From 0331df86e46af7d371fc1b525f55140a66b0f650 Mon Sep 17 00:00:00 2001
From: Rich <33289025+rijobro@users.noreply.github.com>
Date: Wed, 27 Jan 2021 15:39:14 +0000
Subject: [PATCH 01/12] run modified notebooks

---
 .github/workflows/pep8.yml | 13 ++++++++-----
 requirements.txt           |  1 +
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/pep8.yml b/.github/workflows/pep8.yml
index 587472e4a5..dc5853659b 100644
--- a/.github/workflows/pep8.yml
+++ b/.github/workflows/pep8.yml
@@ -8,11 +8,7 @@ on:
   pull_request:
 
 jobs:
-  # caching of these jobs:
-  #   - docker-20-03-py3-pip- (shared)
-  #   - ubuntu py37 pip-
-  #   - os-latest-pip- (shared)
-  pep8:
+  build:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
@@ -34,6 +30,13 @@ jobs:
       run: |
         python -m pip install --upgrade pip wheel
         python -m pip install -r requirements.txt
+        python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/master/requirements.txt
+        python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/master/requirements-dev.txt
     - name: PEP8 check
       run: |
         $(pwd)/runner.sh --no-run
+    - name: Run changed files
+      run: |
+        python -c "import torch; print(torch.cuda.is_available())"
+        git fetch origin master:master
+        git diff --name-only master | while read line; do [[ $line == *.ipynb ]] && ./runner.sh --file "$line" --no-checks; done
diff --git a/requirements.txt b/requirements.txt
index 8bd733221f..193df2c022 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,3 +3,4 @@ papermill
 autopep8
 jupytext
 autoflake
+ipykernel

From fb027577ef14b01e90ff83bcff7bc75796271d0f Mon Sep 17 00:00:00 2001
From: Richard Brown <33289025+rijobro@users.noreply.github.com>
Date: Wed, 27 Jan 2021 15:43:33 +0000
Subject: [PATCH 02/12] add pip install

---
 requirements.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements.txt b/requirements.txt
index 193df2c022..646fdfdbd5 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,3 +4,4 @@ autopep8
 jupytext
 autoflake
 ipykernel
+scikit-learn

From 12e76d946d501d675198e6a10768f261e12b0452 Mon Sep 17 00:00:00 2001
From: Richard Brown <33289025+rijobro@users.noreply.github.com>
Date: Wed, 27 Jan 2021 15:45:41 +0000
Subject: [PATCH 03/12] separate lines

---
 .github/workflows/pep8.yml | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pep8.yml b/.github/workflows/pep8.yml
index dc5853659b..eb36fdc815 100644
--- a/.github/workflows/pep8.yml
+++ b/.github/workflows/pep8.yml
@@ -34,9 +34,15 @@ jobs:
         python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/master/requirements-dev.txt
     - name: PEP8 check
       run: |
-        $(pwd)/runner.sh --no-run
+        git diff --name-only master | \
+          while read line; do 
+            [[ $line == *.ipynb ]] && ./runner.sh --file "$line" --no-run
+          done
     - name: Run changed files
       run: |
         python -c "import torch; print(torch.cuda.is_available())"
         git fetch origin master:master
-        git diff --name-only master | while read line; do [[ $line == *.ipynb ]] && ./runner.sh --file "$line" --no-checks; done
+        git diff --name-only master | \
+          while read line; do
+            [[ $line == *.ipynb ]] && ./runner.sh --file "$line" --no-checks
+          done

From 5d3f609aabbc6fc74672b8d20b068413ca701bdd Mon Sep 17 00:00:00 2001
From: Richard Brown <33289025+rijobro@users.noreply.github.com>
Date: Wed, 27 Jan 2021 15:48:26 +0000
Subject: [PATCH 04/12] cancel workflows and pip install monai-weekly

---
 .github/workflows/cleanup.yml | 20 ++++++++++++++++++++
 .github/workflows/pep8.yml    |  1 +
 2 files changed, 21 insertions(+)
 create mode 100644 .github/workflows/cleanup.yml

diff --git a/.github/workflows/cleanup.yml b/.github/workflows/cleanup.yml
new file mode 100644
index 0000000000..d30caf36b1
--- /dev/null
+++ b/.github/workflows/cleanup.yml
@@ -0,0 +1,20 @@
+name: cleanup-workflow
+
+on:
+  workflow_run:
+    workflows:
+      - "build"
+    types: ["requested"]
+
+jobs:
+  cancel-duplicated-workflow:
+    name: "Cancel duplicated workflow"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: potiuk/cancel-workflow-runs@953e057dc81d3458935a18d1184c386b0f6b5738 # tested
+        name: "Cancel duplicate workflows"
+        with:
+          cancelMode: allDuplicates
+          token: ${{ secrets.GITHUB_TOKEN }}
+          sourceRunId: ${{ github.event.workflow_run.id }}
+          skipEventTypes: '["schedule"]'
\ No newline at end of file
diff --git a/.github/workflows/pep8.yml b/.github/workflows/pep8.yml
index eb36fdc815..8b59821684 100644
--- a/.github/workflows/pep8.yml
+++ b/.github/workflows/pep8.yml
@@ -30,6 +30,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip wheel
         python -m pip install -r requirements.txt
+        python -m pip install monai-weekly
         python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/master/requirements.txt
         python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/master/requirements-dev.txt
     - name: PEP8 check

