Mewu/fix issues (#2)

* change devcontainer path

* Ignore devcontainer folder changes

* use add to install in current location

* add more checks

* fix wrong arguments

* simplify the postXrate script

* adding docker build job

* workaround for extenion path and use prebuilt image to address slowness

* fix publish index link

* add some delay

* specify port

* use default option

.devcontainer/devcontainer.json

@@ -1,9 +1,10 @@
 {
     "name": "Python and R Dev Container",
-    "build": {
-        "dockerfile": "../Dockerfile",
-        "context": "."
-    },
+    "image": "mewu/data_access:latest",   // Use pre-built image
+//    "build": {
+//        "dockerfile": "../Dockerfile",
+//        "context": ".."
+//    },
     "customizations": {
         "vscode": {
             "extensions": [
@@ -25,15 +26,13 @@
 //    "source=${localWorkspaceFolder},target=/workspaces/${localWorkspaceFolder},type=bind,consistency=cached"
 //    ],
     "postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh",
-	"postStartCommand:": "rstudio-server restart && jupyter lab --ip=0.0.0.0 --no-browser --allow-root --NotebookApp.token=''",
+	"postStartCommand": "bash ./.devcontainer/postStartCommand.sh",
     "portsAttributes": {
         "8888": {
-            "label": "Jupyter Lab",
-            "onAutoForward": "always",
+            "label": "Jupyter Lab"
         },
         "8787": {
-          "label": "R studio",
-          "onAutoForward": "always"
+          "label": "R studio"
         }
     },
     "forwardPorts": [8787, 8888]

.devcontainer/postCreateCommand.sh

@@ -19,10 +19,4 @@ fi
 #    cd r && R -e 'renv::restore()'
 #fi
 
-# change the default working directory for RStudio
-echo "session-default-working-dir=${CODESPACE_VSCODE_FOLDER}" | sudo tee -a /etc/rstudio/rsession.conf
-
-rstudio-server start > rstudio_server.log 2>&1 &
-jupyter lab --ip=0.0.0.0 --no-browser --allow-root --NotebookApp.token='' 2>&1 &
-
 echo "Dev environment setup completed!"

.devcontainer/postStartCommand.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+
+# change the default working directory for RStudio
+echo "session-default-working-dir=${CODESPACE_VSCODE_FOLDER}" | sudo tee -a /etc/rstudio/rsession.conf
+
+# Start RStudio Server
+echo "Start R studeio Server"
+rstudio-server start > rstudio_server.log 2>&1 &
+sleep 5  # Give some time for the service to start
+if ! pgrep -x "rstudio-server" > /dev/null; then
+    echo "RStudio Server failed to start. Restarting..."
+    rstudio-server restart > rstudio_server.log 2>&1 &
+fi
+
+sleep 5
+echo "Setup Jupyter-lab"
+# Start Jupyter Lab
+jupyter lab --ip=0.0.0.0 --port=8888 --no-browser --allow-root --NotebookApp.token='' > jupyter_lab.log 2>&1 &
+sleep 5
+if ! pgrep -x "jupyter-lab" > /dev/null; then
+    echo "Jupyter Lab failed to start. Restarting..."
+    jupyter lab --ip=0.0.0.0 --port=8888 --no-browser --allow-root --NotebookApp.token='' > jupyter_lab.log 2>&1 &
+fi
+
+echo "Dev environment startup completed!"

.github/workflows/publish.yml

@@ -4,9 +4,8 @@ on:
   push:
     branches:
       - main
-  pull_request:
-    branches:
-      - main
+    paths-ignore:
+      - '.devcontainer/**'  
   workflow_dispatch: # Manual trigger
 
 jobs:
@@ -17,9 +16,9 @@ jobs:
     - name: Checkout repository
       uses: actions/checkout@v3
 
-    - name: Build Docker image
-      run: |
-        docker build -t demo-quarto-image .
+    # - name: Build Docker image
+    #   run: |
+    #     docker build -t demo-quarto-image .
 
     - name: Create gallery directory on the host
       run: |
@@ -29,7 +28,7 @@ jobs:
 
     - name: Run Quarto in Docker container
       run: |
-        docker run --rm -v ${{ github.workspace }}:/workspace -w /workspace demo-quarto-image bash -c "
+        docker run --rm -v ${{ github.workspace }}:/workspace -w /workspace mewu/data_access:latest bash -c "
         
           source /opt/venv/bin/activate
           echo 'activated virtualenv.'
@@ -52,6 +51,12 @@ jobs:
               echo \"Processing file: \$file\"
               # Remove the /workspace prefix from the file path
               relative_dir=\$(dirname \"\${file#'/workspace/'}\")
+        
+              # Install extension to the folder directly
+              pushd \$relative_dir
+              /workspace/r/install_quarto_extensions.expect
+              popd
+        
               target_dir=\"/workspace/gallery/\$relative_dir\"
               echo \"Creating target directory: \$target_dir\"
               mkdir -p \"\$target_dir\" && echo \"Directory \$target_dir created.\"
@@ -76,11 +81,11 @@ jobs:
       run: |
         ls -laR gallery
         echo "<html><body><h1>Gallery Index</h1><ul>" > gallery/index.html
-        find gallery -name "*.html" | while read -r file; do
+        find gallery -name "*.html" -not -name "index.html" | while read -r file; do
           # Remove the 'gallery/' prefix from the file path
           relative_path="${file#gallery/}"
           file_name=$(basename "$file")
-          echo "<li><a href=\"./$relative_path\">$file_name</a></li>" >> gallery/index.html
+          echo "<li><a href=\"./$relative_path\">$relative_path</a></li>" >> gallery/index.html
         done
         echo "</ul></body></html>" >> gallery/index.html
 
@@ -100,4 +105,4 @@ jobs:
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: ./gallery  # Path to the folder that you want to publish (the gallery folder)
-        publish_branch: docs  # The branch used for GitHub Pages
+        publish_branch: docs  # The branch used for GitHub Pages

.github/workflows/update_docker.yml

@@ -0,0 +1,33 @@
+name: update docker image
+
+on:
+  workflow_dispatch:
+   inputs:
+     tags:
+       description: 'image tags'
+       required: false
+       default: mewu/data_access:latest
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    environment: test
+    steps:
+      -
+        name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+      -
+        name: Login to Docker Hub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      -
+        name: Build and push
+        uses: docker/build-push-action@v6
+        with:
+          push: true
+          tags: ${{ github.event.inputs.tags }}

r/install_quarto_extensions.expect

@@ -1,7 +1,7 @@
 #!/usr/bin/expect
 
 # Start the quarto command
-spawn quarto install extension quarto-ext/shinylive
+spawn quarto add quarto-ext/shinylive
 
 # Look for the prompt and send "y"
 expect "*Do you trust the authors of this extension*" {