Update ci_build_merge_manual.yml

.github/workflows/ci_build_merge_manual.yml

@@ -113,27 +113,35 @@ jobs:
           git config pull.rebase false
           git config --global user.name "GitHub Actions"
           git config --global user.email "[email protected]"
-
+  
       - name: Replace files with the executed notebooks
         run: |
           git fetch --all
-          for branch in $(git branch -r | grep 'storage-' | sed 's/origin\///'); do
-            echo "Replacing files in gh-storage with the ones from $branch"
-            git fetch origin $branch
-            git checkout $branch -- .
-            git commit -am "Replaced executed notebook ${{ matrix.notebook }} from $branch" || echo "No changes to commit for ${{ matrix.notebook }}"
-          done
-  
-      - name: Push changes to gh-storage
-        run: |
-          git push origin gh-storage --force
-  
-      - name: Delete unique branches
-        run: |
-          git fetch --prune
-          for branch in $(git branch -r | grep 'storage-' | sed 's/origin\///'); do
-            git push origin --delete $branch
+          BRANCHES=$(git branch -r | grep 'storage-' | sed 's/origin\///')
+          for BRANCH in $BRANCHES; do
+            # Extract the notebook path from the branch name
+            NOTEBOOK=$(echo $BRANCH | sed 's/storage-[0-9]*-//; s/_/\//g')
+            echo "Replacing file in gh-storage with the one from $BRANCH"
+            git fetch origin $BRANCH
+            git checkout "origin/$BRANCH" -- "$NOTEBOOK"
+            # If the notebook exists and was checked out, commit it to gh-storage
+            if [ -f "$NOTEBOOK" ]; then
+              git add "$NOTEBOOK"
+              git commit -m "Update executed notebook from $BRANCH" -- "$NOTEBOOK"
+              # Push the change to the gh-storage branch
+              git push origin gh-storage
+            else
+              echo "Notebook file $NOTEBOOK was not found in $BRANCH."
+            fi
           done
+
+    - name: Delete unique branches
+      run: |
+        git fetch --prune
+        BRANCHES=$(git branch -r | grep 'storage-' | sed 's/origin\///')
+        for BRANCH in $BRANCHES; do
+          git push origin --delete $BRANCH
+        done
           
   generate_html:
     runs-on: ubuntu-latest