latest.Dockerfile

ARG BASE_IMAGE=debian
ARG BASE_IMAGE_TAG=12
ARG BUILD_ON_IMAGE=glcr.b-data.ch/r/ver
ARG R_VERSION
ARG CUDA_IMAGE_FLAVOR

ARG NB_USER=jovyan
ARG NB_UID=1000
ARG JUPYTERHUB_VERSION=5.2.1
ARG JUPYTERLAB_VERSION=4.3.5
ARG CODE_BUILTIN_EXTENSIONS_DIR=/opt/code-server/lib/vscode/extensions
ARG CODE_SERVER_VERSION=4.96.4
ARG RSTUDIO_VERSION
ARG NEOVIM_VERSION=0.10.4
ARG GIT_VERSION=2.48.1
ARG GIT_LFS_VERSION=3.6.1
ARG PANDOC_VERSION=3.4

FROM ${BUILD_ON_IMAGE}:${R_VERSION}${CUDA_IMAGE_FLAVOR:+-}${CUDA_IMAGE_FLAVOR} AS files

ARG RSTUDIO_VERSION

ARG NB_UID
ENV NB_GID=100

RUN mkdir /files

COPY assets /files
COPY conf/ipython /files
COPY conf/jupyter /files
COPY conf/jupyterlab /files
COPY conf/rstudio /files
COPY conf/shell /files
COPY conf${CUDA_IMAGE:+/cuda}/shell /files
COPY conf/user /files
COPY scripts /files

  ## Copy content of skel directory to backup
RUN cp -a /files/etc/skel/. /files/var/backups/skel \
  && chown -R ${NB_UID}:${NB_GID} /files/var/backups/skel \
  ## Copy custom fonts
  && mkdir -p /files/usr/local/share/jupyter/lab/static/assets \
  && cp -a /files/opt/code-server/src/browser/media/css \
    /files/usr/local/share/jupyter/lab/static/assets \
  && cp -a /files/opt/code-server/src/browser/media/fonts \
    /files/usr/local/share/jupyter/lab/static/assets \
  && mkdir -p /files/etc/rstudio/fonts \
  && cp "/files/opt/code-server/src/browser/media/fonts/MesloLGS NF Regular.woff" \
    "/files/etc/rstudio/fonts/MesloLGS NF.woff" \
  && cp "/files/opt/code-server/src/browser/media/fonts/MesloLGS NF Regular.woff2" \
    "/files/etc/rstudio/fonts/MesloLGS NF.woff2" \
  && if [ -n "${CUDA_VERSION}" ]; then \
    ## Use standard R terminal for CUDA images
    ## radian forces usage of /usr[/local]/bin/python
    sed -i 's|/usr/local/bin/radian|/usr/local/bin/R|g' \
      /files/var/backups/skel/.local/share/code-server/User/settings.json; \
    ## Use entrypoint of CUDA image
    mv /opt/nvidia/entrypoint.d /opt/nvidia/nvidia_entrypoint.sh \
      /files/usr/local/bin; \
    mv /files/usr/local/bin/start.sh \
      /files/usr/local/bin/entrypoint.d/99-start.sh; \
    mv /files/usr/local/bin/nvidia_entrypoint.sh \
      /files/usr/local/bin/start.sh; \
  fi \
  && if [ -z "${RSTUDIO_VERSION}" ]; then \
    rm -rf /files/etc/rstudio \
      /files/usr/local/bin/before-notebook.d/*-rstudio.sh \
      /files/var/backups/skel/.config; \
  fi \
  ## Ensure file modes are correct when using CI
  ## Otherwise set to 777 in the target image
  && find /files -type d -exec chmod 755 {} \; \
  && find /files -type f -exec chmod 644 {} \; \
  && find /files/usr/local/bin -type f -exec chmod 755 {} \; \
  && find /files/etc/profile.d -type f -exec chmod 755 {} \;

FROM glcr.b-data.ch/neovim/nvsi:${NEOVIM_VERSION} AS nvsi
FROM glcr.b-data.ch/git/gsi/${GIT_VERSION}/${BASE_IMAGE}:${BASE_IMAGE_TAG} AS gsi
FROM glcr.b-data.ch/git-lfs/glfsi:${GIT_LFS_VERSION} AS glfsi

