From b95b7b713d379f269ca854e32b1371d10ae56c78 Mon Sep 17 00:00:00 2001
From: Richard Brown <33289025+rijobro@users.noreply.github.com>
Date: Tue, 16 Mar 2021 16:42:21 +0000
Subject: [PATCH 01/12] cron tutorial notebooks

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
---
 .github/workflows/cron.yml | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml
index 90abb5d7e4..c35aad8ed2 100644
--- a/.github/workflows/cron.yml
+++ b/.github/workflows/cron.yml
@@ -128,3 +128,26 @@ jobs:
       with:
         fail_ci_if_error: false
         file: ./coverage.xml
+
+  cron-tutorial-notebooks:
+    if: github.repository == 'Project-MONAI/MONAI'
+    container:
+      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 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
+    - name: Checkout tutorials and install their requirements
+      run: |
+        git clone https://github.com/Project-MONAI/tutorials.git
+        cd tutorials
+        python -m pip install -r requirements.txt
+    - name: Run tutorial notebooks
+      run: |
+        sh ./runtests.sh

From e327d0a3541893694f85f9295f8720ee9d181ee0 Mon Sep 17 00:00:00 2001
From: Richard Brown <33289025+rijobro@users.noreply.github.com>
Date: Tue, 16 Mar 2021 17:30:42 +0000
Subject: [PATCH 02/12] update script name

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
---
 .github/workflows/cron.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml
index c35aad8ed2..9162227606 100644
--- a/.github/workflows/cron.yml
+++ b/.github/workflows/cron.yml
@@ -150,4 +150,4 @@ jobs:
         python -m pip install -r requirements.txt
     - name: Run tutorial notebooks
       run: |
-        sh ./runtests.sh
+        $(pwd)/runner.sh

From 3e26957e14ea05182d267c240c99248358844326 Mon Sep 17 00:00:00 2001
From: Wenqi Li <wenqil@nvidia.com>
Date: Tue, 16 Mar 2021 18:51:55 +0000
Subject: [PATCH 03/12] revise cmds

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
---
 .github/workflows/cron.yml | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml
index 9162227606..cea33e5601 100644
--- a/.github/workflows/cron.yml
+++ b/.github/workflows/cron.yml
@@ -137,17 +137,22 @@ jobs:
     runs-on: [self-hosted, linux, x64, common]
     steps:
     - uses: actions/checkout@v2
-    - name: Install dependencies
+    - name: Install MONAI
       run: |
         which python
         python -m pip install --upgrade pip wheel
-        python -m pip install ${{ matrix.pytorch }}
         python -m pip install -r requirements-dev.txt
+        BUILD_MONAI=0 python setup.py develop  # install monai
     - name: Checkout tutorials and install their requirements
       run: |
-        git clone https://github.com/Project-MONAI/tutorials.git
+        nvidia-smi
+        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+        echo $CUDA_VISIBLE_DEVICES
+        cd /opt
+        git clone --depth 1 https://github.com/Project-MONAI/tutorials.git  # latest commit
         cd tutorials
         python -m pip install -r requirements.txt
     - name: Run tutorial notebooks
       run: |
+        cd /opt/tutorials
         $(pwd)/runner.sh

From dcc6656054a141504080fd5e4f70b019f50aa14a Mon Sep 17 00:00:00 2001
From: Wenqi Li <wenqil@nvidia.com>
Date: Tue, 16 Mar 2021 18:54:12 +0000
Subject: [PATCH 04/12] temp tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
---
 .github/workflows/cron.yml | 253 +++++++++++++++++++------------------
 1 file changed, 128 insertions(+), 125 deletions(-)

diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml
index cea33e5601..58a900ca40 100644
--- a/.github/workflows/cron.yml
+++ b/.github/workflows/cron.yml
@@ -1,133 +1,136 @@
 name: crons
 
 on:
-  schedule:
-    - cron: "0 2 * * *"  # at 02:00 UTC
+#  schedule:
+#    - cron: "0 2 * * *"  # at 02:00 UTC
+  push:
+    branches:
+      - cron_tutorials
 
