add misiing libraries

InstituteforDiseaseModeling · Sep 26, 2024 · fa2564f · fa2564f
1 parent 0f5c234
commit fa2564f
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Showing 3 changed files with 36 additions and 8 deletions.
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -21,16 +21,22 @@ jobs:
       run: |
         docker build -t demo-quarto-image .
 
+    - name: Create gallery directory on the host
+      run: |
+        echo 'Creating gallery directory...'
+        mkdir -p gallery && chmod -R 777 gallery
+        echo 'gallery directory created.'
+
     - name: Run Quarto in Docker container
       run: |
         docker run --rm -v ${{ github.workspace }}:/workspace -w /workspace demo-quarto-image bash -c "
-          echo 'Creating gallery directory...'
-          mkdir -p gallery && chmod -R 777 gallery && \
-          echo 'gallery directory created.'
-          
+        
           source /opt/venv/bin/activate
           echo 'activated virtualenv.'
           
+          ./r/install_quarto_extensions.expect
+          quarto list extensions
+          
           FOLDERS=(python r)
           echo 'Folders to process: \${FOLDERS[@]}'
 
@@ -58,7 +64,6 @@ jobs:
             done
           done"
 
-
     - name: Generate Index HTML
       run: |
         echo "<html><body><h1>Gallery Index</h1><ul>" > gallery/index.html
@@ -69,10 +74,10 @@ jobs:
         echo "</ul></body></html>" >> gallery/index.html
         
     - name: Upload HTML output
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: gallery
-        path: gallery
+        path: gallery/
 
     - name: Set up Git user
       run: |

diff --git a/r/install_packages.R b/r/install_packages.R
@@ -11,7 +11,8 @@ pkgnames <- c(
 'devtools', 'DT', 'languageserver', 'styler', 'httpgd',
 'shiny', 'shinyjs', 'shinyalert', 'shinyWidgets', 'shinythemes', 'shinycssloaders', 'shinyBS', 'shinylive',
 'dplyr','ggplot2', 'plotly', 'tidyr', 'stringr', 'logr', 'tidyverse', 
-'knitr', 'rmarkdown'
+'knitr', 'rmarkdown',
+"leaflet", "leaflet.extras"
 )
 
 print(paste0("Install Packages from Cran : ", pkgnames))

diff --git a/r/install_quarto_extensions.expect b/r/install_quarto_extensions.expect
@@ -0,0 +1,22 @@
+#!/usr/bin/expect
+
+# Start the quarto command
+spawn quarto install extension quarto-ext/shinylive
+
+# Look for the prompt and send "y"
+expect "*Do you trust the authors of this extension*" {
+    send "Y\r"; exp_continue
+}
+
+# Expect the second prompt and send "y" again
+expect "*Would you like to continue*" {
+    send "Y\r"; exp_continue
+}
+
+# Expect the third prompt and send "y"
+expect "*View documentation using default browser?*" {
+    send "n\r";
+}
+
+# Wait for the process to finish
+expect eof