FROM ${BUILD_ON_IMAGE}:${R_VERSION}${CUDA_IMAGE_FLAVOR:+-}${CUDA_IMAGE_FLAVOR} AS base

FROM ${BUILD_ON_IMAGE}:${R_VERSION}${CUDA_IMAGE_FLAVOR:+-}${CUDA_IMAGE_FLAVOR} AS base-rstudio

ARG RSTUDIO_VERSION

ENV RSTUDIO_VERSION=${RSTUDIO_VERSION}

## Connect to RStudio via unix socket
ENV JUPYTER_RSESSION_PROXY_USE_SOCKET=1

FROM base${RSTUDIO_VERSION:+-rstudio}

ARG NCPUS=1

ARG DEBIAN_FRONTEND=noninteractive

ARG BUILD_ON_IMAGE
ARG CUDA_IMAGE_FLAVOR
ARG NB_USER
ARG NB_UID
ARG JUPYTERHUB_VERSION
ARG JUPYTERLAB_VERSION
ARG CODE_BUILTIN_EXTENSIONS_DIR
ARG CODE_SERVER_VERSION
ARG NEOVIM_VERSION
ARG GIT_VERSION
ARG GIT_LFS_VERSION
ARG PANDOC_VERSION
ARG BUILD_START

ARG CODE_WORKDIR

ARG CUDA_IMAGE_LICENSE=${CUDA_VERSION:+"NVIDIA Deep Learning Container License"}
ARG IMAGE_LICENSE=${CUDA_IMAGE_LICENSE:-"MIT"}
ARG IMAGE_SOURCE=https://gitlab.b-data.ch/jupyterlab/r/docker-stack
ARG IMAGE_VENDOR="b-data GmbH"
ARG IMAGE_AUTHORS="Olivier Benz <olivier.benz@b-data.ch>"

LABEL org.opencontainers.image.licenses="$IMAGE_LICENSE" \
      org.opencontainers.image.source="$IMAGE_SOURCE" \
      org.opencontainers.image.vendor="$IMAGE_VENDOR" \
      org.opencontainers.image.authors="$IMAGE_AUTHORS"

ENV PARENT_IMAGE=${BUILD_ON_IMAGE}:${R_VERSION}${CUDA_IMAGE_FLAVOR:+-}${CUDA_IMAGE_FLAVOR} \
    NB_USER=${NB_USER} \
    NB_UID=${NB_UID} \
    JUPYTERHUB_VERSION=${JUPYTERHUB_VERSION} \
    JUPYTERLAB_VERSION=${JUPYTERLAB_VERSION} \
    CODE_SERVER_VERSION=${CODE_SERVER_VERSION} \
    NEOVIM_VERSION=${NEOVIM_VERSION} \
    GIT_VERSION=${GIT_VERSION} \
    GIT_LFS_VERSION=${GIT_LFS_VERSION} \
    PANDOC_VERSION=${PANDOC_VERSION} \
    BUILD_DATE=${BUILD_START}

ENV NB_GID=100

## Installing V8 on Linux, the alternative way
## https://ropensci.org/blog/2020/11/12/installing-v8
ENV DOWNLOAD_STATIC_LIBV8=1

## Disable prompt to install miniconda
ENV RETICULATE_MINICONDA_ENABLED=0

## Install Neovim
COPY --from=nvsi /usr/local /usr/local
## Install Git
COPY --from=gsi /usr/local /usr/local
## Install Git LFS
COPY --from=glfsi /usr/local /usr/local

