update docker image to install required libraries

.devcontainer/postCreateCommand.sh

@@ -9,9 +9,9 @@ if [ -f "python/requirements.txt" ]; then
 fi
 
 # Install R dependencies
-if [ -f "r/install_packages.R" ]; then
-    Rscript r/install_packages.R
-fi
+#if [ -f "r/install_packages.R" ]; then
+#    Rscript r/install_packages.R
+#fi
 
 # This may be done by the user
 # Set up renv for R
@@ -20,8 +20,9 @@ fi
 #fi
 
 # change the default working directory for RStudio
-echo "session-default-working-dir=${CODESPACE_VSCODE_FOLDER}" >> /etc/rstudio/rsession.conf
+echo "session-default-working-dir=${CODESPACE_VSCODE_FOLDER}" | sudo tee -a /etc/rstudio/rsession.conf
 
-rstudio-server start && jupyter lab --ip=0.0.0.0 --no-browser --allow-root --NotebookApp.token=''
+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!"

.github/workflows/publish.yml

@@ -23,12 +23,12 @@ jobs:
 
     - name: Run Quarto in Docker container
       run: |
-        docker run --rm -v ${{ github.workspace }}:/workspace -w /workspace my-quarto-image bash -c "
+        docker run --rm -v ${{ github.workspace }}:/workspace -w /workspace demo-quarto-image bash -c "
           echo 'Creating gallery directory...'
           mkdir -p gallery && \
           echo 'gallery directory created.'
 
-          FOLDERS=(python, R)
+          FOLDERS=(python R)
           echo 'Folders to process: ${FOLDERS[@]}'
 
           for FOLDER in \"\${FOLDERS[@]}\"; do

Dockerfile

@@ -57,14 +57,19 @@ RUN dpkg -i quarto-1.5.57-linux-amd64.deb
 
 # Expose ports for RStudio (8787) and Jupyter (8888)
 
-#WORKDIR /workspaces
+WORKDIR /app
+
+COPY r /app/r
 
 EXPOSE 8787
 EXPOSE 8888
 
 # Install renv globally for all users
 RUN R -e "install.packages('renv', repos='https://cran.rstudio.com/')"
 
+# Install R packages
+RUN Rscript /app/r/install_packages.R
+
 # Add /usr/local/bin to the PATH for all users
 ENV PATH="/usr/local/bin:$PATH"