merge master

.dockerignore

@@ -4,8 +4,10 @@ __pycache__/
 docs/
 
 .coverage
+.coverage.*
+.coverage/
+coverage.xml
 .readthedocs.yml
-*.md
 *.toml
 
 !README.md

.github/pull_request_template.md

@@ -11,7 +11,7 @@ A few sentences describing the changes proposed in this pull request.
 - [x] Non-breaking change (fix or new feature that would not break existing functionality).
 - [ ] Breaking change (fix or new feature that would cause existing functionality to change).
 - [ ] New tests added to cover the changes.
-- [ ] Integration tests passed locally by running `./runtests.sh --codeformat --coverage`.
-- [ ] Quick tests passed locally by running `./runtests.sh --quick`.
+- [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`.
+- [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests`.
 - [ ] In-line docstrings updated.
 - [ ] Documentation updated, tested `make html` command in the `docs/` folder.

.github/workflows/blossom-ci.yml

@@ -0,0 +1,105 @@
+# A workflow to trigger ci on hybrid infra (github + self hosted runner)
+name: Blossom-CI
+on:
+  issue_comment:
+    types: [created]
+  workflow_dispatch:
+      inputs:
+          platform:
+            description: 'runs-on argument'
+            required: false
+          args:
+            description: 'argument'
+            required: false
+
+concurrency:
+  # automatically cancel the previously triggered workflows when there's a newer version
+  group: blossom-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  actions: write
+  checks: write
+  contents: write
+  issues: write
+  pull-requests: write
+  repository-projects: write
+  statuses: write
+
+jobs:
+  Authorization:
+    name: Authorization
+    runs-on: blossom
+    outputs:
+      args: ${{ env.args }}
+
+    # This job only runs for pull request comments
+    if: |
+         contains( 'madil90,Nic-Ma,wyli', format('{0},', github.actor)) &&
+         github.event.comment.body == '/build'
+    steps:
+      - name: Check if comment is issued by authorized person
+        run: blossom-ci
+        env:
+          OPERATION: 'AUTH'
+          REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          REPO_KEY_DATA: ${{ secrets.BLOSSOM_KEY }}
+
+  Vulnerability-scan:
+    name: Vulnerability scan
+    needs: [Authorization]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+        with:
+          repository: ${{ fromJson(needs.Authorization.outputs.args).repo }}
+          ref: ${{ fromJson(needs.Authorization.outputs.args).ref }}
+          lfs: 'true'
+
+      # repo specific steps
+      #- name: Setup java
+      #  uses: actions/setup-java@v1
+      #  with:
+      #    java-version: 1.8
+
+      # add blackduck properties https://synopsys.atlassian.net/wiki/spaces/INTDOCS/pages/631308372/Methods+for+Configuring+Analysis#Using-a-configuration-file
+      #- name: Setup blackduck properties
+      #  run: |
+      #       PROJECTS=$(mvn -am dependency:tree | grep maven-dependency-plugin | awk '{ out="com.nvidia:"$(NF-1);print out }' | grep rapids | xargs | sed -e 's/ /,/g')
+      #       echo detect.maven.build.command="-pl=$PROJECTS -am" >> application.properties
+      #       echo detect.maven.included.scopes=compile >> application.properties
+
+      - name: Run blossom action
+        uses: NVIDIA/blossom-action@main
+        env:
+          REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          REPO_KEY_DATA: ${{ secrets.BLOSSOM_KEY }}
+        with:
+          args1: ${{ fromJson(needs.Authorization.outputs.args).args1 }}
+          args2: ${{ fromJson(needs.Authorization.outputs.args).args2 }}
+          args3: ${{ fromJson(needs.Authorization.outputs.args).args3 }}
+
+  Job-trigger:
+    name: Start ci job
+    needs: [Vulnerability-scan]
+    runs-on: blossom
+    steps:
+      - name: Start ci job
+        run: blossom-ci
+        env:
+          OPERATION: 'START-CI-JOB'
+          CI_SERVER: ${{ secrets.CI_SERVER }}
+          REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+  Post-processing:
+    name: Post processing
+    runs-on: blossom
+    if : github.event_name == 'workflow_dispatch'
+    steps:
+      - name: Start post processing
+        run: blossom-ci
+        env:
+          OPERATION: 'POST-PROCESSING'
+          CI_SERVER: ${{ secrets.CI_SERVER }}
+          REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/cron.yml

