merge master

.dockerignore

@@ -4,6 +4,9 @@ __pycache__/
 docs/
 
 .coverage
+.coverage.*
+.coverage/
+coverage.xml
 .readthedocs.yml
 *.md
 *.toml

.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

@@ -13,7 +13,7 @@ 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 +23,12 @@ 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 [ ${{ matrix.pytorch-version }} == "1.7.1" ]; then
+          python -m pip install torch==1.7.1 torchvision==0.8.2
         fi
         python -m pip install -r requirements-dev.txt
         python -m pip list
@@ -43,9 +40,16 @@ jobs:
         nvidia-smi
         export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
         echo $CUDA_VISIBLE_DEVICES
+        stop_time=$((LAUNCH_DELAY + $(date +%s)))
+        while [ $(date +%s) -lt $stop_time ]; do
+          python -c 'import torch; torch.rand(5, 3, device=torch.device("cuda:0"))';
+        done
         python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
-        python -c 'import torch; print(torch.rand(5,3, device=torch.device("cuda:0")))'
-        BUILD_MONAI=1 ./runtests.sh --coverage
+        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
+        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
+        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+        echo $CUDA_VISIBLE_DEVICES
+        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
         coverage xml
     - name: Upload coverage
       uses: codecov/codecov-action@v1
@@ -56,12 +60,16 @@ jobs:
   cron-pt-image:
     if: github.repository == 'Project-MONAI/MONAI'
     container:
-      image: nvcr.io/nvidia/pytorch:20.12-py3  # testing with the latest pytorch base image
+      image: nvcr.io/nvidia/pytorch:21.02-py3  # testing with the latest pytorch base image
       options: "--gpus all"
     runs-on: [self-hosted, linux, x64, common]
     steps:
     - uses: actions/checkout@v2
-    - name: Install the dependencies
+    - name: Install APT dependencies
+      run: |
+        apt-get update
+        DEBIAN_FRONTEND="noninteractive" apt-get install -y libopenslide0
+    - name: Install Python dependencies
       run: |
         which python
         python -m pip install --upgrade pip wheel
@@ -75,9 +83,16 @@ jobs:
         nvidia-smi
         export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
         echo $CUDA_VISIBLE_DEVICES
+        stop_time=$((LAUNCH_DELAY + $(date +%s)))
+        while [ $(date +%s) -lt $stop_time ]; do
+          python -c 'import torch; torch.rand(5, 3, device=torch.device("cuda:0"))';
+        done
         python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
-        python -c 'import torch; print(torch.rand(5,3, device=torch.device("cuda:0")))'
-        BUILD_MONAI=1 ./runtests.sh --coverage
+        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
+        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
+        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+        echo $CUDA_VISIBLE_DEVICES
+        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
         coverage xml
     - name: Upload coverage
       uses: codecov/codecov-action@v1
@@ -103,10 +118,46 @@ jobs:
         python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
         python -c 'import torch; print(torch.rand(5,3, device=torch.device("cuda:0")))'
         ngc --version
-        BUILD_MONAI=1 ./runtests.sh --coverage --pytype
+        BUILD_MONAI=1 ./runtests.sh --coverage --pytype --unittests  # unit tests with pytype checks, coverage report
+        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+        echo $CUDA_VISIBLE_DEVICES
+        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
         coverage xml
     - name: Upload coverage
       uses: codecov/codecov-action@v1
       with:
         fail_ci_if_error: false
         file: ./coverage.xml
+
+  cron-tutorial-notebooks:
+    if: github.repository == 'Project-MONAI/MONAI'
+    needs: cron-gpu  # so that monai itself is verified first
+    container:
+      image: nvcr.io/nvidia/pytorch:21.02-py3  # testing with the latest pytorch base image
+      options: "--gpus all --ipc=host"
+    runs-on: [self-hosted, linux, x64, common]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Install MONAI
+      id: monai-install
+      run: |
+        which python
+        python -m pip install --upgrade pip wheel
+        python -m pip install -r requirements-dev.txt
+        BUILD_MONAI=0 python setup.py develop  # install monai
+        nvidia-smi
+        export CUDA_VISIBLE_DEVICES=$(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
+      run: |
+        export CUDA_VISIBLE_DEVICES=${{ steps.monai-install.outputs.devices }}
+        echo $CUDA_VISIBLE_DEVICES
+        cd /opt/tutorials
+        $(pwd)/runner.sh