 jobs:
-  cron-gpu:
-    if: github.repository == 'Project-MONAI/MONAI'
-    container:
-      image: nvcr.io/nvidia/pytorch:20.03-py3  # CUDA 10.2
-      options: "--gpus all"
-    runs-on: [self-hosted, linux, x64, common]
-    strategy:
-      matrix:
-        pytorch-version: [1.5.1, 1.6.0, 1.7.1, latest]
-    steps:
-    - uses: actions/checkout@v2
-    - name: Install the dependencies
-      run: |
-        which python
-        python -m pip install --upgrade pip wheel
-        python -m pip uninstall -y torch torchvision
-        if [ ${{ matrix.pytorch-version }} == "latest" ]; then
-          python -m pip install torch torchvision
-        elif [ ${{ matrix.pytorch-version }} == "1.5.1" ]; then
-          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 torchvision==0.7.0
-        elif [ ${{ matrix.pytorch-version }} == "1.7.1" ]; then
-          python -m pip install torch==1.7.1 torchvision==0.8.2
-        fi
-        python -m pip install -r requirements-dev.txt
-        python -m pip list
-    - name: Run tests report coverage
-      run: |
-        export LAUNCH_DELAY=$[ $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 $stop_time ]; do
-          python -c 'import torch; torch.rand(5, 3, device=torch.device("cuda:0"))';
-        done
-        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
-        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
-        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
-        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
-        echo $CUDA_VISIBLE_DEVICES
-        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
-        coverage xml
-    - name: Upload coverage
-      uses: codecov/codecov-action@v1
-      with:
-        fail_ci_if_error: false
-        file: ./coverage.xml
-
-  cron-pt-image:
-    if: github.repository == 'Project-MONAI/MONAI'
-    container:
-      image: nvcr.io/nvidia/pytorch:21.02-py3  # testing with the latest pytorch base image
-      options: "--gpus all"
-    runs-on: [self-hosted, linux, x64, common]
-    steps:
-    - uses: actions/checkout@v2
-    - name: Install APT dependencies
-      run: |
-        apt-get update
-        DEBIAN_FRONTEND="noninteractive" apt-get install -y libopenslide0
-    - name: Install Python dependencies
-      run: |
-        which python
-        python -m pip install --upgrade pip wheel
-        python -m pip install -r requirements-dev.txt
-        python -m pip list
-    - name: Run tests report coverage
-      run: |
-        export LAUNCH_DELAY=$[ $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 $stop_time ]; do
-          python -c 'import torch; torch.rand(5, 3, device=torch.device("cuda:0"))';
-        done
-        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
-        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
-        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
-        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
-        echo $CUDA_VISIBLE_DEVICES
-        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
-        coverage xml
-    - name: Upload coverage
-      uses: codecov/codecov-action@v1
-      with:
-        fail_ci_if_error: false
-        file: ./coverage.xml
-
-  cron-docker:
-    if: github.repository == 'Project-MONAI/MONAI'
-    container:
-      image: localhost:5000/local_monai:dockerhub # use currently latest, locally available dockerhub image
-      options: "--gpus all"
-    runs-on: [self-hosted, linux, x64, common]
-    steps:
-    - name: Run tests report coverage
-      # The docker image process has done the compilation.
-      # BUILD_MONAI=1 is necessary for triggering the USE_COMPILED flag.
-      run: |
-        cd /opt/monai
-        nvidia-smi
-        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
-        echo $CUDA_VISIBLE_DEVICES
-        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
-        python -c 'import torch; print(torch.rand(5,3, device=torch.device("cuda:0")))'
-        ngc --version
-        BUILD_MONAI=1 ./runtests.sh --coverage --pytype --unittests  # unit tests with pytype checks, coverage report
-        export CUDA_VISIBLE_DEVICES=$(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-gpu:
+#    if: github.repository == 'Project-MONAI/MONAI'
+#    container:
+#      image: nvcr.io/nvidia/pytorch:20.03-py3  # CUDA 10.2
+#      options: "--gpus all"
+#    runs-on: [self-hosted, linux, x64, common]
+#    strategy:
+#      matrix:
+#        pytorch-version: [1.5.1, 1.6.0, 1.7.1, latest]
+#    steps:
+#    - uses: actions/checkout@v2
+#    - name: Install the dependencies
+#      run: |
+#        which python
+#        python -m pip install --upgrade pip wheel
+#        python -m pip uninstall -y torch torchvision
+#        if [ ${{ matrix.pytorch-version }} == "latest" ]; then
+#          python -m pip install torch torchvision
+#        elif [ ${{ matrix.pytorch-version }} == "1.5.1" ]; then
+#          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 torchvision==0.7.0
+#        elif [ ${{ matrix.pytorch-version }} == "1.7.1" ]; then
+#          python -m pip install torch==1.7.1 torchvision==0.8.2
+#        fi
+#        python -m pip install -r requirements-dev.txt
+#        python -m pip list
+#    - name: Run tests report coverage
+#      run: |
+#        export LAUNCH_DELAY=$[ $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 $stop_time ]; do
+#          python -c 'import torch; torch.rand(5, 3, device=torch.device("cuda:0"))';
+#        done
+#        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
+#        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
+#        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
+#        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+#        echo $CUDA_VISIBLE_DEVICES
+#        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
+#        coverage xml
+#    - name: Upload coverage
+#      uses: codecov/codecov-action@v1
+#      with:
+#        fail_ci_if_error: false
+#        file: ./coverage.xml
+#
+#  cron-pt-image:
+#    if: github.repository == 'Project-MONAI/MONAI'
+#    container:
+#      image: nvcr.io/nvidia/pytorch:21.02-py3  # testing with the latest pytorch base image
+#      options: "--gpus all"
+#    runs-on: [self-hosted, linux, x64, common]
+#    steps:
+#    - uses: actions/checkout@v2
+#    - name: Install APT dependencies
+#      run: |
+#        apt-get update
+#        DEBIAN_FRONTEND="noninteractive" apt-get install -y libopenslide0
+#    - name: Install Python dependencies
+#      run: |
+#        which python
+#        python -m pip install --upgrade pip wheel
+#        python -m pip install -r requirements-dev.txt
+#        python -m pip list
+#    - name: Run tests report coverage
+#      run: |
+#        export LAUNCH_DELAY=$[ $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 $stop_time ]; do
+#          python -c 'import torch; torch.rand(5, 3, device=torch.device("cuda:0"))';
+#        done
+#        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
+#        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
+#        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
+#        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+#        echo $CUDA_VISIBLE_DEVICES
+#        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
+#        coverage xml
+#    - name: Upload coverage
+#      uses: codecov/codecov-action@v1
+#      with:
+#        fail_ci_if_error: false
+#        file: ./coverage.xml
+#
+#  cron-docker:
+#    if: github.repository == 'Project-MONAI/MONAI'
+#    container:
+#      image: localhost:5000/local_monai:dockerhub # use currently latest, locally available dockerhub image
+#      options: "--gpus all"
+#    runs-on: [self-hosted, linux, x64, common]
+#    steps:
+#    - name: Run tests report coverage
+#      # The docker image process has done the compilation.
+#      # BUILD_MONAI=1 is necessary for triggering the USE_COMPILED flag.
+#      run: |
+#        cd /opt/monai
+#        nvidia-smi
+#        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+#        echo $CUDA_VISIBLE_DEVICES
+#        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
+#        python -c 'import torch; print(torch.rand(5,3, device=torch.device("cuda:0")))'
+#        ngc --version
+#        BUILD_MONAI=1 ./runtests.sh --coverage --pytype --unittests  # unit tests with pytype checks, coverage report
+#        export CUDA_VISIBLE_DEVICES=$(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'