From 1fab60602c68b25703c9f9f104dce7ab502a2a7c Mon Sep 17 00:00:00 2001
From: Richard Brown <33289025+rijobro@users.noreply.github.com>
Date: Wed, 27 Jan 2021 15:50:33 +0000
Subject: [PATCH 05/12] combine check and run

---
 .github/workflows/pep8.yml | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/pep8.yml b/.github/workflows/pep8.yml
index 8b59821684..05b2f79a70 100644
--- a/.github/workflows/pep8.yml
+++ b/.github/workflows/pep8.yml
@@ -33,17 +33,9 @@ jobs:
         python -m pip install monai-weekly
         python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/master/requirements.txt
         python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/master/requirements-dev.txt
-    - name: PEP8 check
+    - name: PEP8 check and execute
       run: |
         git diff --name-only master | \
           while read line; do 
-            [[ $line == *.ipynb ]] && ./runner.sh --file "$line" --no-run
-          done
-    - name: Run changed files
-      run: |
-        python -c "import torch; print(torch.cuda.is_available())"
-        git fetch origin master:master
-        git diff --name-only master | \
-          while read line; do
-            [[ $line == *.ipynb ]] && ./runner.sh --file "$line" --no-checks
+            [[ $line == *.ipynb ]] && ./runner.sh --file "$line"
           done

From 88be176e5494bb648131d89429f3b5998d6ed159 Mon Sep 17 00:00:00 2001
From: Richard Brown <33289025+rijobro@users.noreply.github.com>
Date: Wed, 27 Jan 2021 15:52:01 +0000
Subject: [PATCH 06/12] bug fix

---
 .github/workflows/pep8.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pep8.yml b/.github/workflows/pep8.yml
index 05b2f79a70..1040290c6a 100644
--- a/.github/workflows/pep8.yml
+++ b/.github/workflows/pep8.yml
@@ -35,7 +35,9 @@ jobs:
         python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/master/requirements-dev.txt
     - name: PEP8 check and execute
       run: |
+        python -c "import torch; print(torch.cuda.is_available())"
+        git fetch origin master:master
         git diff --name-only master | \
-          while read line; do 
+          while read line; do
             [[ $line == *.ipynb ]] && ./runner.sh --file "$line"
           done

From ab1995eb48ed2e150c5e4a1eacbd7dadfd5ca3f4 Mon Sep 17 00:00:00 2001
From: Richard Brown <33289025+rijobro@users.noreply.github.com>
Date: Wed, 27 Jan 2021 15:55:50 +0000
Subject: [PATCH 07/12] install master branch

---
 .github/workflows/pep8.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pep8.yml b/.github/workflows/pep8.yml
index 1040290c6a..278cb41999 100644
--- a/.github/workflows/pep8.yml
+++ b/.github/workflows/pep8.yml
@@ -30,7 +30,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip wheel
         python -m pip install -r requirements.txt
-        python -m pip install monai-weekly
+        BUILD_MONAI=1 python -m pip install git+https://github.com/Project-MONAI/MONAI#egg=MONAI
         python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/master/requirements.txt
         python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/master/requirements-dev.txt
     - name: PEP8 check and execute

From 835533eacdd1329453d1a2c27695c9ffa947ca6a Mon Sep 17 00:00:00 2001
From: Richard Brown <33289025+rijobro@users.noreply.github.com>
Date: Wed, 27 Jan 2021 15:56:39 +0000
Subject: [PATCH 08/12] remove cuda print

---
 .github/workflows/pep8.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pep8.yml b/.github/workflows/pep8.yml
index 278cb41999..735e9c1431 100644
--- a/.github/workflows/pep8.yml
+++ b/.github/workflows/pep8.yml
@@ -35,7 +35,7 @@ jobs:
         python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/master/requirements-dev.txt
     - name: PEP8 check and execute
       run: |
-        python -c "import torch; print(torch.cuda.is_available())"
+        # python -c "import torch; print(torch.cuda.is_available())"
         git fetch origin master:master
         git diff --name-only master | \
           while read line; do