USER root

RUN dpkgArch="$(dpkg --print-architecture)" \
  ## Unminimise if the system has been minimised
  && if [ $(command -v unminimize) ]; then \
    yes | unminimize; \
  fi \
  && apt-get update \
  && apt-get -y install --no-install-recommends \
    bash-completion \
    build-essential \
    curl \
    file \
    fontconfig \
    g++ \
    gcc \
    gfortran \
    gnupg \
    htop \
    info \
    jq \
    libclang-dev \
    man-db \
    nano \
    ncdu \
    procps \
    psmisc \
    screen \
    sudo \
    swig \
    tmux \
    vim-tiny \
    wget \
    zsh \
    ## Neovim: Additional runtime recommendations
    ripgrep \
    ## Git: Additional runtime dependencies
    libcurl3-gnutls \
    liberror-perl \
    ## Git: Additional runtime recommendations
    less \
    ssh-client \
  ## Python: Additional dev dependencies
  && if [ -z "$PYTHON_VERSION" ]; then \
    apt-get -y install --no-install-recommends \
      python3-dev \
      ## Install Python package installer
      ## (dep: python3-distutils, python3-setuptools and python3-wheel)
      python3-pip \
      ## Install venv module for python3
      python3-venv; \
    ## make some useful symlinks that are expected to exist
    ## ("/usr/bin/python" and friends)
    for src in pydoc3 python3 python3-config; do \
      dst="$(echo "$src" | tr -d 3)"; \
      if [ -s "/usr/bin/$src" ] && [ ! -e "/usr/bin/$dst" ]; then \
        ln -svT "$src" "/usr/bin/$dst"; \
      fi \
    done; \
  else \
    ## Force update pip, setuptools and wheel
    pip install --upgrade --force-reinstall \
      pip \
      setuptools \
      wheel; \
  fi \
  ## Install font MesloLGS NF
  && mkdir -p /usr/share/fonts/truetype/meslo \
  && curl -sL https://github.com/romkatv/powerlevel10k-media/raw/master/MesloLGS%20NF%20Regular.ttf -o "/usr/share/fonts/truetype/meslo/MesloLGS NF Regular.ttf" \
  && curl -sL https://github.com/romkatv/powerlevel10k-media/raw/master/MesloLGS%20NF%20Bold.ttf -o "/usr/share/fonts/truetype/meslo/MesloLGS NF Bold.ttf" \
  && curl -sL https://github.com/romkatv/powerlevel10k-media/raw/master/MesloLGS%20NF%20Italic.ttf -o "/usr/share/fonts/truetype/meslo/MesloLGS NF Italic.ttf" \
  && curl -sL https://github.com/romkatv/powerlevel10k-media/raw/master/MesloLGS%20NF%20Bold%20Italic.ttf -o "/usr/share/fonts/truetype/meslo/MesloLGS NF Bold Italic.ttf" \
  && fc-cache -fsv \
  ## Git: Set default branch name to main
  && git config --system init.defaultBranch main \
  ## Git: Store passwords for one hour in memory
  && git config --system credential.helper "cache --timeout=3600" \
  ## Git: Merge the default branch from the default remote when "git pull" is run
  && git config --system pull.rebase false \
  ## Install pandoc
  && curl -sLO https://github.com/jgm/pandoc/releases/download/${PANDOC_VERSION}/pandoc-${PANDOC_VERSION}-1-${dpkgArch}.deb \
  && dpkg -i pandoc-${PANDOC_VERSION}-1-${dpkgArch}.deb \
  && rm pandoc-${PANDOC_VERSION}-1-${dpkgArch}.deb \
  ## Delete potential user with UID 1000
  && if grep -q 1000 /etc/passwd; then \
    userdel --remove $(id -un 1000); \
  fi \
  ## Do not set user limits for sudo/sudo-i
  && sed -i 's/.*pam_limits.so/#&/g' /etc/pam.d/sudo \
  && if [ -f "/etc/pam.d/sudo-i" ]; then \
    sed -i 's/.*pam_limits.so/#&/g' /etc/pam.d/sudo-i; \
  fi \
  ## Add user
  && useradd -l -m -s $(which zsh) -N -u ${NB_UID} ${NB_USER} \
  ## Mark home directory as populated
  && touch /home/${NB_USER}/.populated \
  && chown ${NB_UID}:${NB_GID} /home/${NB_USER}/.populated \
  && chmod go+w /home/${NB_USER}/.populated \
  ## Create backup directory for home directory
  && mkdir -p /var/backups/skel \
  && chown ${NB_UID}:${NB_GID} /var/backups/skel \
  ## Install Tini
  && curl -sL https://github.com/krallin/tini/releases/download/v0.19.0/tini-${dpkgArch} -o /usr/local/bin/tini \
  && chmod +x /usr/local/bin/tini \
  ## Clean up
  && rm -rf /tmp/* \
  && rm -rf /var/lib/apt/lists/* \
    ${HOME}/.cache