From 7303b610c4e4d7b431685383284bcc33068763a5 Mon Sep 17 00:00:00 2001
From: Wenqi Li <wenqil@nvidia.com>
Date: Tue, 16 Mar 2021 21:24:46 +0000
Subject: [PATCH 05/12] Revert "temp tests"

This reverts commit dcc6656054a141504080fd5e4f70b019f50aa14a.

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
---
 .github/workflows/cron.yml | 253 ++++++++++++++++++-------------------
 1 file changed, 125 insertions(+), 128 deletions(-)

diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml
index 58a900ca40..cea33e5601 100644
--- a/.github/workflows/cron.yml
+++ b/.github/workflows/cron.yml
@@ -1,136 +1,133 @@
 name: crons
 
 on:
-#  schedule:
-#    - cron: "0 2 * * *"  # at 02:00 UTC
-  push:
-    branches:
-      - cron_tutorials
+  schedule:
+    - cron: "0 2 * * *"  # at 02:00 UTC
 
 jobs:
-#  cron-gpu:
-#    if: github.repository == 'Project-MONAI/MONAI'
-#    container:
-#      image: nvcr.io/nvidia/pytorch:20.03-py3  # CUDA 10.2
-#      options: "--gpus all"
-#    runs-on: [self-hosted, linux, x64, common]
-#    strategy:
-#      matrix:
-#        pytorch-version: [1.5.1, 1.6.0, 1.7.1, latest]
-#    steps:
-#    - uses: actions/checkout@v2
-#    - name: Install the dependencies
-#      run: |
-#        which python
-#        python -m pip install --upgrade pip wheel
-#        python -m pip uninstall -y torch torchvision
-#        if [ ${{ matrix.pytorch-version }} == "latest" ]; then
-#          python -m pip install torch torchvision
-#        elif [ ${{ matrix.pytorch-version }} == "1.5.1" ]; then
-#          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 torchvision==0.7.0
-#        elif [ ${{ matrix.pytorch-version }} == "1.7.1" ]; then
-#          python -m pip install torch==1.7.1 torchvision==0.8.2
-#        fi
-#        python -m pip install -r requirements-dev.txt
-#        python -m pip list
-#    - name: Run tests report coverage
-#      run: |
-#        export LAUNCH_DELAY=$[ $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 $stop_time ]; do
-#          python -c 'import torch; torch.rand(5, 3, device=torch.device("cuda:0"))';
-#        done
-#        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
-#        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
-#        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
-#        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
-#        echo $CUDA_VISIBLE_DEVICES
-#        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
-#        coverage xml
-#    - name: Upload coverage
-#      uses: codecov/codecov-action@v1
-#      with:
-#        fail_ci_if_error: false
-#        file: ./coverage.xml
-#
-#  cron-pt-image:
-#    if: github.repository == 'Project-MONAI/MONAI'
-#    container:
-#      image: nvcr.io/nvidia/pytorch:21.02-py3  # testing with the latest pytorch base image
-#      options: "--gpus all"
-#    runs-on: [self-hosted, linux, x64, common]
-#    steps:
-#    - uses: actions/checkout@v2
-#    - name: Install APT dependencies
-#      run: |
-#        apt-get update
-#        DEBIAN_FRONTEND="noninteractive" apt-get install -y libopenslide0
-#    - name: Install Python dependencies
-#      run: |
-#        which python
-#        python -m pip install --upgrade pip wheel
-#        python -m pip install -r requirements-dev.txt
-#        python -m pip list
-#    - name: Run tests report coverage
-#      run: |
-#        export LAUNCH_DELAY=$[ $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 $stop_time ]; do
-#          python -c 'import torch; torch.rand(5, 3, device=torch.device("cuda:0"))';
-#        done
-#        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
-#        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
-#        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
-#        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
-#        echo $CUDA_VISIBLE_DEVICES
-#        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
-#        coverage xml
-#    - name: Upload coverage
-#      uses: codecov/codecov-action@v1
-#      with:
-#        fail_ci_if_error: false
-#        file: ./coverage.xml
-#
-#  cron-docker:
-#    if: github.repository == 'Project-MONAI/MONAI'
-#    container:
-#      image: localhost:5000/local_monai:dockerhub # use currently latest, locally available dockerhub image
-#      options: "--gpus all"
-#    runs-on: [self-hosted, linux, x64, common]
-#    steps:
-#    - name: Run tests report coverage
-#      # The docker image process has done the compilation.
-#      # BUILD_MONAI=1 is necessary for triggering the USE_COMPILED flag.
-#      run: |
-#        cd /opt/monai
-#        nvidia-smi
-#        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
-#        echo $CUDA_VISIBLE_DEVICES
-#        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
-#        python -c 'import torch; print(torch.rand(5,3, device=torch.device("cuda:0")))'
-#        ngc --version
-#        BUILD_MONAI=1 ./runtests.sh --coverage --pytype --unittests  # unit tests with pytype checks, coverage report
-#        export CUDA_VISIBLE_DEVICES=$(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-gpu:
+    if: github.repository == 'Project-MONAI/MONAI'
+    container:
+      image: nvcr.io/nvidia/pytorch:20.03-py3  # CUDA 10.2
+      options: "--gpus all"
+    runs-on: [self-hosted, linux, x64, common]
+    strategy:
+      matrix:
+        pytorch-version: [1.5.1, 1.6.0, 1.7.1, latest]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Install the dependencies
+      run: |
+        which python
+        python -m pip install --upgrade pip wheel
+        python -m pip uninstall -y torch torchvision
+        if [ ${{ matrix.pytorch-version }} == "latest" ]; then
+          python -m pip install torch torchvision
+        elif [ ${{ matrix.pytorch-version }} == "1.5.1" ]; then
+          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 torchvision==0.7.0
+        elif [ ${{ matrix.pytorch-version }} == "1.7.1" ]; then
+          python -m pip install torch==1.7.1 torchvision==0.8.2
+        fi
+        python -m pip install -r requirements-dev.txt
+        python -m pip list
+    - name: Run tests report coverage
+      run: |
+        export LAUNCH_DELAY=$[ $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 $stop_time ]; do
+          python -c 'import torch; torch.rand(5, 3, device=torch.device("cuda:0"))';
+        done
+        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
+        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
+        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
+        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+        echo $CUDA_VISIBLE_DEVICES
+        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
+        coverage xml
+    - name: Upload coverage
+      uses: codecov/codecov-action@v1
+      with:
+        fail_ci_if_error: false
+        file: ./coverage.xml
+
+  cron-pt-image:
+    if: github.repository == 'Project-MONAI/MONAI'
+    container:
+      image: nvcr.io/nvidia/pytorch:21.02-py3  # testing with the latest pytorch base image
+      options: "--gpus all"
+    runs-on: [self-hosted, linux, x64, common]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Install APT dependencies
+      run: |
+        apt-get update
+        DEBIAN_FRONTEND="noninteractive" apt-get install -y libopenslide0
+    - name: Install Python dependencies
+      run: |
+        which python
+        python -m pip install --upgrade pip wheel
+        python -m pip install -r requirements-dev.txt
+        python -m pip list
+    - name: Run tests report coverage
+      run: |
+        export LAUNCH_DELAY=$[ $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 $stop_time ]; do
+          python -c 'import torch; torch.rand(5, 3, device=torch.device("cuda:0"))';
+        done
+        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
+        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
+        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
+        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+        echo $CUDA_VISIBLE_DEVICES
+        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
+        coverage xml
+    - name: Upload coverage
+      uses: codecov/codecov-action@v1
+      with:
+        fail_ci_if_error: false
+        file: ./coverage.xml
+
+  cron-docker:
+    if: github.repository == 'Project-MONAI/MONAI'
+    container:
+      image: localhost:5000/local_monai:dockerhub # use currently latest, locally available dockerhub image
+      options: "--gpus all"
+    runs-on: [self-hosted, linux, x64, common]
+    steps:
+    - name: Run tests report coverage
+      # The docker image process has done the compilation.
+      # BUILD_MONAI=1 is necessary for triggering the USE_COMPILED flag.
+      run: |
+        cd /opt/monai
+        nvidia-smi
+        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+        echo $CUDA_VISIBLE_DEVICES
+        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
+        python -c 'import torch; print(torch.rand(5,3, device=torch.device("cuda:0")))'
+        ngc --version
+        BUILD_MONAI=1 ./runtests.sh --coverage --pytype --unittests  # unit tests with pytype checks, coverage report
+        export CUDA_VISIBLE_DEVICES=$(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'

From e47dbdfb7d8dd66642ca2be9731fb31ed3d538ad Mon Sep 17 00:00:00 2001
From: Richard Brown <33289025+rijobro@users.noreply.github.com>
Date: Tue, 16 Mar 2021 16:42:21 +0000
Subject: [PATCH 06/12] cron tutorial notebooks

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
---
 .github/workflows/cron.yml | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml
index 90abb5d7e4..c35aad8ed2 100644
--- a/.github/workflows/cron.yml
+++ b/.github/workflows/cron.yml
@@ -128,3 +128,26 @@ jobs:
       with:
         fail_ci_if_error: false
         file: ./coverage.xml
+
+  cron-tutorial-notebooks:
+    if: github.repository == 'Project-MONAI/MONAI'
+    container:
+      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 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
+    - name: Checkout tutorials and install their requirements
+      run: |
+        git clone https://github.com/Project-MONAI/tutorials.git
+        cd tutorials
+        python -m pip install -r requirements.txt
+    - name: Run tutorial notebooks
+      run: |
+        sh ./runtests.sh