From a02bc57f9a60fd18a0747ad1e134ea99257dba02 Mon Sep 17 00:00:00 2001
From: Richard Brown <33289025+rijobro@users.noreply.github.com>
Date: Thu, 19 May 2022 11:34:46 +0100
Subject: [PATCH 09/12] run modified notebooks

---
 .github/workflows/cleanup.yml | 20 --------------------
 .github/workflows/pep8.yml    | 11 +++++------
 requirements.txt              |  2 --
 3 files changed, 5 insertions(+), 28 deletions(-)
 delete mode 100644 .github/workflows/cleanup.yml

diff --git a/.github/workflows/cleanup.yml b/.github/workflows/cleanup.yml
deleted file mode 100644
index d30caf36b1..0000000000
--- a/.github/workflows/cleanup.yml
+++ /dev/null
@@ -1,20 +0,0 @@
-name: cleanup-workflow
-
-on:
-  workflow_run:
-    workflows:
-      - "build"
-    types: ["requested"]
-
-jobs:
-  cancel-duplicated-workflow:
-    name: "Cancel duplicated workflow"
-    runs-on: ubuntu-latest
-    steps:
-      - uses: potiuk/cancel-workflow-runs@953e057dc81d3458935a18d1184c386b0f6b5738 # tested
-        name: "Cancel duplicate workflows"
-        with:
-          cancelMode: allDuplicates
-          token: ${{ secrets.GITHUB_TOKEN }}
-          sourceRunId: ${{ github.event.workflow_run.id }}
-          skipEventTypes: '["schedule"]'
\ No newline at end of file
diff --git a/.github/workflows/pep8.yml b/.github/workflows/pep8.yml
index 735e9c1431..d71150de4f 100644
--- a/.github/workflows/pep8.yml
+++ b/.github/workflows/pep8.yml
@@ -4,7 +4,7 @@ on:
   # quick tests for every pull request
   push:
     branches:
-      - master
+      - main
   pull_request:
 
 jobs:
@@ -31,13 +31,12 @@ jobs:
         python -m pip install --upgrade pip wheel
         python -m pip install -r requirements.txt
         BUILD_MONAI=1 python -m pip install git+https://github.com/Project-MONAI/MONAI#egg=MONAI
-        python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/master/requirements.txt
-        python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/master/requirements-dev.txt
+        python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/main/requirements.txt
+        python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/main/requirements-dev.txt
     - name: PEP8 check and execute
       run: |
-        # python -c "import torch; print(torch.cuda.is_available())"
-        git fetch origin master:master
-        git diff --name-only master | \
+        git fetch origin main:main
+        git diff --name-only main | \
           while read line; do
             [[ $line == *.ipynb ]] && ./runner.sh --file "$line"
           done
diff --git a/requirements.txt b/requirements.txt
index ab0e6bdfb5..096c01c178 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,6 +3,4 @@ papermill
 autopep8
 jupytext
 autoflake
-ipykernel
-scikit-learn
 tensorboard>=2.4.0

From 5bdc2efea281fd4af3964bf108c2a8cc73a0c1b0 Mon Sep 17 00:00:00 2001
From: Wenqi Li <wenqil@nvidia.com>
Date: Tue, 11 Oct 2022 09:06:31 +0100
Subject: [PATCH 10/12] update runner

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
---
 .github/workflows/pep8.yml          | 24 +++++++++----------
 .github/workflows/test-modified.yml | 37 +++++++++++++++++++++++++++++
 2 files changed, 48 insertions(+), 13 deletions(-)
 create mode 100644 .github/workflows/test-modified.yml

diff --git a/.github/workflows/pep8.yml b/.github/workflows/pep8.yml
index d71150de4f..f33c3a3f41 100644
--- a/.github/workflows/pep8.yml
+++ b/.github/workflows/pep8.yml
@@ -8,12 +8,16 @@ on:
   pull_request:
 