.github/workflows/integration.yml

@@ -7,7 +7,7 @@ on:
 jobs:
   integration-py3:
     container:
-      image: nvcr.io/nvidia/pytorch:20.03-py3  # CUDA 10.2
+      image: nvcr.io/nvidia/pytorch:20.12-py3  # CUDA 11.1, default for PT 1.8.0
       options: --gpus all
     runs-on: [self-hosted, linux, x64, common]
     steps:
@@ -28,13 +28,13 @@ jobs:
         path: |
           ~/.cache/pip
           ~/.cache/torch
-        key: docker-20-03-py3-pip-${{ steps.pip-cache.outputs.datew }}
+        key: docker-py3-pip-${{ steps.pip-cache.outputs.datew }}
     - name: Install the dependencies
       run: |
         which python
         python -m pip install --upgrade pip wheel
         python -m pip uninstall -y torch torchvision
-        python -m pip install torch==1.7.1 torchvision==0.8.2
+        python -m pip install torch==1.8.0 torchvision==0.9.0
         python -m pip install -r requirements-dev.txt
     - name: Run integration tests
       run: |
@@ -44,7 +44,7 @@ jobs:
         echo $CUDA_VISIBLE_DEVICES
         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 --net
+        BUILD_MONAI=1 ./runtests.sh --unittests --net
     - name: Add reaction
       uses: peter-evans/create-or-update-comment@v1
       with:

.github/workflows/pythonapp.yml

@@ -9,7 +9,7 @@ on:
 
 jobs:
   # caching of these jobs:
-  #   - docker-20-03-py3-pip- (shared)
+  #   - docker-py3-pip- (shared)
   #   - ubuntu py37 pip-
   #   - os-latest-pip- (shared)
   flake8-py3:
@@ -39,7 +39,7 @@ jobs:
         # clean up temporary files
         $(pwd)/runtests.sh --clean
         # Git hub actions have 2 cores, so parallize pytype
-        $(pwd)/runtests.sh --nounittests --codeformat -j 2
+        $(pwd)/runtests.sh --codeformat -j 2
 
   quick-py3:  # full dependencies installed
     runs-on: ${{ matrix.os }}
@@ -80,13 +80,16 @@ jobs:
     - if: runner.os == 'windows'
       name: Install torch cpu from pytorch.org (Windows only)
       run: |
-        python -m pip install torch==1.7.1+cpu torchvision==0.8.2+cpu -f https://download.pytorch.org/whl/torch_stable.html
+        python -m pip install torch==1.8.0+cpu torchvision==0.9.0+cpu -f https://download.pytorch.org/whl/torch_stable.html
         # min. requirements for windows instances
         python -c "f=open('requirements-dev.txt', 'r'); txt=f.readlines(); f.close(); print(txt); f=open('requirements-dev.txt', 'w'); f.writelines(txt[1:12]); f.close()"
+    - if: runner.os == 'macos'
+      name: Remove cucim installation (Mac only)
+      run: |
+        python -c "f=open('requirements-dev.txt', 'r'); txt=f.readlines(); f.close(); print(txt); f=open('requirements-dev.txt', 'w'); f.writelines([t for t in txt if not t.startswith('cucim')]); f.close()"
     - name: Install the dependencies
       run: |
-        python -m pip install torch==1.7.1
-        python -m pip install torchvision==0.8.2
+        python -m pip install torch==1.8.0 torchvision==0.9.0
         cat "requirements-dev.txt"
         python -m pip install -r requirements-dev.txt
         python -m pip list
@@ -134,11 +137,11 @@ jobs:
     - if: runner.os == 'windows'
       name: Install torch cpu from pytorch.org (Windows only)
       run: |
-        python -m pip install torch==1.7.1+cpu -f https://download.pytorch.org/whl/torch_stable.html
+        python -m pip install torch==1.8.0+cpu -f https://download.pytorch.org/whl/torch_stable.html
     - name: Install the dependencies
       run: |
         # min. requirements
-        python -m pip install torch==1.7.1
+        python -m pip install torch==1.8.0
         python -m pip install -r requirements-min.txt
         python -m pip list
         BUILD_MONAI=0 python setup.py develop  # no compile of extensions
@@ -156,15 +159,13 @@ jobs:
     strategy:
       matrix:
         environment:
-          - "PT15+CUDA101"
           - "PT16+CUDA102"
           - "PT16+CUDA110"
           - "PT17+CUDA102"
           - "PT17+CUDA110"
+          - "PT18+CUDA102"
+          - "PT18+CUDA112"
         include:
-          - environment: PT15+CUDA101
-            pytorch: "torch==1.5.0+cu101 torchvision==0.6.0+cu101 -f https://download.pytorch.org/whl/torch_stable.html"
-            base: "nvcr.io/nvidia/cuda:10.1-devel-ubuntu18.04"
           - environment: PT16+CUDA102
             pytorch: "torch==1.6.0 torchvision==0.7.0"
             base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
@@ -179,6 +180,13 @@ jobs:
             # 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==1.8.0 torchvision==0.9.0"
+            base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
+          - environment: PT18+CUDA112
+            # we explicitly set pytorch to -h to avoid pip install error
+            pytorch: "-h"
+            base: "nvcr.io/nvidia/pytorch:21.02-py3"
     container:
       image: ${{ matrix.base }}
       options: --gpus all
@@ -187,7 +195,10 @@ jobs:
     - uses: actions/checkout@v2
     - name: apt install
       run: |
-        if [ ${{ matrix.environment }} != "PT16+CUDA110" ]; then \
+        if [ ${{ matrix.environment }} = "PT16+CUDA102" ] || \
+           [ ${{ matrix.environment }} = "PT17+CUDA102" ] || \
+           [ ${{ matrix.environment }} = "PT18+CUDA102" ]
+        then
         PYVER=3.6 PYSFX=3 DISTUTILS=python3-distutils && \
         apt-get update && apt-get install -y --no-install-recommends \
           curl \
@@ -217,7 +228,8 @@ jobs:
         ln -s /usr/bin/python$PYVER /usr/bin/python`echo $PYVER | cut -c1-1` &&
         curl -O https://bootstrap.pypa.io/get-pip.py && \
         python get-pip.py && \
-        rm get-pip.py ; fi
+        rm get-pip.py;
+        fi
     - name: Install dependencies
       run: |
         which python
@@ -231,10 +243,10 @@ jobs:
         export CUDA_VISIBLE_DEVICES=$(coverage run -m tests.utils)
         echo $CUDA_VISIBLE_DEVICES
         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 torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
         python -c "import monai; monai.config.print_config()"
-        BUILD_MONAI=1 ./runtests.sh --quick
-        if [ ${{ matrix.environment }} == "PT16+CUDA110" ]; then
+        BUILD_MONAI=1 ./runtests.sh --quick --unittests
+        if [ ${{ matrix.environment }} == "PT18+CUDA112" ]; then
           # test the clang-format tool downloading once
           coverage run -m tests.clang_format_utils
         fi