From 27104f8c6fdceb1866afedb0b82c4ed0198baa67 Mon Sep 17 00:00:00 2001
From: Richard Brown <33289025+rijobro@users.noreply.github.com>
Date: Tue, 16 Mar 2021 17:30:42 +0000
Subject: [PATCH 07/12] update script name

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
---
 .github/workflows/cron.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml
index c35aad8ed2..9162227606 100644
--- a/.github/workflows/cron.yml
+++ b/.github/workflows/cron.yml
@@ -150,4 +150,4 @@ jobs:
         python -m pip install -r requirements.txt
     - name: Run tutorial notebooks
       run: |
-        sh ./runtests.sh
+        $(pwd)/runner.sh

From 44252252b98547fee6efb41bae519bc57227c388 Mon Sep 17 00:00:00 2001
From: Richard Brown <33289025+rijobro@users.noreply.github.com>
Date: Wed, 17 Mar 2021 09:51:28 +0000
Subject: [PATCH 08/12] single branch checkout

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
---
 .github/workflows/cron.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml
index cea33e5601..f47263a5c2 100644
--- a/.github/workflows/cron.yml
+++ b/.github/workflows/cron.yml
@@ -149,7 +149,7 @@ jobs:
         export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
         echo $CUDA_VISIBLE_DEVICES
         cd /opt
-        git clone --depth 1 https://github.com/Project-MONAI/tutorials.git  # latest commit
+        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

From 96176f41f586392cbb9b91f7248e6997462b844d Mon Sep 17 00:00:00 2001
From: Wenqi Li <wenqil@nvidia.com>
Date: Tue, 16 Mar 2021 18:51:55 +0000
Subject: [PATCH 09/12] revise cmds

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
---
 .github/workflows/cron.yml | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml
index 9162227606..443b43334c 100644
--- a/.github/workflows/cron.yml
+++ b/.github/workflows/cron.yml
@@ -131,23 +131,33 @@ jobs:
 
   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"
+      options: "--gpus all --ipc=host"
     runs-on: [self-hosted, linux, x64, common]
     steps:
     - uses: actions/checkout@v2
-    - name: Install dependencies
+    - name: Install MONAI
+      id: monai-install
       run: |
         which python
         python -m pip install --upgrade pip wheel
-        python -m pip install ${{ matrix.pytorch }}
         python -m pip install -r requirements-dev.txt
+        BUILD_MONAI=0 python setup.py develop  # install monai
+        nvidia-smi
+        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+        echo $CUDA_VISIBLE_DEVICES
+        echo "::set-output name=devices::$CUDA_VISIBLE_DEVICES"
     - name: Checkout tutorials and install their requirements
       run: |
-        git clone https://github.com/Project-MONAI/tutorials.git
+        cd /opt
+        git clone --depth 1 https://github.com/Project-MONAI/tutorials.git  # latest commit
         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

From f8e9d6f0e026c60c62e2f732204d4db2fe6b85d8 Mon Sep 17 00:00:00 2001
From: Wenqi Li <wenqil@nvidia.com>
Date: Tue, 16 Mar 2021 18:54:12 +0000
Subject: [PATCH 10/12] temp tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
---
 .github/workflows/cron.yml | 255 +++++++++++++++++++------------------
 1 file changed, 129 insertions(+), 126 deletions(-)

diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml
index 443b43334c..6ad950336d 100644
--- a/.github/workflows/cron.yml
+++ b/.github/workflows/cron.yml
@@ -1,137 +1,140 @@
 name: crons
 
 on:
-  schedule:
-    - cron: "0 2 * * *"  # at 02:00 UTC
+#  schedule:
+#    - cron: "0 2 * * *"  # at 02:00 UTC
+  push:
+    branches:
+      - cron_tutorials_test
 