ENV PATH=/opt/code-server/bin:$PATH \
    CS_DISABLE_GETTING_STARTED_OVERRIDE=1

## Install code-server
RUN mkdir /opt/code-server \
  && cd /opt/code-server \
  && curl -sL https://github.com/coder/code-server/releases/download/v${CODE_SERVER_VERSION}/code-server-${CODE_SERVER_VERSION}-linux-$(dpkg --print-architecture).tar.gz | tar zxf - --no-same-owner --strip-components=1 \
  ## Copy custom fonts
  && mkdir -p /opt/code-server/src/browser/media/fonts \
  && cp -a /usr/share/fonts/truetype/meslo/*.ttf /opt/code-server/src/browser/media/fonts \
  ## Include custom fonts
  && sed -i 's|</head>|	<link rel="preload" href="{{BASE}}/_static/src/browser/media/fonts/MesloLGS NF Regular.woff2" as="font" type="font/woff2" crossorigin="anonymous">\n	</head>|g' /opt/code-server/lib/vscode/out/vs/code/browser/workbench/workbench.html \
  && sed -i 's|</head>|	<link rel="preload" href="{{BASE}}/_static/src/browser/media/fonts/MesloLGS NF Italic.woff2" as="font" type="font/woff2" crossorigin="anonymous">\n	</head>|g' /opt/code-server/lib/vscode/out/vs/code/browser/workbench/workbench.html \
  && sed -i 's|</head>|	<link rel="preload" href="{{BASE}}/_static/src/browser/media/fonts/MesloLGS NF Bold.woff2" as="font" type="font/woff2" crossorigin="anonymous">\n	</head>|g' /opt/code-server/lib/vscode/out/vs/code/browser/workbench/workbench.html \
  && sed -i 's|</head>|	<link rel="preload" href="{{BASE}}/_static/src/browser/media/fonts/MesloLGS NF Bold Italic.woff2" as="font" type="font/woff2" crossorigin="anonymous">\n	</head>|g' /opt/code-server/lib/vscode/out/vs/code/browser/workbench/workbench.html \
  && sed -i 's|</head>|	<link rel="stylesheet" type="text/css" href="{{BASE}}/_static/src/browser/media/css/fonts.css">\n	</head>|g' /opt/code-server/lib/vscode/out/vs/code/browser/workbench/workbench.html \
  ## Install code-server extensions
  && cd /tmp \
  && curl -sLO https://dl.b-data.ch/vsix/piotrpalarz.vscode-gitignore-generator-1.0.3.vsix \
  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension piotrpalarz.vscode-gitignore-generator-1.0.3.vsix \
  && curl -sLO https://dl.b-data.ch/vsix/mutantdino.resourcemonitor-1.0.7.vsix \
  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension mutantdino.resourcemonitor-1.0.7.vsix \
  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension alefragnani.project-manager \
  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension GitHub.vscode-pull-request-github \
  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension GitLab.gitlab-workflow \
  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension ms-python.python \
  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension ms-toolsai.jupyter \
  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension christian-kohler.path-intellisense \
  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension eamodio.gitlens@11.7.0 \
  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension mhutchie.git-graph \
  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension redhat.vscode-yaml \
  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension grapecity.gc-excelviewer \
  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension editorconfig.editorconfig \
  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension DavidAnson.vscode-markdownlint \
  ## Create folders temp and tmp for Jupyter extension
  && cd /opt/code-server/lib/vscode/extensions/ms-toolsai.jupyter-* \
  && mkdir -m 1777 temp \
  && mkdir -m 1777 tmp \
  ## Clean up
  && rm -rf /tmp/* \
    ${HOME}/.config \
    ${HOME}/.local

