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/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, latest]
     steps:
     - uses: actions/checkout@v2
     - name: Install the dependencies
@@ -23,15 +25,12 @@ 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 [ ${{ matrix.pytorch-version }} == "1.7.1" ]; then
+          python -m pip install torch==1.7.1 torchvision==0.8.2
         fi
         python -m pip install -r requirements-dev.txt
         python -m pip list
@@ -43,10 +42,14 @@ jobs:
         nvidia-smi
         export CUDA_VISIBLE_DEVICES=$(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 +58,20 @@ 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/${{ matrix.container }}-py3  # testing with the latest pytorch base image
       options: "--gpus all"
     runs-on: [self-hosted, linux, x64, common]
     steps:
     - uses: actions/checkout@v2
-    - name: Install the dependencies
+    - name: Install APT dependencies
+      run: |
+        apt-get update
+        DEBIAN_FRONTEND="noninteractive" apt-get install -y libopenslide0
+    - name: Install Python dependencies
       run: |
         which python
         python -m pip install --upgrade pip wheel
@@ -75,16 +85,87 @@ jobs:
         nvidia-smi
         export CUDA_VISIBLE_DEVICES=$(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/${{ matrix.container }}-py3  # testing with the latest pytorch base image
+      options: "--gpus all"
+    runs-on: [self-hosted, linux, x64, common]
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - name: Install the dependencies
+        run: |
+          which python
+          python -m pip install --upgrade pip wheel twine
+          python -m pip uninstall -y torch torchvision
+          python -m pip list
+      - name: Run tests report coverage
+        run: |
+          pip uninstall monai
+          pip list | grep -iv monai
+          git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+          root_dir=$PWD
+          echo "$root_dir"
+          set -e
+
+          # build tar.gz and wheel
+          python setup.py check -m -s
+          python setup.py sdist bdist_wheel
+          python -m twine check dist/*
+
+          # move packages to a temp dir
+          tmp_dir=$(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 $name[all]
+          python -c 'import monai; monai.config.print_config()' 2>&1 | grep -iv "unknown"
+          python -c 'import monai; print(monai.__file__)'
+
+          # run tests
+          export LAUNCH_DELAY=$[ $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()))"
+
+          cp $root_dir/requirements*.txt "$tmp_dir"
+          cp -r $root_dir/tests "$tmp_dir"
+          pwd
+          ls -al
+          python -m pip install -r requirements-dev.txt
+          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 +181,54 @@ 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

.github/workflows/docker.yml

@@ -0,0 +1,124 @@
+name: docker
+# versioning: compute a static version file
+# local_docker: use the version file to build docker images
+# docker_test_latest: test the latest internal docker image (has flake)
+# docker_test_dockerhub: test the latest dockerhub release (no flake)
+on:
+  # dev only docker deployment and quick tests
+  push:
+    branches:
+      - dev
+  # Allows you to run this workflow manually from the Actions tab
+  # This is to trigger building/testing docker image from dev only.
+  workflow_dispatch:
+
+jobs:
+  versioning:
+    # compute versioning file from python setup.py
+    # upload as artifact
+    # (also used in release.yml)
+    if: github.repository == 'Project-MONAI/MONAI'
+    container:
+      image: localhost:5000/local_monai:latest
+    runs-on: [self-hosted, linux, x64, build_only]
+    steps:
+      - uses: actions/checkout@v2
+        # full history so that we can git describe
+        with:
+          ref: dev
+          fetch-depth: 0
+      - shell: bash
+        run: |
+          git describe
+          python setup.py build
+          cat build/lib/monai/_version.py
+      - name: Upload version
+        uses: actions/upload-artifact@v2
+        with:
+          name: _version.py
+          path: build/lib/monai/_version.py
+      - name: Clean up directory
+        shell: bash
+        run: |
+          ls -al
+          rm -rf {*,.[^.]*}
+
+  local_docker:
+    # builds two versions: local_monai:latest and local_monai:dockerhub
+    # latest: used for local tests
+    # dockerhub: release, no flake package
+    if: github.repository == 'Project-MONAI/MONAI'
+    needs: versioning
+    runs-on: [self-hosted, linux, x64, build_only]
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        ref: dev
+    - name: Download version
+      uses: actions/download-artifact@v2
+      with:
+        name: _version.py
+    - name: docker_build
+      shell: bash
+      run: |
+        # get tag info for versioning
+        cat _version.py
+        mv _version.py monai/
+        # build and run original docker image for local registry
+        docker build -t localhost:5000/local_monai:latest -f Dockerfile .
+        docker push localhost:5000/local_monai:latest
+        # build once more w/ tag "latest": remove flake package as it is not needed on hub.docker.com
+        sed -i '/flake/d' requirements-dev.txt
+        docker build -t projectmonai/monai:latest -f Dockerfile .
+        # also push as tag "dockerhub" to local registry
+        docker image tag projectmonai/monai:latest localhost:5000/local_monai:dockerhub
+        docker push localhost:5000/local_monai:dockerhub
+        # distribute as always w/ tag "latest" to hub.docker.com
+        echo "${{ secrets.DOCKER_PW }}" | docker login -u projectmonai --password-stdin
+        docker push projectmonai/monai:latest
+        docker logout
+        docker image prune -f
+
+  docker_test_latest:
+    if: github.repository == 'Project-MONAI/MONAI'
+    needs: local_docker
+    container:
+      image: localhost:5000/local_monai:latest
+    runs-on: [self-hosted, linux, x64, common]
+    steps:
+    - name: Import
+      run: |
+        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+        echo $CUDA_VISIBLE_DEVICES
+        trap 'if pgrep python; then pkill python; fi;' ERR
+        python -c $'import torch\na,b=torch.zeros(1,device="cuda:0"),torch.zeros(1,device="cuda:1");\nwhile True:print(a,b)' > /dev/null &
+        python -c 'import monai; monai.config.print_config()'
+        cd /opt/monai
+        ls -al
+        ngc --version
+        python -m tests.min_tests
+        if pgrep python; then pkill python; fi
+      env:
+        QUICKTEST: True
+
+  docker_test_dockerhub:
+    if: github.repository == 'Project-MONAI/MONAI'
+    needs: local_docker
+    container:
+      image: localhost:5000/local_monai:dockerhub
+    runs-on: [self-hosted, linux, x64, common]
+    steps:
+    - name: Import
+      run: |
+        export CUDA_VISIBLE_DEVICES=$(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 monai; monai.config.print_config()'
+        cd /opt/monai
+        ls -al
+        ngc --version
+        python -m tests.min_tests
+        if pgrep python; then pkill python; fi
+      env:
+        QUICKTEST: True