.github/workflows/setupapp.yml

@@ -8,7 +8,7 @@ on:
 
 jobs:
   # caching of these jobs:
-  #   - docker-20-03-py3-pip- (shared)
+  #   - docker-py3-pip- (shared)
   #   - ubuntu py36 37 38-pip-
   #   - os-latest-pip (shared)
   coverage-py3:
@@ -30,7 +30,7 @@ jobs:
         path: |
           ~/.cache/pip
           ~/.cache/torch
-        key: docker-20-03-py3-pip-${{ steps.pip-cache.outputs.datew }}
+        key: docker-py3-pip-${{ steps.pip-cache.outputs.datew }}
     - name: Install the dependencies
       run: |
         which python
@@ -41,17 +41,27 @@ jobs:
     - name: Run unit tests report coverage
       run: |
         python -m pip list
+        export LAUNCH_DELAY=$[ $RANDOM % 16 * 60 ]
+        echo "Sleep $LAUNCH_DELAY"
+        sleep $LAUNCH_DELAY
         nvidia-smi
         export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
         echo $CUDA_VISIBLE_DEVICES
+        stop_time=$((LAUNCH_DELAY + $(date +%s)))
+        while [ $(date +%s) -lt $stop_time ]; do
+          python -c 'import torch; torch.rand(5, 3, device=torch.device("cuda:0"))';
+        done
         python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
-        python -c 'import torch; print(torch.rand(5,3, device=torch.device("cuda:0")))'
-        BUILD_MONAI=1 ./runtests.sh --coverage
+        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
+        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
+        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+        echo $CUDA_VISIBLE_DEVICES
+        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
         coverage xml
     - name: Upload coverage
       uses: codecov/codecov-action@v1
       with:
-        fail_ci_if_error: true
+        fail_ci_if_error: false
         file: ./coverage.xml
 
   test-py3x:
@@ -88,7 +98,7 @@ jobs:
       run: |
         python -m pip list
         python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
-        BUILD_MONAI=1 ./runtests.sh --quick
+        BUILD_MONAI=1 ./runtests.sh --quick --unittests
         coverage xml
     - name: Upload coverage
       uses: codecov/codecov-action@v1

.gitignore

@@ -40,6 +40,7 @@ htmlcov/
 .tox/
 .coverage
 .coverage.*
+.coverage/
 .cache
 nosetests.xml
 coverage.xml
@@ -124,6 +125,7 @@ temp/
 # temporary testing data MedNIST
 tests/testing_data/MedNIST*
 tests/testing_data/*Hippocampus*
+tests/testing_data/CMU-1.tiff
 
 # clang format tool
 .clang-format-bin/