## Install RStudio
RUN if [ -n "${RSTUDIO_VERSION}" ]; then \
    dpkgArch="$(dpkg --print-architecture)"; \
    . /etc/os-release; \
    apt-get update; \
    ## Install lsb-release
    if [ "$ID" = "debian" ]; then \
      dpkg --compare-versions "$VERSION_ID" lt "12"; \
      condDebian=$?; \
    fi; \
    if [ "$ID" = "ubuntu" ]; then \
      dpkg --compare-versions "$VERSION_ID" lt "23.04"; \
      condUbuntu=$?; \
    fi; \
    if [ "$condDebian" = "0" ]; then \
      curl -sL \
        http://mirrors.kernel.org/debian/pool/main/l/lsb-release-minimal/lsb-release_12.0-1_all.deb \
        -o lsb-release.deb; \
      dpkg -i lsb-release.deb; \
      rm lsb-release.deb; \
    elif [ "$condUbuntu" = "0" ]; then \
      curl -sL \
        http://mirrors.kernel.org/ubuntu/pool/main/l/lsb-release-minimal/lsb-release_12.0-2_all.deb \
        -o lsb-release.deb; \
      dpkg -i lsb-release.deb; \
      rm lsb-release.deb; \
    else \
      apt-get -y install --no-install-recommends lsb-release; \
    fi; \
    ## Map Ubuntu codename
    if [ "$ID" = "debian" ]; then \
      case "$VERSION_CODENAME" in \
        bullseye) UBUNTU_CODENAME="focal" ;; \
        bookworm) UBUNTU_CODENAME="jammy" ;; \
        *) echo "error: Debian $VERSION unsupported"; exit 1 ;; \
      esac; \
    fi; \
    ## Install RStudio
    apt-get -y install --no-install-recommends \
      libapparmor1 \
      libpq5 \
      libssl-dev; \
    rm -rf /var/lib/apt/lists/*; \
    DOWNLOAD_FILE=rstudio-server-$(echo $RSTUDIO_VERSION | tr + -)-$dpkgArch.deb; \
    wget --progress=dot:mega \
      "https://download2.rstudio.org/server/$UBUNTU_CODENAME/$dpkgArch/$DOWNLOAD_FILE" || \
      wget --progress=dot:mega \
      "https://s3.amazonaws.com/rstudio-ide-build/server/$UBUNTU_CODENAME/$dpkgArch/$DOWNLOAD_FILE"; \
    dpkg -i "$DOWNLOAD_FILE"; \
    rm "$DOWNLOAD_FILE"; \
    ## Enable rstudio-server and rserver system-wide
    ln -fs /usr/lib/rstudio-server/bin/rstudio-server /usr/local/bin; \
    ln -fs /usr/lib/rstudio-server/bin/rserver /usr/local/bin; \
    ## Copy custom fonts
    cp "/opt/code-server/src/browser/media/fonts/MesloLGS NF Regular.ttf" \
      "/etc/rstudio/fonts/MesloLGS NF.ttf"; \
  fi

## Install JupyterLab
RUN export PIP_BREAK_SYSTEM_PACKAGES=1 \
  && pip install \
    jupyter-server-proxy \
    jupyterhub==${JUPYTERHUB_VERSION} \
    jupyterlab==${JUPYTERLAB_VERSION} \
    jupyterlab-git \
    jupyterlab-lsp \
    notebook \
    nbclassic \
    nbconvert \
    python-lsp-server[all] \
    ${RSTUDIO_VERSION:+jupyter-rsession-proxy} \
  ## Jupyter Server Proxy: Set maximum allowed HTTP body size to 10 GiB
  && sed -i 's/AsyncHTTPClient(/AsyncHTTPClient(max_body_size=10737418240, /g' \
    /usr/local/lib/python*/*-packages/jupyter_server_proxy/handlers.py \
  ## Jupyter Server Proxy: Set maximum allowed websocket message size to 1 GiB
  && sed -i 's/"_default_max_message_size",.*$/"_default_max_message_size", 1024 \* 1024 \* 1024/g' \
    /usr/local/lib/python*/*-packages/jupyter_server_proxy/websocket.py \
  && sed -i 's/_default_max_message_size =.*$/_default_max_message_size = 1024 \* 1024 \* 1024/g' \
    /usr/local/lib/python*/*-packages/tornado/websocket.py \
  ## Copy custom fonts
  && mkdir -p /usr/local/share/jupyter/lab/static/assets/fonts \
  && cp -a /usr/share/fonts/truetype/meslo/*.ttf /usr/local/share/jupyter/lab/static/assets/fonts \
  ## Include custom fonts
  && sed -i 's|</head>|<link rel="preload" href="{{page_config.fullStaticUrl}}/assets/fonts/MesloLGS NF Regular.woff2" as="font" type="font/woff2" crossorigin="anonymous"></head>|g' /usr/local/share/jupyter/lab/static/index.html \
  && sed -i 's|</head>|<link rel="preload" href="{{page_config.fullStaticUrl}}/assets/fonts/MesloLGS NF Italic.woff2" as="font" type="font/woff2" crossorigin="anonymous"></head>|g' /usr/local/share/jupyter/lab/static/index.html \
  && sed -i 's|</head>|<link rel="preload" href="{{page_config.fullStaticUrl}}/assets/fonts/MesloLGS NF Bold.woff2" as="font" type="font/woff2" crossorigin="anonymous"></head>|g' /usr/local/share/jupyter/lab/static/index.html \
  && sed -i 's|</head>|<link rel="preload" href="{{page_config.fullStaticUrl}}/assets/fonts/MesloLGS NF Bold Italic.woff2" as="font" type="font/woff2" crossorigin="anonymous"></head>|g' /usr/local/share/jupyter/lab/static/index.html \
  && sed -i 's|</head>|<link rel="stylesheet" type="text/css" href="{{page_config.fullStaticUrl}}/assets/css/fonts.css"></head>|g' /usr/local/share/jupyter/lab/static/index.html \
  ## Clean up
  && rm -rf /tmp/* \
    ${HOME}/.cache

