run modified notebooks (#117)

Author: rijobro

.github/workflows/pep8.yml

@@ -15,24 +15,25 @@ jobs:
   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
       id: pip-cache
       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
         key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
     - 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
     - name: PEP8 check
       run: |

.github/workflows/test-modified.yml

@@ -0,0 +1,37 @@
+name: build
+
+on:
+  # quick tests of modified notebooks for every pull request
+  push:
+    branches:
+      - main
+  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
+        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"

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",

runner.sh

@@ -141,7 +141,8 @@ do
             failfast=true
         ;;
         -p|--pattern)
-            pattern="$2"
+            pattern+="$2"
+            echo $pattern
             shift
         ;;
         -k|--kernelspec)