@@ -3,6 +3,8 @@ name: crons
 on:
   schedule:
     - cron: "0 2 * * *"  # at 02:00 UTC
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
 
 jobs:
   cron-gpu:
@@ -13,7 +15,7 @@ jobs:
     runs-on: [self-hosted, linux, x64, common]
     strategy:
       matrix:
-        pytorch-version: [1.5.0, 1.5.1, 1.6.0, latest]
+        pytorch-version: [1.5.1, 1.6.0, 1.7.1, 1.8.1, latest]
     steps:
     - uses: actions/checkout@v2
     - name: Install the dependencies
@@ -23,15 +25,14 @@ jobs:
         python -m pip uninstall -y torch torchvision
         if [ ${{ matrix.pytorch-version }} == "latest" ]; then
           python -m pip install torch torchvision
-        elif [ ${{ matrix.pytorch-version }} == "1.5.0" ]; then
-          python -m pip install torch==1.5.0
-          python -m pip install torchvision==0.6.0
         elif [ ${{ matrix.pytorch-version }} == "1.5.1" ]; then
-          python -m pip install torch==1.5.1
-          python -m pip install torchvision==0.6.1
+          python -m pip install torch==1.5.1 torchvision==0.6.1
         elif [ ${{ matrix.pytorch-version }} == "1.6.0" ]; then
-          python -m pip install torch==1.6.0
-          python -m pip install torchvision==0.7.0
+          python -m pip install torch==1.6.0 torchvision==0.7.0
+        elif [ ${{ matrix.pytorch-version }} == "1.7.1" ]; then
+          python -m pip install torch==1.7.1 torchvision==0.8.2
+        elif [ ${{ matrix.pytorch-version }} == "1.8.1" ]; then
+          python -m pip install torch==1.8.1 torchvision==0.9.1
         fi
         python -m pip install -r requirements-dev.txt
         python -m pip list
@@ -43,10 +44,14 @@ jobs:
         nvidia-smi
         export CUDA_VISIBLE_DEVICES=$(python -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")))'
-        BUILD_MONAI=1 ./runtests.sh --coverage
+        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
+        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
+        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
         coverage xml
+        if pgrep python; then pkill python; fi
     - name: Upload coverage
       uses: codecov/codecov-action@v1
       with:
@@ -55,13 +60,20 @@ jobs:
 