## Install R related stuff
RUN apt-get update \
  && apt-get -y install --no-install-recommends \
    ## Current ZeroMQ library for R pbdZMQ
    libzmq3-dev \
    ## Required for R extension
    libcairo2-dev \
    libcurl4-openssl-dev \
    libfontconfig1-dev \
    libssl-dev \
    libtiff-dev \
    libxml2-dev \
  ## Install radian
  && export PIP_BREAK_SYSTEM_PACKAGES=1 \
  && pip install radian \
  ## Provide NVBLAS-enabled radian_
  ## Enabled at runtime and only if nvidia-smi and at least one GPU are present
  && if [ ! -z "$CUDA_IMAGE" ]; then \
    nvblasLib="$(cd $CUDA_HOME/lib* && ls libnvblas.so* | head -n 1)"; \
    cp -a $(which radian) $(which radian)_; \
    echo '#!/bin/bash' > $(which radian)_; \
    echo "command -v nvidia-smi >/dev/null && nvidia-smi -L | grep 'GPU[[:space:]]\?[[:digit:]]\+' >/dev/null && export LD_PRELOAD=$nvblasLib" \
      >> $(which radian)_; \
    echo "$(which radian) \"\${@}\"" >> $(which radian)_; \
  fi \
  ## Install the R kernel for Jupyter, languageserver and httpgd
  && install2.r --error --deps TRUE --skipinstalled -n $NCPUS \
    IRkernel \
    languageserver \
    httpgd \
  && Rscript -e "IRkernel::installspec(user = FALSE, displayname = paste('R', Sys.getenv('R_VERSION')))" \
  ## Get rid of libcairo2-dev and its dependencies (incl. python3)
  && apt-get -y purge libcairo2-dev \
  && apt-get -y autoremove \
  ## IRkernel: Enable 'image/svg+xml' instead of 'image/png' for plot display
  ## IRkernel: Enable 'application/pdf' for PDF conversion
  && echo "options(jupyter.plot_mimetypes = c('text/plain', 'image/svg+xml', 'application/pdf'))" \
    >> $(R RHOME)/etc/Rprofile.site \
  ## IRkernel: Include user's private bin in PATH
  && echo "if (dir.exists(file.path(Sys.getenv('HOME'), 'bin')) &&" \
    >> $(R RHOME)/etc/Rprofile.site \
  && echo '  !grepl(file.path(Sys.getenv('\''HOME'\''), '\''bin'\''), Sys.getenv('\''PATH'\''))) {' \
    >> $(R RHOME)/etc/Rprofile.site \
  && echo "  Sys.setenv(PATH = paste(file.path(Sys.getenv('HOME'), 'bin'), Sys.getenv('PATH')," \
    >> $(R RHOME)/etc/Rprofile.site \
  && echo "    sep = .Platform\$path.sep))}" \
    >> $(R RHOME)/etc/Rprofile.site \
  && echo "if (dir.exists(file.path(Sys.getenv('HOME'), '.local', 'bin')) &&" \
    >> $(R RHOME)/etc/Rprofile.site \
  && echo '  !grepl(file.path(Sys.getenv('\''HOME'\''), '\''.local'\'', '\''bin'\''), Sys.getenv('\''PATH'\''))) {' \
    >> $(R RHOME)/etc/Rprofile.site \
  && echo "  Sys.setenv(PATH = paste(file.path(Sys.getenv('HOME'), '.local', 'bin'), Sys.getenv('PATH')," \
    >> $(R RHOME)/etc/Rprofile.site \
  && echo "    sep = .Platform\$path.sep))}" \
    >> $(R RHOME)/etc/Rprofile.site \
  ## Install code-server extension
  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension REditorSupport.r \
  ## REditorSupport.r: Disable help panel and revert to old behaviour
  && echo "options(vsc.helpPanel = FALSE)" >> $(R RHOME)/etc/Rprofile.site \
  ## Change ownership and permission of $(R RHOME)/etc/*.site
  && chown :"$NB_GID" "$(R RHOME)/etc" "$(R RHOME)/etc/"*.site \
  && chmod g+w "$(R RHOME)/etc" "$(R RHOME)/etc/"*.site \
  ## Strip libraries of binary packages installed from P3M
  && RLS=$(Rscript -e "cat(Sys.getenv('R_LIBS_SITE'))") \
  && strip ${RLS}/*/libs/*.so \
  ## Clean up
  && rm -rf /tmp/* \
    /var/lib/apt/lists/* \
    ${HOME}/.cache \
    ${HOME}/.config \
    ${HOME}/.ipython \
    ${HOME}/.local

