Merge pull request #214 from Project-MONAI/dev

merge master

.deepsource.toml

@@ -24,4 +24,4 @@ enabled = true
 
 [[analyzers]]
 name = "shell"
-enabled = true
+enabled = true

.dockerignore

@@ -11,4 +11,3 @@ coverage.xml
 *.toml
 
 !README.md
-

.github/ISSUE_TEMPLATE/question.md

@@ -9,4 +9,4 @@ assignees: ''
 **Please use MONAI's Discussions tab**
 For questions relating to MONAI usage, please do not create an issue.
 
-Instead, use [MONAI's GitHub Discussions tab](https://github.com/Project-MONAI/MONAI/discussions). This can be found next to Issues and Pull Requests along the top of our repository.
+Instead, use [MONAI's GitHub Discussions tab](https://github.com/Project-MONAI/MONAI/discussions). This can be found next to Issues and Pull Requests along the top of our repository.

.github/workflows/cron.yml

@@ -1,8 +1,8 @@
 name: crons
 
 on:
- schedule:
- - cron: "0 2 * * *" # at 02:00 UTC
+ # schedule:
+ #  - cron: "0 2 * * *" # at 02:00 UTC
  # Allows you to run this workflow manually from the Actions tab
  workflow_dispatch:
 
@@ -62,7 +62,7 @@ jobs:
  if: github.repository == 'Project-MONAI/MONAI'
  strategy:
  matrix:
- container: ["pytorch:21.02", "pytorch:21.06"] # 21.02 for backward comp.
+ container: ["pytorch:21.02", "pytorch:21.08"] # 21.02 for backward comp.
  container:
  image: nvcr.io/nvidia/${{ matrix.container }}-py3 # testing with the latest pytorch base image
  options: "--gpus all"
@@ -106,7 +106,7 @@ jobs:
  if: github.repository == 'Project-MONAI/MONAI'
  strategy:
  matrix:
- container: ["pytorch:21.02", "pytorch:21.06"] # 21.02 for backward comp.
+ container: ["pytorch:21.02", "pytorch:21.08"] # 21.02 for backward comp.
  container:
  image: nvcr.io/nvidia/${{ 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:21.06-py3 # testing with the latest pytorch base image
+ image: nvcr.io/nvidia/pytorch:21.08-py3 # testing with the latest pytorch base image
  options: "--gpus all --ipc=host"
  runs-on: [self-hosted, linux, x64, common]
  steps:

