Dockerfile

# Stage 1: Build stage
FROM ubuntu:22.04 AS build

USER root

### BASICS ###
# Technical Environment Variables
ENV \
    SHELL="/bin/bash" \
    HOME="/root"  \
    # Notebook server user: https://github.com/jupyter/docker-stacks/blob/master/base-notebook/Dockerfile#L33
    NB_USER="root" \
    USER_GID=0 \
    XDG_CACHE_HOME="/root/.cache/" \
    XDG_RUNTIME_DIR="/tmp" \
    DISPLAY=":1" \
    TERM="xterm" \
    DEBIAN_FRONTEND="noninteractive" \
    RESOURCES_PATH="/resources" \
    SSL_RESOURCES_PATH="/resources/ssl" \
    WORKSPACE_HOME="/workspace"

WORKDIR $HOME

# Make folders
RUN \
    mkdir $RESOURCES_PATH && chmod a+rwx $RESOURCES_PATH && \
    mkdir $WORKSPACE_HOME && chmod a+rwx $WORKSPACE_HOME && \
    mkdir $SSL_RESOURCES_PATH && chmod a+rwx $SSL_RESOURCES_PATH

# Layer cleanup script
COPY resources/scripts/clean-layer.sh  /usr/bin/clean-layer.sh
COPY resources/scripts/fix-permissions.sh  /usr/bin/fix-permissions.sh

# Make clean-layer and fix-permissions executable
RUN \
    chmod a+rwx /usr/bin/clean-layer.sh && \
    chmod a+rwx /usr/bin/fix-permissions.sh

# Generate and Set locals
# https://stackoverflow.com/questions/28405902/how-to-set-the-locale-inside-a-debian-ubuntu-docker-container#38553499
RUN \
    apt-get update && \
    apt-get install -y locales && \
    # install locales-all?
    sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen && \
    locale-gen && \
    dpkg-reconfigure --frontend=noninteractive locales && \
    update-locale LANG=en_US.UTF-8 && \
    # Cleanup
    clean-layer.sh

ENV LC_ALL="en_US.UTF-8" \
    LANG="en_US.UTF-8" \
    LANGUAGE="en_US:en"

# Install basics
RUN \
    apt-get update --fix-missing && \
    apt-get install -y sudo apt-utils && \
    apt-get upgrade -y && \
    apt-get update && \
    apt-get install -y --no-install-recommends \
        apt-transport-https \
        gnupg-agent \
        gpg-agent \
        gnupg2 \
        ca-certificates \
        build-essential \
        pkg-config \
        software-properties-common \
        lsof \
        net-tools \
        libcurl4 \
        curl \
        wget \
        cron \
        openssl \
        iproute2 \
        psmisc \
        tmux \
        dpkg-sig \
        uuid-dev \
        csh \
        xclip \
        clinfo \
        time \
        libssl-dev \
        libgdbm-dev \
        libncurses5-dev \
        libncursesw5-dev \
        libreadline-dev \
        libedit-dev \
        xz-utils \
        gawk \
        swig \
        graphviz \
        libgraphviz-dev \
        screen \
        nano \
        locate \
        sqlite3 \
        xmlstarlet \
        parallel \
        libspatialindex-dev \
        yara \
        libhiredis-dev \
        libpq-dev \
        libmysqlclient-dev \
        libleptonica-dev \
        libgeos-dev \
        less \
        tree \
        bash-completion \
        iputils-ping \
        socat \
        jq \
        rsync \
        libsqlite3-dev \
        git \
        subversion \
        jed \
        unixodbc \
        unixodbc-dev \
        libtiff-dev \
        libjpeg-dev \
        libpng-dev \
        libglib2.0-0 \
        libxext6 \
        libsm6 \
        libxext-dev \
        libxrender1 \
        libzmq3-dev \
        protobuf-compiler \
        libprotobuf-dev \
        libprotoc-dev \
        autoconf \
        automake \
        libtool \
        cmake  \
        fonts-liberation \
        google-perftools \
        zip \
        gzip \
        unzip \
        bzip2 \
        lzop \
        libarchive-tools \
        unp \
        libbz2-dev \
        liblzma-dev \
        zlib1g-dev && \
    add-apt-repository -y ppa:git-core/ppa && \
    apt-get update && \
    apt-get install -y --no-install-recommends git && \
    chmod -R a+rwx /usr/local/bin/ && \
    ldconfig && \
    fix-permissions.sh $HOME && \
    clean-layer.sh

# Add tini
RUN wget --no-verbose https://github.com/krallin/tini/releases/download/v0.19.0/tini -O /tini && \
    chmod +x /tini

