ignore deleted files for conversion to ipynb

Author: cbielow

.github/workflows/test-pr.yaml

@@ -1,60 +1,60 @@
-name: Build and Test code in notebooks
-
-on:
-  pull_request:
-    branches:
-      - master
-
-jobs:
-
-  build-test:
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v3
-
-    - uses: actions/setup-python@v4
-      with:
-        python-version: '3.10' # Version range or exact version of a Python version to use, using SemVer's version range syntax    
-
-    - name: Get changed files
-      id: changed-files
-      uses: tj-actions/changed-files@v41
-      with:
-          dir_names_max_depth: 0
-          files: |
-            docs/source/*.rst
-            docs/source/**/*.rst
-            !docs/source/**/_templates
-      
-    - uses: r-lib/actions/setup-pandoc@v2
-      with:
-        pandoc-version: '3.1.2'
-
-#    - uses: actions/setup-python@v4
-#      with:
-#        python-version: '3.7' # Version range or exact version of a Python version to use, using SemVer's version range syntax
-        
-    - name: Installing Dependencies
-      run: |
-        python3 -m pip install --upgrade pip
-        python3 -m pip install --upgrade pandocfilters jupyter
-        python3 -m pip install --upgrade -r requirements.txt
-
-    
-    - name: Generating notebooks
-      run: |
-        pushd docs/source
-          ./generate_ipynb.sh
-        popd
-
-    - name: Execute all notebooks generated from modified files
-      run: |
-        for file in ${{ steps.changed-files.outputs.all_modified_files }}; do
-          jupyter nbconvert --to notebook --inplace --execute ${file%.rst}.ipynb || (echo "${file%.rst}" >> failed_nbs.txt)
-        done
-        if [ -f "failed_nbs.txt" ]; then
-          echo "Some notebooks failed to run. Please check logs."
-          cat failed_nbs.txt
-          exit 1
-        fi
+name: Build and Test code in notebooks
+
+on:
+  pull_request:
+    branches:
+      - master
+
+jobs:
+
+  build-test:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.10' # Version range or exact version of a Python version to use, using SemVer's version range syntax    
+
+    - name: Get changed files
+      id: changed-files
+      uses: tj-actions/changed-files@v45
+      with:
+          dir_names_max_depth: 0
+          files: |
+            docs/source/*.rst
+            docs/source/**/*.rst
+            !docs/source/**/_templates
+      
+    - uses: r-lib/actions/setup-pandoc@v2
+      with:
+        pandoc-version: '3.1.2'
+
+#    - uses: actions/setup-python@v4
+#      with:
+#        python-version: '3.7' # Version range or exact version of a Python version to use, using SemVer's version range syntax
+        
+    - name: Installing Dependencies
+      run: |
+        python3 -m pip install --upgrade pip
+        python3 -m pip install --upgrade pandocfilters jupyter
+        python3 -m pip install --upgrade -r requirements.txt
+
+    
+    - name: Generating notebooks
+      run: |
+        pushd docs/source
+          ./generate_ipynb.sh
+        popd
+
+    - name: Execute all notebooks generated from modified files
+      run: |
+        for file in ${{ steps.changed-files.outputs.all_changed_files }}; do
+          jupyter nbconvert --to notebook --inplace --execute ${file%.rst}.ipynb || (echo "${file%.rst}" >> failed_nbs.txt)
+        done
+        if [ -f "failed_nbs.txt" ]; then
+          echo "Some notebooks failed to run. Please check logs."
+          cat failed_nbs.txt
+          exit 1
+        fi