Merge pull request #180 from Project-MONAI/dev

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 +1,103 @@
+# 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
+
+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: Setup blackduck properties
+ run: |
+ echo detect.excluded.detector.types=PIP >> 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:21.06"] # 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:21.06"] # 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 $'import torch\na,b=torch.zeros(1,device="cuda:0"),torch.zeros(1,device="cuda:1");\nwhile True:print(a,b)' > /dev/null &
  python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
  python -c 'import torch; print(torch.rand(5,3, device=torch.device("cuda:0")))'
  ngc --version
- BUILD_MONAI=1 ./runtests.sh --coverage --pytype
+ BUILD_MONAI=1 ./runtests.sh --coverage --pytype --unittests # unit tests with pytype checks, coverage report
+ BUILD_MONAI=1 ./runtests.sh --coverage --net # integration tests with coverage report
  coverage xml
+ if pgrep python; then pkill python; fi
  - name: Upload coverage
  uses: codecov/codecov-action@v1
  with:
  fail_ci_if_error: false
  file: ./coverage.xml
+
+ cron-tutorial-notebooks:
+ if: github.repository == 'Project-MONAI/MONAI'
+ needs: cron-gpu # so that monai itself is verified first
+ container:
+ image: nvcr.io/nvidia/pytorch:21.06-py3 # testing with the latest pytorch base image
+ options: "--gpus all --ipc=host"
+ runs-on: [self-hosted, linux, x64, common]
+ steps:
+ - uses: actions/checkout@v2
+ - name: Install MONAI
+ id: monai-install
+ run: |
+ which python
+ python -m pip install --upgrade pip wheel
+ python -m pip install -r requirements-dev.txt
+ BUILD_MONAI=0 python setup.py develop # install monai
+ nvidia-smi
+ export CUDA_VISIBLE_DEVICES=$(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