.github/workflows/pythonapp-gpu.yml

@@ -0,0 +1,134 @@
+name: build-gpu
+
+on:
+ # quick tests for pull requests and the releasing branches
+ push:
+ branches:
+ - main
+ - releasing/*
+ pull_request:
+
+concurrency:
+ # automatically cancel the previously triggered workflows when there's a newer version
+ group: build-gpu-${{ github.event.pull_request.number || github.ref }}
+ cancel-in-progress: true
+
+jobs:
+ GPU-quick-py3: # GPU with full dependencies
+ if: github.repository == 'Project-MONAI/MONAI'
+ strategy:
+ matrix:
+ environment:
+ - "PT16+CUDA110"
+ - "PT17+CUDA102"
+ - "PT17+CUDA110"
+ - "PT18+CUDA102"
+ - "PT19+CUDA114"
+ - "PT19+CUDA102"
+ include:
+ - environment: PT16+CUDA110
+ # we explicitly set pytorch to -h to avoid pip install error
+ pytorch: "-h"
+ base: "nvcr.io/nvidia/pytorch:20.07-py3"
+ - environment: PT17+CUDA102
+ pytorch: "torch==1.7.1 torchvision==0.8.2"
+ base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
+ - environment: PT17+CUDA110
+ # we explicitly set pytorch to -h to avoid pip install error
+ pytorch: "-h"
+ base: "nvcr.io/nvidia/pytorch:20.09-py3"
+ - environment: PT18+CUDA102
+ pytorch: "torch==1.8.1 torchvision==0.9.1"
+ base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
+ - 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
+ pytorch: "-h"
+ base: "nvcr.io/nvidia/pytorch:21.08-py3"
+ - environment: PT19+CUDA102
+ pytorch: "torch==1.9.0 torchvision==0.10.0"
+ base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
+ container:
+ image: ${{ matrix.base }}
+ options: --gpus all
+ runs-on: [self-hosted, linux, x64, common]
+ steps:
+ - uses: actions/checkout@v2
+ - name: apt install
+ run: |
+ if [ ${{ matrix.environment }} = "PT17+CUDA102" ] || \
+ [ ${{ matrix.environment }} = "PT18+CUDA102" ] || \
+ [ ${{ matrix.environment }} = "PT19+CUDA102" ]
+ then
+ PYVER=3.6 PYSFX=3 DISTUTILS=python3-distutils && \
+ apt-get update && apt-get install -y --no-install-recommends \
+ curl \
+ pkg-config \
+ python$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
+ - if: matrix.environment == 'PT19+CUDA114'
+ name: Optional Cupy dependency (cuda114)
+ run: echo "cupy-cuda114" >> requirements-dev.txt
+ - name: Install dependencies
+ run: |
+ which python
+ python -m pip install --upgrade pip wheel
+ python -m pip install ${{ matrix.pytorch }}
+ python -m pip install -r requirements-dev.txt
+ python -m pip list
+ - name: Run quick tests (GPU)
+ run: |
+ git clone --depth 1 \
+ https://github.com/Project-MONAI/MONAI-extra-test-data.git /MONAI-extra-test-data
+ export MONAI_EXTRA_TEST_DATA="/MONAI-extra-test-data"
+ nvidia-smi
+ export LAUNCH_DELAY=$(python -c "import numpy; print(numpy.random.randint(30) * 10)")
+ echo "Sleep $LAUNCH_DELAY"
+ sleep $LAUNCH_DELAY
+ export CUDA_VISIBLE_DEVICES=$(coverage run -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")))'
+ python -c "import monai; monai.config.print_config()"
+ # build for the current self-hosted CI Tesla V100
+ BUILD_MONAI=1 TORCH_CUDA_ARCH_LIST="7.0" ./runtests.sh --quick --unittests
+ if [ ${{ matrix.environment }} = "PT19+CUDA102" ]; then
+ # test the clang-format tool downloading once
+ coverage run -m tests.clang_format_utils
+ fi
+ coverage xml
+ if pgrep python; then pkill python; fi
+ shell: bash
+ - name: Upload coverage
+ uses: codecov/codecov-action@v1
+ with:
+ file: ./coverage.xml

