-        container: ["pytorch:21.02", "pytorch:21.08"]  # 21.02 for backward comp.
+        container: ["pytorch:21.02", "pytorch:21.09"]  # 21.02 for backward comp.
     container:
       image: nvcr.io/nvidia/${{ 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:21.08-py3  # testing with the latest pytorch base image
+      image: nvcr.io/nvidia/pytorch:21.09-py3  # testing with the latest pytorch base image
       options: "--gpus all --ipc=host"
     runs-on: [self-hosted, linux, x64, common]
     steps:
@@ -215,7 +215,7 @@ jobs:
         which python
         python -m pip install --upgrade pip wheel
         python -m pip install -r requirements-dev.txt
-        BUILD_MONAI=0 python setup.py develop  # install monai
+        BUILD_MONAI=1 python setup.py develop  # install monai
         nvidia-smi
         export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
         echo $CUDA_VISIBLE_DEVICES
@@ -234,5 +234,7 @@ jobs:
         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 &
         cd /opt/tutorials
+        python -c 'import monai; monai.config.print_debug_info()'
         $(pwd)/runner.sh
+        python -c 'import monai; monai.config.print_debug_info()'
         if pgrep python; then pkill python; fi

.github/workflows/integration.yml

@@ -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==1.9.0+cu111 torchvision==0.10.0+cu111 -f https://download.pytorch.org/whl/torch_stable.html
+        python -m pip install torch==1.9.1+cu111 torchvision==0.10.1+cu111 -f https://download.pytorch.org/whl/torch_stable.html
         python -m pip install -r requirements-dev.txt
     - name: Run integration tests
       run: |

.github/workflows/pythonapp-gpu.yml

@@ -43,11 +43,11 @@ jobs:
           - 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
+            # 21.09: 1.10.0a0+3fd9dcf
             pytorch: "-h"
-            base: "nvcr.io/nvidia/pytorch:21.08-py3"
+            base: "nvcr.io/nvidia/pytorch:21.09-py3"
           - environment: PT19+CUDA102
-            pytorch: "torch==1.9.0 torchvision==0.10.0"
+            pytorch: "torch==1.9.1 torchvision==0.10.1"
             base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
     container:
       image: ${{ matrix.base }}
@@ -100,6 +100,8 @@ jobs:
       run: |
         which python
         python -m pip install --upgrade pip wheel
+        # fixes preinstalled ruamel_yaml error from the docker image
+        rm -rf $(python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())")/ruamel*
         python -m pip install ${{ matrix.pytorch }}
         python -m pip install -r requirements-dev.txt
         python -m pip list

.github/workflows/pythonapp-min.yml

@@ -0,0 +1,170 @@
+name: build-min
+
+on:
+  # quick tests for pull requests and the releasing branches
+  push:
+    branches:
+      - dev
+      - main
+      - releasing/*
+  pull_request:
+
+concurrency:
+  # automatically cancel the previously triggered workflows when there's a newer version
+  group: build-min-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  # caching of these jobs:
+  #   - docker-py3-pip- (shared)
+  #   - ubuntu py37 pip-
+  #   - os-latest-pip- (shared)
+  min-dep-os:  # min dependencies installed tests for different OS
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [windows-latest, macOS-latest, ubuntu-latest]
+    timeout-minutes: 40
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Prepare pip wheel
+      run: |
+        which python
+        python -m pip install --upgrade pip wheel
+    - name: cache weekly timestamp
+      id: pip-cache
+      run: |
+        echo "::set-output name=datew::$(date '+%Y-%V')"
+        echo "::set-output name=dir::$(pip cache dir)"
+      shell: bash
+    - name: cache for pip
+      uses: actions/cache@v2
+      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==1.9.1+cpu -f https://download.pytorch.org/whl/torch_stable.html
+    - name: Install the dependencies
+      run: |
+        # min. requirements
+        python -m pip install torch==1.9.1
+        python -m pip install -r requirements-min.txt
+        python -m pip list
+        BUILD_MONAI=0 python setup.py develop  # no compile of extensions
+      shell: bash
+    - name: Run quick tests (CPU ${{ runner.os }})
+      run: |
+        python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
+        python -c "import monai; monai.config.print_config()"
+        ./runtests.sh --min
+      shell: bash
+      env:
+        QUICKTEST: True
+
+  min-dep-py3:  # min dependencies installed tests for different python
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.6, 3.7, 3.8, 3.9]
+    timeout-minutes: 40
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Prepare pip wheel
+      run: |
+        which python
+        python -m pip install --user --upgrade pip setuptools wheel
+    - name: cache weekly timestamp
+      id: pip-cache
+      run: |
+        echo "::set-output name=datew::$(date '+%Y-%V')"
+        echo "::set-output name=dir::$(pip cache dir)"
+      shell: bash
+    - name: cache for pip
+      uses: actions/cache@v2
+      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==1.9.1
+        python -m pip install -r requirements-min.txt
+        python -m pip list
+        BUILD_MONAI=0 python setup.py develop  # no compile of extensions
+      shell: bash
+    - name: Run quick tests (CPU ${{ runner.os }})
+      run: |
+        python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
+        python -c "import monai; monai.config.print_config()"
+        ./runtests.sh --min
+      env:
+        QUICKTEST: True
+
+  min-dep-pytorch:  # min dependencies installed tests for different pytorch
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        pytorch-version: [1.5.1, 1.6.0, 1.7.1, 1.8.1, latest]
+    timeout-minutes: 40
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Prepare pip wheel
+      run: |
+        which python
+        python -m pip install --user --upgrade pip setuptools wheel
+    - name: cache weekly timestamp
+      id: pip-cache
+      run: |
+        echo "::set-output name=datew::$(date '+%Y-%V')"
+        echo "::set-output name=dir::$(pip cache dir)"
+      shell: bash
+    - name: cache for pip
+      uses: actions/cache@v2
+      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
+        if [ ${{ matrix.pytorch-version }} == "latest" ]; then
+          python -m pip install torch
+        elif [ ${{ matrix.pytorch-version }} == "1.5.1" ]; then
+          python -m pip install torch==1.5.1
+        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
+        fi
+        python -m pip install -r requirements-min.txt
+        python -m pip list
+        BUILD_MONAI=0 python setup.py develop  # no compile of extensions
+      shell: bash
+    - name: Run quick tests (pytorch ${{ matrix.pytorch-version }})
+      run: |
+        python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
+        python -c "import monai; monai.config.print_config()"
+        ./runtests.sh --min
+      env:
+        QUICKTEST: True