## Switch back to ${NB_USER} to avoid accidental container runs as root
USER ${NB_USER}

ENV HOME=/home/${NB_USER} \
    CODE_WORKDIR=${CODE_WORKDIR:-/home/${NB_USER}/projects} \
    SHELL=/usr/bin/zsh \
    TERM=xterm-256color

WORKDIR ${HOME}

## Install Oh My Zsh with Powerlevel10k theme
RUN sh -c "$(curl -fsSL https://raw.githubusercontent.com/ohmyzsh/ohmyzsh/master/tools/install.sh)" "" --unattended \
  && git clone --depth=1 https://github.com/romkatv/powerlevel10k.git ${HOME}/.oh-my-zsh/custom/themes/powerlevel10k \
  && ${HOME}/.oh-my-zsh/custom/themes/powerlevel10k/gitstatus/install -f \
  && sed -i 's/ZSH="\/home\/jovyan\/.oh-my-zsh"/ZSH="$HOME\/.oh-my-zsh"/g' ${HOME}/.zshrc \
  && sed -i 's/ZSH_THEME="robbyrussell"/ZSH_THEME="powerlevel10k\/powerlevel10k"/g' ${HOME}/.zshrc \
  && echo "\n# set PATH so it includes user's private bin if it exists\nif [ -d \"\$HOME/bin\" ] && [[ \"\$PATH\" != *\"\$HOME/bin\"* ]] ; then\n    PATH=\"\$HOME/bin:\$PATH\"\nfi" | tee -a ${HOME}/.bashrc ${HOME}/.zshrc \
  && echo "\n# set PATH so it includes user's private bin if it exists\nif [ -d \"\$HOME/.local/bin\" ] && [[ \"\$PATH\" != *\"\$HOME/.local/bin\"* ]] ; then\n    PATH=\"\$HOME/.local/bin:\$PATH\"\nfi" | tee -a ${HOME}/.bashrc ${HOME}/.zshrc \
  && echo "\n# Update last-activity timestamps while in screen/tmux session\nif [ ! -z \"\$TMUX\" -o ! -z \"\$STY\" ] ; then\n    busy &\nfi" >> ${HOME}/.bashrc \
  && echo "\n# Update last-activity timestamps while in screen/tmux session\nif [ ! -z \"\$TMUX\" -o ! -z \"\$STY\" ] ; then\n    setopt nocheckjobs\n    busy &\nfi" >> ${HOME}/.zshrc \
  && echo "\n# To customize prompt, run \`p10k configure\` or edit ~/.p10k.zsh." >> ${HOME}/.zshrc \
  && echo "[[ ! -f ~/.p10k.zsh ]] || source ~/.p10k.zsh" >> ${HOME}/.zshrc \
  ## Create user's private bin
  && mkdir -p ${HOME}/.local/bin \
  ## Record population timestamp
  && date -uIseconds > ${HOME}/.populated \
  ## Create backup of home directory
  && cp -a ${HOME}/. /var/backups/skel

## Copy files as late as possible to avoid cache busting
COPY --from=files /files /
COPY --from=files /files/var/backups/skel ${HOME}

ARG JUPYTER_PORT=8888
ENV JUPYTER_PORT=${JUPYTER_PORT}

EXPOSE $JUPYTER_PORT

## Configure container startup
ENTRYPOINT ["tini", "-g", "--", "start.sh"]
CMD ["start-notebook.sh"]