 jobs:
-  cron-gpu:
-    if: github.repository == 'Project-MONAI/MONAI'
-    container:
-      image: nvcr.io/nvidia/pytorch:20.03-py3  # CUDA 10.2
-      options: "--gpus all"
-    runs-on: [self-hosted, linux, x64, common]
-    strategy:
-      matrix:
-        pytorch-version: [1.5.1, 1.6.0, 1.7.1, latest]
-    steps:
-    - uses: actions/checkout@v2
-    - name: Install the dependencies
-      run: |
-        which python
-        python -m pip install --upgrade pip wheel
-        python -m pip uninstall -y torch torchvision
-        if [ ${{ matrix.pytorch-version }} == "latest" ]; then
-          python -m pip install torch torchvision
-        elif [ ${{ matrix.pytorch-version }} == "1.5.1" ]; then
-          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 torchvision==0.7.0
-        elif [ ${{ matrix.pytorch-version }} == "1.7.1" ]; then
-          python -m pip install torch==1.7.1 torchvision==0.8.2
-        fi
-        python -m pip install -r requirements-dev.txt
-        python -m pip list
-    - name: Run tests report coverage
-      run: |
-        export LAUNCH_DELAY=$[ $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 $stop_time ]; do
-          python -c 'import torch; torch.rand(5, 3, device=torch.device("cuda:0"))';
-        done
-        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
-        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
-        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
-        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
-        echo $CUDA_VISIBLE_DEVICES
-        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
-        coverage xml
-    - name: Upload coverage
-      uses: codecov/codecov-action@v1
-      with:
-        fail_ci_if_error: false
-        file: ./coverage.xml
-
-  cron-pt-image:
-    if: github.repository == 'Project-MONAI/MONAI'
-    container:
-      image: nvcr.io/nvidia/pytorch:21.02-py3  # testing with the latest pytorch base image
-      options: "--gpus all"
-    runs-on: [self-hosted, linux, x64, common]
-    steps:
-    - uses: actions/checkout@v2
-    - name: Install APT dependencies
-      run: |
-        apt-get update
-        DEBIAN_FRONTEND="noninteractive" apt-get install -y libopenslide0
-    - name: Install Python dependencies
-      run: |
-        which python
-        python -m pip install --upgrade pip wheel
-        python -m pip install -r requirements-dev.txt
-        python -m pip list
-    - name: Run tests report coverage
-      run: |
-        export LAUNCH_DELAY=$[ $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 $stop_time ]; do
-          python -c 'import torch; torch.rand(5, 3, device=torch.device("cuda:0"))';
-        done
-        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
-        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
-        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
-        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
-        echo $CUDA_VISIBLE_DEVICES
-        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
-        coverage xml
-    - name: Upload coverage
-      uses: codecov/codecov-action@v1
-      with:
-        fail_ci_if_error: false
-        file: ./coverage.xml
-
-  cron-docker:
-    if: github.repository == 'Project-MONAI/MONAI'
-    container:
-      image: localhost:5000/local_monai:dockerhub # use currently latest, locally available dockerhub image
-      options: "--gpus all"
-    runs-on: [self-hosted, linux, x64, common]
-    steps:
-    - name: Run tests report coverage
-      # The docker image process has done the compilation.
-      # BUILD_MONAI=1 is necessary for triggering the USE_COMPILED flag.
-      run: |
-        cd /opt/monai
-        nvidia-smi
-        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
-        echo $CUDA_VISIBLE_DEVICES
-        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
-        python -c 'import torch; print(torch.rand(5,3, device=torch.device("cuda:0")))'
-        ngc --version
-        BUILD_MONAI=1 ./runtests.sh --coverage --pytype --unittests  # unit tests with pytype checks, coverage report
-        export CUDA_VISIBLE_DEVICES=$(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-gpu:
+#    if: github.repository == 'Project-MONAI/MONAI'
+#    container:
+#      image: nvcr.io/nvidia/pytorch:20.03-py3  # CUDA 10.2
+#      options: "--gpus all"
+#    runs-on: [self-hosted, linux, x64, common]
+#    strategy:
+#      matrix:
+#        pytorch-version: [1.5.1, 1.6.0, 1.7.1, latest]
+#    steps:
+#    - uses: actions/checkout@v2
+#    - name: Install the dependencies
+#      run: |
+#        which python
+#        python -m pip install --upgrade pip wheel
+#        python -m pip uninstall -y torch torchvision
+#        if [ ${{ matrix.pytorch-version }} == "latest" ]; then
+#          python -m pip install torch torchvision
+#        elif [ ${{ matrix.pytorch-version }} == "1.5.1" ]; then
+#          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 torchvision==0.7.0
+#        elif [ ${{ matrix.pytorch-version }} == "1.7.1" ]; then
+#          python -m pip install torch==1.7.1 torchvision==0.8.2
+#        fi
+#        python -m pip install -r requirements-dev.txt
+#        python -m pip list
+#    - name: Run tests report coverage
+#      run: |
+#        export LAUNCH_DELAY=$[ $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 $stop_time ]; do
+#          python -c 'import torch; torch.rand(5, 3, device=torch.device("cuda:0"))';
+#        done
+#        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
+#        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
+#        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
+#        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+#        echo $CUDA_VISIBLE_DEVICES
+#        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
+#        coverage xml
+#    - name: Upload coverage
+#      uses: codecov/codecov-action@v1
+#      with:
+#        fail_ci_if_error: false
+#        file: ./coverage.xml
+#
+#  cron-pt-image:
+#    if: github.repository == 'Project-MONAI/MONAI'
+#    container:
+#      image: nvcr.io/nvidia/pytorch:21.02-py3  # testing with the latest pytorch base image
+#      options: "--gpus all"
+#    runs-on: [self-hosted, linux, x64, common]
+#    steps:
+#    - uses: actions/checkout@v2
+#    - name: Install APT dependencies
+#      run: |
+#        apt-get update
+#        DEBIAN_FRONTEND="noninteractive" apt-get install -y libopenslide0
+#    - name: Install Python dependencies
+#      run: |
+#        which python
+#        python -m pip install --upgrade pip wheel
+#        python -m pip install -r requirements-dev.txt
+#        python -m pip list
+#    - name: Run tests report coverage
+#      run: |
+#        export LAUNCH_DELAY=$[ $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 $stop_time ]; do
+#          python -c 'import torch; torch.rand(5, 3, device=torch.device("cuda:0"))';
+#        done
+#        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
+#        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
+#        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
+#        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+#        echo $CUDA_VISIBLE_DEVICES
+#        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
+#        coverage xml
+#    - name: Upload coverage
+#      uses: codecov/codecov-action@v1
+#      with:
+#        fail_ci_if_error: false
+#        file: ./coverage.xml
+#
+#  cron-docker:
+#    if: github.repository == 'Project-MONAI/MONAI'
+#    container:
+#      image: localhost:5000/local_monai:dockerhub # use currently latest, locally available dockerhub image
+#      options: "--gpus all"
+#    runs-on: [self-hosted, linux, x64, common]
+#    steps:
+#    - name: Run tests report coverage
+#      # The docker image process has done the compilation.
+#      # BUILD_MONAI=1 is necessary for triggering the USE_COMPILED flag.
+#      run: |
+#        cd /opt/monai
+#        nvidia-smi
+#        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+#        echo $CUDA_VISIBLE_DEVICES
+#        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
+#        python -c 'import torch; print(torch.rand(5,3, device=torch.device("cuda:0")))'
+#        ngc --version
+#        BUILD_MONAI=1 ./runtests.sh --coverage --pytype --unittests  # unit tests with pytype checks, coverage report
+#        export CUDA_VISIBLE_DEVICES=$(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
+#    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"

