Merge pull request #160 from nmfs-opensci/eeholmes-patch-1

Update install-vscode-extensions.sh

appendix

@@ -55,6 +55,9 @@ RUN mkdir -p /pyrocket_scripts && cp -r ${REPO_DIR}/scripts/* /pyrocket_scripts/
 RUN chown -R root:staff /pyrocket_scripts && \
     chmod -R 775 /pyrocket_scripts
 
+# Debugging
+RUN /pyrocket_scripts/test.sh
+
 # Some basic VS Code extensions
 RUN /pyrocket_scripts/install-vscode-extensions.sh ${REPO_DIR}/vscode-extensions.txt
 

scripts/install-conda-packages.sh

@@ -16,6 +16,7 @@ fi
 
 # Main script execution as NB_USER
 echo "Running install-conda-packages.sh as ${NB_USER}"
+echo "NB_PYTHON_PREFIX: $NB_PYTHON_PREFIX, CONDA_ENV: $CONDA_ENV, CONDA_DIR: $CONDA_DIR"
 
 # Set the file variable to the provided argument
 ENV_FILE="$1"
@@ -58,15 +59,19 @@ if [ "$INSTALLATION_HAPPENED" = true ]; then
     # Updating the notebook environment sometimes gets rid of pip installed packages.
     # Make sure the core environment didn't get damaged.
     # Check if jupyterlab-quarto is installed, and reinstall if missing
-    if ! python -m pip show jupyterlab-quarto > /dev/null 2>&1; then
+    if ! ${NB_PYTHON_PREFIX}/bin/pip show jupyterlab-quarto > /dev/null 2>&1; then
         echo "  Reinstalling jupyterlab-quarto..."
-        python -m pip install jupyterlab-quarto
+        if ! ${NB_PYTHON_PREFIX}/bin/pip install jupyterlab-quarto; then
+           echo "  Error: Failed to reinstall jupyterlab-quarto. Continuing with the process." >&2
+        fi    
     fi
 
     # Check if jupyter-remote-desktop-proxy is installed, and reinstall if missing
-    if ! python -m pip show jupyter-remote-desktop-proxy > /dev/null 2>&1; then
+    if ! ${NB_PYTHON_PREFIX}/bin/pip show jupyter-remote-desktop-proxy > /dev/null 2>&1; then
         echo "  Reinstalling jupyter-remote-desktop-proxy..."
-        python -m pip install jupyter-remote-desktop-proxy
+        if ! ${NB_PYTHON_PREFIX}/bin/pip install jupyter-remote-desktop-proxy; then
+           echo "  Error: Failed to reinstall jupyter-remote-desktop-proxy. Continuing with the process." >&2
+        fi    
     fi
 fi
 

scripts/install-pip-packages.sh

@@ -16,7 +16,7 @@ fi
 
 # Main script execution as NB_USER
 echo "Running install-pip-packages.sh as ${NB_USER}"
-
+echo "NB_PYTHON_PREFIX: $NB_PYTHON_PREFIX, CONDA_ENV: $CONDA_ENV, CONDA_DIR: $CONDA_DIR"
 
 # Set variable for the provided file
 requirements_file="$1"

scripts/install-r-packages.sh

@@ -16,6 +16,7 @@ fi
 
 # Main script execution as NB_USER
 echo "Running install-r-packages.sh as ${NB_USER}"
+echo "Rscript location: $(which Rscript)"
 
 # Set the file variable to the provided argument
 INSTALL_FILE="$1"
@@ -29,7 +30,7 @@ fi
 
 echo "  Found file: $INSTALL_FILE"
 
-# Install R packages using the provided R script
+# Install R packages using the provided R script; should be /usr/local/bin/Rscript
 if ! Rscript "$INSTALL_FILE"; then
     echo "  Error: Installation of packages from '$INSTALL_FILE' failed. Please check the script for errors." >&2
     exit 1

scripts/install-vscode-extensions.sh

@@ -29,11 +29,9 @@ fi
 
 # Install each extension listed in the file
 while IFS= read -r EXT; do
-    if code-server --install-extension "$EXT"; then
+    if ${NB_PYTHON_PREFIX}/bin/code-server --install-extension "$EXT"; then
         echo "  Successfully installed extension: $EXT"
     else
         echo "  Failed to install extension: $EXT" >&2
     fi
 done < "$ext_file"
-
-echo "  Success! install-vscode-extensions.sh"

scripts/test.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+# Required User: NB_USER
+
+echo "user is root"
+echo "NB_PYTHON_PREFIX: $NB_PYTHON_PREFIX"
+echo "CONDA_ENV: $CONDA_ENV"
+echo "CONDA_DIR: $CONDA_DIR"
+
+# Check if running as root and switch to NB_USER if needed
+if [[ $(id -u) -eq 0 ]]; then
+    echo "Switching to ${NB_USER} to run install-conda-packages.sh"
+    exec su "${NB_USER}" -c "/bin/bash $0 $1"  # Pass along the filename argument
+fi
+
+echo "user is jovyan"
+echo "NB_PYTHON_PREFIX: $NB_PYTHON_PREFIX"
+echo "CONDA_ENV: $CONDA_ENV"
+echo "CONDA_DIR: $CONDA_DIR"