 jobs:
-  build:
+  # caching of these jobs:
+  #   - docker-20-03-py3-pip- (shared)
+  #   - ubuntu py37 pip-
+  #   - os-latest-pip- (shared)
+  pep8:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version: 3.8
     - name: cache weekly timestamp
@@ -21,7 +25,7 @@ jobs:
       run: |
         echo "::set-output name=datew::$(date '+%Y-%V')"
     - name: cache for pip
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache
       with:
         path: ~/.cache/pip
@@ -29,14 +33,8 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip wheel
+        python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/dev/requirements-dev.txt
         python -m pip install -r requirements.txt
-        BUILD_MONAI=1 python -m pip install git+https://github.com/Project-MONAI/MONAI#egg=MONAI
-        python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/main/requirements.txt
-        python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/main/requirements-dev.txt
-    - name: PEP8 check and execute
+    - name: PEP8 check
       run: |
-        git fetch origin main:main
-        git diff --name-only main | \
-          while read line; do
-            [[ $line == *.ipynb ]] && ./runner.sh --file "$line"
-          done
+        $(pwd)/runner.sh --no-run
diff --git a/.github/workflows/test-modified.yml b/.github/workflows/test-modified.yml
new file mode 100644
index 0000000000..0a7ed6b910
--- /dev/null
+++ b/.github/workflows/test-modified.yml
@@ -0,0 +1,37 @@
+name: build
+
+on:
+  # quick tests of modified notebooks for every pull request
+  push:
+    branches:
+      - main
+      - update-runner
+  pull_request:
+
+concurrency:
+  # automatically cancel the previously triggered workflows when there's a newer version
+  group: build-gpu-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    if: github.repository == 'Project-MONAI/tutorials'
+    container:
+      image: nvcr.io/nvidia/pytorch:21.06-py3  # CUDA 11.3
+      options: "--gpus 0"
+    runs-on: [self-hosted, linux, x64]
+    steps:
+    - name: Install MONAI
+      id: monai-install
+      run: |
+        which python
+        python -m pip install --upgrade pip wheel
+        BUILD_MONAI=0 python -m pip install git+https://github.com/Project-MONAI/MONAI#egg=MONAI
+        python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/main/requirements-dev.txt
+    - uses: actions/checkout@v3
+    - name: Notebook quick check
+      shell: bash
+      run: |
+        git fetch origin main
+        git diff --name-only origin/main | while read line; do if [[ $line == *.ipynb ]]; then ./runner.sh --file "$line"; fi; done;
+          # [[ $line == *.ipynb ]] && ./runner.sh --file "$line"

From 3732c054acdad74d93a3043229c56e18570879c8 Mon Sep 17 00:00:00 2001
From: Wenqi Li <wenqil@nvidia.com>
Date: Tue, 11 Oct 2022 10:06:14 +0100
Subject: [PATCH 11/12] update

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
---
 .github/workflows/test-modified.yml      | 3 ++-
 modules/2d_slices_from_3d_training.ipynb | 2 +-
 runner.sh                                | 3 ++-
 3 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test-modified.yml b/.github/workflows/test-modified.yml
index 0a7ed6b910..17c45a5b78 100644
--- a/.github/workflows/test-modified.yml
+++ b/.github/workflows/test-modified.yml
@@ -33,5 +33,6 @@ jobs:
       shell: bash
       run: |
         git fetch origin main
-        git diff --name-only origin/main | while read line; do if [[ $line == *.ipynb ]]; then ./runner.sh --file "$line"; fi; done;
+        python -m pip install -r requirements.txt; python -m pip list
+        git diff --name-only origin/main | while read line; do if [[ $line == *.ipynb ]]; then ./runner.sh -p "-and -wholename './${line}'"; fi; done;
           # [[ $line == *.ipynb ]] && ./runner.sh --file "$line"
diff --git a/modules/2d_slices_from_3d_training.ipynb b/modules/2d_slices_from_3d_training.ipynb
index c99d58ffb4..a547dcbcf3 100644
--- a/modules/2d_slices_from_3d_training.ipynb
+++ b/modules/2d_slices_from_3d_training.ipynb
@@ -6,7 +6,7 @@
    "source": [
     "# Training with 2D slices from volumes\n",
     "\n",
-    "This tutorial shows how to train a network with 2D samples from 3D inputs.\n",
+    "This tutorial shows how to train a network with 2D slice samples from 3D inputs.\n",
     "\n",
     "It mainly demonstrates 2d slice dataset using `monai.data.PatchIterd` and `monai.data.GridPatchDataset`.\n",
     "\n",
diff --git a/runner.sh b/runner.sh
index 108c57330f..0c4db3be67 100755
--- a/runner.sh
+++ b/runner.sh
@@ -141,7 +141,8 @@ do
             failfast=true
         ;;
         -p|--pattern)
-            pattern="$2"
+            pattern+="$2"
+            echo $pattern
             shift
         ;;
         -k|--kernelspec)

From b771bd8536e9e3fb355db61ece5ddf375f83cb68 Mon Sep 17 00:00:00 2001
From: Wenqi Li <wenqil@nvidia.com>
Date: Tue, 11 Oct 2022 10:55:18 +0100
Subject: [PATCH 12/12] remove temp tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
---
 .github/workflows/test-modified.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/test-modified.yml b/.github/workflows/test-modified.yml
index 17c45a5b78..422e8e8526 100644
--- a/.github/workflows/test-modified.yml
+++ b/.github/workflows/test-modified.yml
@@ -5,7 +5,6 @@ on:
   push:
     branches:
       - main
-      - update-runner
   pull_request:
 
 concurrency: