use utilities file

images/Dockerfile

@@ -1,8 +1,9 @@
 FROM quay.io/jupyter/minimal-notebook:ubuntu-24.04
 
-# persistent storage (e.g. code-server extensions)
+# Make code-server extensions etc persist to container, not hub
 ENV XDG_DATA_HOME=/opt/share
 
+# Python environment
 COPY jupyter-ai.yml environment.yml
 RUN conda update -n base -c conda-forge conda && \
     conda env update --file environment.yml
@@ -22,11 +23,8 @@ ENV PATH=$PATH:/usr/lib/rstudio-server/bin/quarto/bin
 # When run as root, install.r automagically handles any necessary apt-gets
 COPY install.r install.r
 RUN Rscript install.r
-
-## switch from BSPM to r-universe for user default 
+## switch from BSPM to r-universe for user default, only after BSPM does install.r! 
 COPY Rprofile /usr/lib/R/etc/Rprofile.site
 
 USER ${NB_USER}
 
-
-

images/install-utilities.sh

@@ -24,6 +24,8 @@ wget https://github.com/git-ecosystem/git-credential-manager/releases/download/v
 
 # ensure user owns all of /opt
 mkdir /opt/share && chown -R ${NB_USER}:users /opt/share
+
+# code-server (VSCode)
 curl -fsSL https://code-server.dev/install.sh | sh && rm -rf .cache 
 sudo -u ${NB_USER} echo "ms-python.python ms-toolsai.jupyter quarto.quarto" | xargs -n 1 code-server --install-extension