experimental r2u

.github/workflows/docker-rstudio.yml

@@ -0,0 +1,34 @@
+name: RStudio 
+on:
+  workflow_dispatch: null
+  push:
+    paths: ['images/*']
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions: write-all
+    steps:
+    # For biggish images, github actions runs out of disk space.
+    # So we cleanup some unwanted things in the disk image, and reclaim that space for our docker use
+    # https://github.com/actions/virtual-environments/issues/2606#issuecomment-772683150
+    # and https://github.com/easimon/maximize-build-space/blob/b4d02c14493a9653fe7af06cc89ca5298071c66e/action.yml#L104
+    # This gives us a total of about 52G of free space, which should be enough for now
+      - name: cleanup disk space
+        run: |
+          sudo rm -rf /usr/local/lib/android /usr/share/dotnet /opt/ghc
+          df -h
+      - uses: actions/checkout@v3
+      - name: Login to GitHub Container Registry
+        if: github.repository == 'boettiger-lab/k8s'
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{github.actor}}
+          password: ${{secrets.GITHUB_TOKEN}}
+      - name: Build the Docker image
+        if: github.repository == 'boettiger-lab/k8s'
+        run: docker build images/ --tag ghcr.io/boettiger-lab/k8s-r:latest
+      - name: Publish
+        if: github.repository == 'boettiger-lab/k8s'
+        run: docker push ghcr.io/boettiger-lab/k8s-r:latest
+

images/Dockerfile.R

@@ -0,0 +1,45 @@
+FROM quay.io/jupyter/pytorch-notebook:cuda12-ubuntu-24.04
+COPY jupyter-ai.yml environment.yml
+
+RUN conda update -n base -c conda-forge conda && \
+    conda env update --file environment.yml
+
+USER root
+RUN curl -fsSL https://code-server.dev/install.sh | sh && rm -rf .cache
+RUN git config --system pull.rebase false && \
+    echo '"\e[5~": history-search-backward' >> /etc/inputrc && \
+    echo '"\e[6~": history-search-forward' >> /etc/inputrc
+
+RUN usermod -a -G staff ${NB_USER} \
+  && echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
+  && locale-gen en_US.utf8 \
+  && /usr/sbin/update-locale LANG=en_US.UTF-8
+
+## Set some variables
+ENV LC_ALL en_US.UTF-8
+ENV LANG en_US.UTF-8
+ENV DEBIAN_FRONTEND noninteractive
+ENV TZ UTC
+
+RUN curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/refs/heads/master/inst/scripts/add_cranapt_noble.sh | sh
+RUN apt-get update && \
+  apt-get install -y --no-install-recommends \
+  r-base r-base-dev r-recommended \
+  r-cran-docopt r-cran-littler r-cran-remotes \
+  python3-dbus python3-gi python3-apt sudo \
+  && Rscript -e 'install.packages("bspm")'  \
+  ## Support user-level installation of R packages
+  && chown root:staff /usr/lib/R/site-library \
+  && chmod g+ws /usr/lib/R/site-library \
+  && echo "options(bspm.sudo = TRUE)" >> /usr/lib/R/etc/Rprofile.site
+
+## add user to sudoers
+RUN echo "${NB_USER} ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
+
+## RStudio
+RUN conda install jupyter-rsession-proxy
+COPY install_rstudio.sh install_rstudio.sh
+RUN bash install_rstudio.sh
+
+USER ${NB_USER}
+

images/install_rstudio.sh

@@ -0,0 +1,75 @@
+#!/bin/bash
+set -e
+
+RSTUDIO_VERSION=${1:-${RSTUDIO_VERSION:-"stable"}}
+DEFAULT_USER=${DEFAULT_USER:-"rstudio"}
+
+apt-get update && apt-get -y install \
+    ca-certificates \
+    gdebi-core \
+    git \
+    libclang-dev \
+    libssl-dev \
+    lsb-release \
+    psmisc \
+    pwgen \
+    sudo \
+    wget
+
+ARCH=$(dpkg --print-architecture)
+UBUNTU_CODENAME="noble"
+
+## Download RStudio Server for Ubuntu 18+
+DOWNLOAD_FILE=rstudio-server.deb
+
+if [ "$RSTUDIO_VERSION" = "latest" ]; then
+    RSTUDIO_VERSION="stable"
+fi
+
+if [ "$UBUNTU_CODENAME" = "focal" ]; then
+    UBUNTU_CODENAME="bionic"
+fi
+
+# TODO: remove this workaround for Ubuntu 24.04
+if [ "$UBUNTU_CODENAME" = "noble" ]; then
+    UBUNTU_CODENAME="jammy"
+fi
+
+if [ "$RSTUDIO_VERSION" = "stable" ] || [ "$RSTUDIO_VERSION" = "preview" ] || [ "$RSTUDIO_VERSION" = "daily" ]; then
+    if [ "$UBUNTU_CODENAME" = "bionic" ]; then
+        UBUNTU_CODENAME="focal"
+    fi
+    wget "https://rstudio.org/download/latest/${RSTUDIO_VERSION}/server/${UBUNTU_CODENAME}/rstudio-server-latest-${ARCH}.deb" -O "$DOWNLOAD_FILE"
+else
+    wget "https://download2.rstudio.org/server/${UBUNTU_CODENAME}/${ARCH}/rstudio-server-${RSTUDIO_VERSION/"+"/"-"}-${ARCH}.deb" -O "$DOWNLOAD_FILE" ||
+        wget "https://s3.amazonaws.com/rstudio-ide-build/server/${UBUNTU_CODENAME}/${ARCH}/rstudio-server-${RSTUDIO_VERSION/"+"/"-"}-${ARCH}.deb" -O "$DOWNLOAD_FILE"
+fi
+
+gdebi --non-interactive "$DOWNLOAD_FILE"
+rm "$DOWNLOAD_FILE"
+
+ln -fs /usr/lib/rstudio-server/bin/rstudio-server /usr/local/bin
+ln -fs /usr/lib/rstudio-server/bin/rserver /usr/local/bin
+
+# https://github.com/rocker-org/rocker-versioned2/issues/137
+rm -f /var/lib/rstudio-server/secure-cookie-key
+
+## RStudio wants an /etc/R, will populate from $R_HOME/etc
+mkdir -p /etc/R
+
+## Make RStudio compatible with case when R is built from source
+## (and thus is at /usr/local/bin/R), because RStudio doesn't obey
+## path if a user apt-get installs a package
+R_BIN="$(which R)"
+echo "rsession-which-r=${R_BIN}" >/etc/rstudio/rserver.conf
+## use more robust file locking to avoid errors when using shared volumes:
+echo "lock-type=advisory" >/etc/rstudio/file-locks
+
+## Prepare optional configuration file to disable authentication
+## To de-activate authentication, `disable_auth_rserver.conf` script
+## will just need to be overwrite /etc/rstudio/rserver.conf.
+## This is triggered by an env var in the user config
+cp /etc/rstudio/rserver.conf /etc/rstudio/disable_auth_rserver.conf
+echo "auth-none=1" >>/etc/rstudio/disable_auth_rserver.conf
+
+

jupyterhub/public-config.yaml

@@ -37,6 +37,8 @@ singleuser:
           # https://github.com/jupyterlab/jupyterlab/issues/11304#issuecomment-945466766
           ContentsManager:
             allow_hidden: true
+          FileContentsManager:
+            always_delete_dir: true
   profileList:
     - display_name: "CPU"
       slug: rocker