From 1f0df15c5c971c4679f233181a073b5c2d0179c4 Mon Sep 17 00:00:00 2001
From: Richard Brown <33289025+rijobro@users.noreply.github.com>
Date: Wed, 17 Mar 2021 09:51:28 +0000
Subject: [PATCH 11/12] single branch checkout

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
---
 .github/workflows/cron.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml
index 6ad950336d..890551e378 100644
--- a/.github/workflows/cron.yml
+++ b/.github/workflows/cron.yml
@@ -155,7 +155,7 @@ jobs:
     - name: Checkout tutorials and install their requirements
       run: |
         cd /opt
-        git clone --depth 1 https://github.com/Project-MONAI/tutorials.git  # latest commit
+        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

From b848404116cb165d1cf46193c779dd691ab0d4b5 Mon Sep 17 00:00:00 2001
From: Wenqi Li <wenqil@nvidia.com>
Date: Wed, 17 Mar 2021 13:22:35 +0000
Subject: [PATCH 12/12] Revert "temp tests"

This reverts commit f8e9d6f0e026c60c62e2f732204d4db2fe6b85d8.

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
---
 .github/workflows/cron.yml | 255 ++++++++++++++++++-------------------
 1 file changed, 126 insertions(+), 129 deletions(-)

diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml
index 890551e378..761b1f7ebc 100644
--- a/.github/workflows/cron.yml
+++ b/.github/workflows/cron.yml
@@ -1,140 +1,137 @@
 name: crons
 
 on:
-#  schedule:
-#    - cron: "0 2 * * *"  # at 02:00 UTC
-  push:
-    branches:
-      - cron_tutorials_test
+  schedule:
+    - cron: "0 2 * * *"  # at 02:00 UTC
 