   cron-pt-image:
     if: github.repository == 'Project-MONAI/MONAI'
+    strategy:
+      matrix:
+        container: ["pytorch:21.02", "pytorch:21.04"]  # 21.02 for backward comp.
     container:
-      image: nvcr.io/nvidia/pytorch:20.12-py3  # testing with the latest pytorch base image
+      image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
     runs-on: [self-hosted, linux, x64, common]
     steps:
     - uses: actions/checkout@v2
-    - name: Install the dependencies
+    - name: Install APT dependencies
+      run: |
+        apt-get update
+        DEBIAN_FRONTEND="noninteractive" apt-get install -y libopenslide0
+    - name: Install Python dependencies
       run: |
         which python
         python -m pip install --upgrade pip wheel
@@ -75,16 +87,89 @@ jobs:
         nvidia-smi
         export CUDA_VISIBLE_DEVICES=$(python -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")))'
-        BUILD_MONAI=1 ./runtests.sh --coverage
+        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
+        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
+        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
         coverage xml
+        if pgrep python; then pkill python; fi
     - name: Upload coverage
       uses: codecov/codecov-action@v1
       with:
         fail_ci_if_error: false
         file: ./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:21.04"]  # 21.02 for backward comp.
+    container:
+      image: nvcr.io/nvidia/${{ matrix.container }}-py3  # testing with the latest pytorch base image
+      options: "--gpus all"
+    runs-on: [self-hosted, linux, x64, common]
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - name: Install the dependencies
+        run: |
+          which python
+          python -m pip install --upgrade pip wheel twine
+          python -m pip list
+      - name: Run tests report coverage
+        run: |
+          pip uninstall monai
+          pip list | grep -iv monai
+          git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+          root_dir=$PWD
+          echo "$root_dir"
+          set -e
+
+          # build tar.gz and wheel
+          bash runtests.sh --clean  # clear any existing dev temp files
+          python -m pip uninstall -y torch torchvision
+          python setup.py check -m -s
+          python setup.py sdist bdist_wheel
+          python -m twine check dist/*
+
+          # move packages to a temp dir
+          tmp_dir=$(mktemp -d)
+          cp dist/monai* "$tmp_dir"
+          rm -r build dist monai.egg-info
+          cd "$tmp_dir"
+          ls -al
+
+          # 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__)'
+
+          # run tests
+          cp $root_dir/requirements*.txt "$tmp_dir"
+          cp -r $root_dir/tests "$tmp_dir"
+          pwd
+          ls -al
+
+          export LAUNCH_DELAY=$[ $RANDOM % 16 * 60 ]
+          echo "Sleep $LAUNCH_DELAY"
+          sleep $LAUNCH_DELAY
+          nvidia-smi
+          export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+          echo $CUDA_VISIBLE_DEVICES
+          trap 'if pgrep python; then pkill python; fi;' ERR
+          python -c $'import torch\na,b=torch.zeros(1,device="cuda:0"),torch.zeros(1,device="cuda:1");\nwhile True:print(a,b)' > /dev/null &
+          python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
+
+          python -m pip install -r requirements-dev.txt
+          PYTHONPATH="$tmp_dir":$PYTHONPATH BUILD_MONAI=1 python ./tests/runner.py -p 'test_((?!integration).)'  # unit tests
+          if pgrep python; then pkill python; fi
+
   cron-docker:
     if: github.repository == 'Project-MONAI/MONAI'
     container:
@@ -100,13 +185,54 @@ jobs:
         nvidia-smi
         export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
         echo $CUDA_VISIBLE_DEVICES
+        trap 'if pgrep python; then pkill python; fi;' ERR
+        python -c $'import torch\na,b=torch.zeros(1,device="cuda:0"),torch.zeros(1,device="cuda:1");\nwhile True:print(a,b)' > /dev/null &
         python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
         python -c 'import torch; print(torch.rand(5,3, device=torch.device("cuda:0")))'
         ngc --version
-        BUILD_MONAI=1 ./runtests.sh --coverage --pytype
+        BUILD_MONAI=1 ./runtests.sh --coverage --pytype --unittests  # unit tests with pytype checks, coverage report
+        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
         coverage xml
+        if pgrep python; then pkill python; fi
     - name: Upload coverage
       uses: codecov/codecov-action@v1
       with:
         fail_ci_if_error: false
         file: ./coverage.xml
+
+  cron-tutorial-notebooks:
+    if: github.repository == 'Project-MONAI/MONAI'
+    needs: cron-gpu  # so that monai itself is verified first
+    container:
+      image: nvcr.io/nvidia/pytorch:21.04-py3  # testing with the latest pytorch base image
+      options: "--gpus all --ipc=host"
+    runs-on: [self-hosted, linux, x64, common]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Install MONAI
+      id: monai-install
+      run: |
+        which python
+        python -m pip install --upgrade pip wheel
+        python -m pip install -r requirements-dev.txt
+        BUILD_MONAI=0 python setup.py develop  # install monai
+        nvidia-smi
+        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+        echo $CUDA_VISIBLE_DEVICES
+        echo "::set-output name=devices::$CUDA_VISIBLE_DEVICES"
+    - 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
+        cd tutorials
+        python -m pip install -r requirements.txt
+    - name: Run tutorial notebooks
+      timeout-minutes: 150
+      run: |
+        export CUDA_VISIBLE_DEVICES=${{ steps.monai-install.outputs.devices }}
+        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 &
+        cd /opt/tutorials
+        $(pwd)/runner.sh
+        if pgrep python; then pkill python; fi