.github/workflows/pythonapp.yml

@@ -200,122 +200,11 @@ jobs:
  env:
  QUICKTEST: True
 
- GPU-quick-py3: # GPU with full dependencies
- if: github.repository == 'Project-MONAI/MONAI'
- strategy:
- matrix:
- environment:
- - "PT16+CUDA110"
- - "PT17+CUDA102"
- - "PT17+CUDA110"
- - "PT18+CUDA102"
- - "PT19+CUDA113"
- - "PT19+CUDA102"
- include:
- - environment: PT16+CUDA110
- # we explicitly set pytorch to -h to avoid pip install error
- pytorch: "-h"
- base: "nvcr.io/nvidia/pytorch:20.07-py3"
- - environment: PT17+CUDA102
- pytorch: "torch==1.7.1 torchvision==0.8.2"
- base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
- - environment: PT17+CUDA110
- # we explicitly set pytorch to -h to avoid pip install error
- pytorch: "-h"
- base: "nvcr.io/nvidia/pytorch:20.09-py3"
- - environment: PT18+CUDA102
- pytorch: "torch==1.8.1 torchvision==0.9.1"
- base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
- - environment: PT19+CUDA113
- # we explicitly set pytorch to -h to avoid pip install error
- pytorch: "-h"
- base: "nvcr.io/nvidia/pytorch:21.06-py3"
- - environment: PT19+CUDA102
- pytorch: "torch==1.9.0 torchvision==0.10.0"
- base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
- container:
- image: ${{ matrix.base }}
- options: --gpus all
- runs-on: [self-hosted, linux, x64, common]
- steps:
- - uses: actions/checkout@v2
- - name: apt install
- run: |
- if [ ${{ matrix.environment }} = "PT17+CUDA102" ] || \
- [ ${{ matrix.environment }} = "PT18+CUDA102" ] || \
- [ ${{ matrix.environment }} = "PT19+CUDA102" ]
- then
- PYVER=3.6 PYSFX=3 DISTUTILS=python3-distutils && \
- apt-get update && apt-get install -y --no-install-recommends \
- curl \
- pkg-config \
- python$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 dependencies
- run: |
- which python
- python -m pip install --upgrade pip wheel
- python -m pip install ${{ matrix.pytorch }}
- python -m pip install -r requirements-dev.txt
- python -m pip list
- - name: Run quick tests (GPU)
- run: |
- git clone --depth 1 \
- https://github.com/Project-MONAI/MONAI-extra-test-data.git /MONAI-extra-test-data
- export MONAI_EXTRA_TEST_DATA="/MONAI-extra-test-data"
- nvidia-smi
- export LAUNCH_DELAY=$(python -c "import numpy; print(numpy.random.randint(30) * 10)")
- echo "Sleep $LAUNCH_DELAY"
- sleep $LAUNCH_DELAY
- export CUDA_VISIBLE_DEVICES=$(coverage run -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")))'
- python -c "import monai; monai.config.print_config()"
- # build for the current self-hosted CI Tesla V100
- BUILD_MONAI=1 TORCH_CUDA_ARCH_LIST="7.0" ./runtests.sh --quick --unittests
- if [ ${{ matrix.environment }} = "PT19+CUDA102" ]; then
- # test the clang-format tool downloading once
- coverage run -m tests.clang_format_utils
- fi
- coverage xml
- if pgrep python; then pkill python; fi
- shell: bash
- - name: Upload coverage
- uses: codecov/codecov-action@v1
- with:
- file: ./coverage.xml
-
  packaging:
  runs-on: ubuntu-latest
+ env:
+ QUICKTEST: True
+ shell: bash
  steps:
  - uses: actions/checkout@v2
  with:
@@ -343,51 +232,57 @@ jobs:
  # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
  # fresh torch installation according to pyproject.toml
  python -m pip install torch>=1.5 torchvision
- - name: Test source archive and wheel file
+ - name: Check packages
  run: |
  pip uninstall monai
  pip list | grep -iv monai
  git fetch --depth=1 origin +refs/tags/*:refs/tags/*
- root_dir=$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/*
-
+ - run: echo "::set-output name=pwd::$PWD"
+ id: root
+ - run: echo "::set-output name=tmp_dir::$(mktemp -d)"
+ id: mktemp
+ - name: Move packages
+ run: |
+ printf ${{ steps.root.outputs.pwd }}
+ printf ${{ steps.mktemp.outputs.tmp_dir }}
  # move packages to a temp dir
- tmp_dir=$(mktemp -d)
- cp dist/monai* "$tmp_dir"
+ cp dist/monai* "${{ steps.mktemp.outputs.tmp_dir }}"
  rm -r build dist monai.egg-info
- cd "$tmp_dir"
+ cd "${{ steps.mktemp.outputs.tmp_dir }}"
  ls -al
-
+ - name: Install wheel file
+ working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
+ run: |
  # install from wheel
  python -m pip install monai*.whl
  python -c 'import monai; monai.config.print_config()' 2>&1 | grep -iv "unknown"
  python -c 'import monai; print(monai.__file__)'
  python -m pip uninstall -y monai
  rm monai*.whl
-
+ - name: Install source archive
+ working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
+ run: |
  # install from tar.gz
  name=$(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__)'
-
+ - name: Quick test
+ working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
+ run: |
  # run min tests
- cp $root_dir/requirements*.txt "$tmp_dir"
- cp -r $root_dir/tests "$tmp_dir"
- pwd
+ cp ${{ steps.root.outputs.pwd }}/requirements*.txt .
+ cp -r ${{ steps.root.outputs.pwd }}/tests .
  ls -al
  python -m pip install -r requirements-dev.txt
  python -m unittest -v
- env:
- QUICKTEST: True
- shell: bash
 
  build-docs:
  runs-on: ubuntu-latest

.github/workflows/setupapp.yml

@@ -4,7 +4,6 @@ on:
  # full tests for all the important branches
  push:
  branches:
- - dev
  - main
  - releasing/*
  - feature/*