 jobs:
-#  cron-gpu:
-#    if: github.repository == 'Project-MONAI/MONAI'
-#    container:
-#      image: nvcr.io/nvidia/pytorch:20.03-py3  # CUDA 10.2
-#      options: "--gpus all"
-#    runs-on: [self-hosted, linux, x64, common]
-#    strategy:
-#      matrix:
-#        pytorch-version: [1.5.1, 1.6.0, 1.7.1, latest]
-#    steps:
-#    - uses: actions/checkout@v2
-#    - name: Install the dependencies
-#      run: |
-#        which python
-#        python -m pip install --upgrade pip wheel
-#        python -m pip uninstall -y torch torchvision
-#        if [ ${{ matrix.pytorch-version }} == "latest" ]; then
-#          python -m pip install torch torchvision
-#        elif [ ${{ matrix.pytorch-version }} == "1.5.1" ]; then
-#          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 torchvision==0.7.0
-#        elif [ ${{ matrix.pytorch-version }} == "1.7.1" ]; then
-#          python -m pip install torch==1.7.1 torchvision==0.8.2
-#        fi
-#        python -m pip install -r requirements-dev.txt
-#        python -m pip list
-#    - name: Run tests report coverage
-#      run: |
-#        export LAUNCH_DELAY=$[ $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 $stop_time ]; do
-#          python -c 'import torch; torch.rand(5, 3, device=torch.device("cuda:0"))';
-#        done
-#        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
-#        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
-#        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
-#        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
-#        echo $CUDA_VISIBLE_DEVICES
-#        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
-#        coverage xml
-#    - name: Upload coverage
-#      uses: codecov/codecov-action@v1
-#      with:
-#        fail_ci_if_error: false
-#        file: ./coverage.xml
-#
-#  cron-pt-image:
-#    if: github.repository == 'Project-MONAI/MONAI'
-#    container:
-#      image: nvcr.io/nvidia/pytorch:21.02-py3  # testing with the latest pytorch base image
-#      options: "--gpus all"
-#    runs-on: [self-hosted, linux, x64, common]
-#    steps:
-#    - uses: actions/checkout@v2
-#    - name: Install APT dependencies
-#      run: |
-#        apt-get update
-#        DEBIAN_FRONTEND="noninteractive" apt-get install -y libopenslide0
-#    - name: Install Python dependencies
-#      run: |
-#        which python
-#        python -m pip install --upgrade pip wheel
-#        python -m pip install -r requirements-dev.txt
-#        python -m pip list
-#    - name: Run tests report coverage
-#      run: |
-#        export LAUNCH_DELAY=$[ $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 $stop_time ]; do
-#          python -c 'import torch; torch.rand(5, 3, device=torch.device("cuda:0"))';
-#        done
-#        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
-#        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
-#        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
-#        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
-#        echo $CUDA_VISIBLE_DEVICES
-#        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
-#        coverage xml
-#    - name: Upload coverage
-#      uses: codecov/codecov-action@v1
-#      with:
-#        fail_ci_if_error: false
-#        file: ./coverage.xml
-#
-#  cron-docker:
-#    if: github.repository == 'Project-MONAI/MONAI'
-#    container:
-#      image: localhost:5000/local_monai:dockerhub # use currently latest, locally available dockerhub image
-#      options: "--gpus all"
-#    runs-on: [self-hosted, linux, x64, common]
-#    steps:
-#    - name: Run tests report coverage
-#      # The docker image process has done the compilation.
-#      # BUILD_MONAI=1 is necessary for triggering the USE_COMPILED flag.
-#      run: |
-#        cd /opt/monai
-#        nvidia-smi
-#        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
-#        echo $CUDA_VISIBLE_DEVICES
-#        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
-#        python -c 'import torch; print(torch.rand(5,3, device=torch.device("cuda:0")))'
-#        ngc --version
-#        BUILD_MONAI=1 ./runtests.sh --coverage --pytype --unittests  # unit tests with pytype checks, coverage report
-#        export CUDA_VISIBLE_DEVICES=$(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-gpu:
+    if: github.repository == 'Project-MONAI/MONAI'
+    container:
+      image: nvcr.io/nvidia/pytorch:20.03-py3  # CUDA 10.2
+      options: "--gpus all"
+    runs-on: [self-hosted, linux, x64, common]
+    strategy:
+      matrix:
+        pytorch-version: [1.5.1, 1.6.0, 1.7.1, latest]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Install the dependencies
+      run: |
+        which python
+        python -m pip install --upgrade pip wheel
+        python -m pip uninstall -y torch torchvision
+        if [ ${{ matrix.pytorch-version }} == "latest" ]; then
+          python -m pip install torch torchvision
+        elif [ ${{ matrix.pytorch-version }} == "1.5.1" ]; then
+          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 torchvision==0.7.0
+        elif [ ${{ matrix.pytorch-version }} == "1.7.1" ]; then
+          python -m pip install torch==1.7.1 torchvision==0.8.2
+        fi
+        python -m pip install -r requirements-dev.txt
+        python -m pip list
+    - name: Run tests report coverage
+      run: |
+        export LAUNCH_DELAY=$[ $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 $stop_time ]; do
+          python -c 'import torch; torch.rand(5, 3, device=torch.device("cuda:0"))';
+        done
+        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
+        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
+        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
+        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+        echo $CUDA_VISIBLE_DEVICES
+        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
+        coverage xml
+    - name: Upload coverage
+      uses: codecov/codecov-action@v1
+      with:
+        fail_ci_if_error: false
+        file: ./coverage.xml
+
+  cron-pt-image:
+    if: github.repository == 'Project-MONAI/MONAI'
+    container:
+      image: nvcr.io/nvidia/pytorch:21.02-py3  # testing with the latest pytorch base image
+      options: "--gpus all"
+    runs-on: [self-hosted, linux, x64, common]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Install APT dependencies
+      run: |
+        apt-get update
+        DEBIAN_FRONTEND="noninteractive" apt-get install -y libopenslide0
+    - name: Install Python dependencies
+      run: |
+        which python
+        python -m pip install --upgrade pip wheel
+        python -m pip install -r requirements-dev.txt
+        python -m pip list
+    - name: Run tests report coverage
+      run: |
+        export LAUNCH_DELAY=$[ $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 $stop_time ]; do
+          python -c 'import torch; torch.rand(5, 3, device=torch.device("cuda:0"))';
+        done
+        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
+        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
+        BUILD_MONAI=1 ./runtests.sh --coverage --unittests  # unit tests with coverage report
+        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+        echo $CUDA_VISIBLE_DEVICES
+        BUILD_MONAI=1 ./runtests.sh --coverage --net  # integration tests with coverage report
+        coverage xml
+    - name: Upload coverage
+      uses: codecov/codecov-action@v1
+      with:
+        fail_ci_if_error: false
+        file: ./coverage.xml
+
+  cron-docker:
+    if: github.repository == 'Project-MONAI/MONAI'
+    container:
+      image: localhost:5000/local_monai:dockerhub # use currently latest, locally available dockerhub image
+      options: "--gpus all"
+    runs-on: [self-hosted, linux, x64, common]
+    steps:
+    - name: Run tests report coverage
+      # The docker image process has done the compilation.
+      # BUILD_MONAI=1 is necessary for triggering the USE_COMPILED flag.
+      run: |
+        cd /opt/monai
+        nvidia-smi
+        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+        echo $CUDA_VISIBLE_DEVICES
+        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
+        python -c 'import torch; print(torch.rand(5,3, device=torch.device("cuda:0")))'
+        ngc --version
+        BUILD_MONAI=1 ./runtests.sh --coverage --pytype --unittests  # unit tests with pytype checks, coverage report
+        export CUDA_VISIBLE_DEVICES=$(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
+    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"