# prepare ssh for inter-container communication for remote python kernel
RUN \
    apt-get update && \
    apt-get install -y --no-install-recommends \
        openssh-client \
        openssh-server \
        sslh \
        autossh \
        mussh && \
    chmod go-w $HOME && \
    mkdir -p $HOME/.ssh/ && \
    touch $HOME/.ssh/config  && \
    sudo chown -R $NB_USER:users $HOME/.ssh && \
    chmod 700 $HOME/.ssh && \
    printenv >> $HOME/.ssh/environment && \
    chmod -R a+rwx /usr/local/bin/ && \
    fix-permissions.sh $HOME && \
    clean-layer.sh

RUN \
    OPEN_RESTY_VERSION="1.19.3.2" && \
    mkdir $RESOURCES_PATH"/openresty" && \
    cd $RESOURCES_PATH"/openresty" && \
    apt-get update && \
    apt-get purge -y nginx nginx-common && \
    apt-get install -y libssl-dev libpcre3 libpcre3-dev apache2-utils && \
    wget --no-verbose https://openresty.org/download/openresty-$OPEN_RESTY_VERSION.tar.gz  -O ./openresty.tar.gz && \
    tar xfz ./openresty.tar.gz && \
    rm ./openresty.tar.gz && \
    cd ./openresty-$OPEN_RESTY_VERSION/ && \
    ./configure --with-http_stub_status_module --with-http_sub_module > /dev/null && \
    make -j2 > /dev/null && \
    make install > /dev/null && \
    mkdir -p /var/log/nginx/ && \
    touch /var/log/nginx/upstream.log && \
    cd $RESOURCES_PATH && \
    rm -r $RESOURCES_PATH"/openresty" && \
    chmod -R a+rwx $RESOURCES_PATH && \
    clean-layer.sh

ENV PATH=/usr/local/openresty/nginx/sbin:$PATH

COPY resources/nginx/lua-extensions /etc/nginx/nginx_plugins

### END BASICS ###

### RUNTIMES ###
# Install Miniconda: https://repo.continuum.io/miniconda/

ENV \
    CONDA_DIR=/opt/conda \
    CONDA_ROOT=/opt/conda \
    PYTHON_VERSION="3.10.4" \
    CONDA_PYTHON_DIR=/opt/conda/lib/python3.10 \
    MINICONDA_VERSION=4.10.3 \
    MINICONDA_MD5=122c8c9beb51e124ab32a0fa6426c656 \
    CONDA_VERSION=4.9.2

# Install a more recent version of Conda
RUN wget --no-verbose https://repo.anaconda.com/miniconda/Miniconda3-py38_${CONDA_VERSION}-Linux-x86_64.sh -O ~/miniconda.sh && \
    echo "${MINICONDA_MD5} *miniconda.sh" | md5sum -c - && \
    /bin/bash ~/miniconda.sh -b -p $CONDA_ROOT && \
    rm ~/miniconda.sh && \
    $CONDA_ROOT/bin/conda init bash && \
    export PATH=$CONDA_ROOT/bin:$PATH && \
    $CONDA_ROOT/bin/conda update -y conda && \
    $CONDA_ROOT/bin/conda install -y conda-build && \
    $CONDA_ROOT/bin/conda install -y python=${PYTHON_VERSION} && \
    ln -s $CONDA_ROOT/bin/python /usr/local/bin/python && \
    ln -s $CONDA_ROOT/bin/conda /usr/bin/conda && \
    $CONDA_ROOT/bin/conda install -y pip && \
    $CONDA_ROOT/bin/pip install --upgrade pip && \
    chmod -R a+rwx /usr/local/bin/

ENV PATH=$CONDA_ROOT/bin:$PATH
ENV RESOURCES_PATH=/opt/resources
ENV LD_LIBRARY_PATH=$CONDA_ROOT/lib

# Install pyenv to allow dynamic creation of python versions
RUN apt-get update && \
    apt-get install -y --no-install-recommends git libffi-dev && \
    git clone https://github.com/pyenv/pyenv.git $RESOURCES_PATH/.pyenv && \
    git clone https://github.com/pyenv/pyenv-virtualenv.git $RESOURCES_PATH/.pyenv/plugins/pyenv-virtualenv && \
    git clone https://github.com/pyenv/pyenv-doctor.git $RESOURCES_PATH/.pyenv/plugins/pyenv-doctor && \
    git clone https://github.com/pyenv/pyenv-update.git $RESOURCES_PATH/.pyenv/plugins/pyenv-update && \
    git clone https://github.com/pyenv/pyenv-which-ext.git $RESOURCES_PATH/.pyenv/plugins/pyenv-which-ext && \
    clean-layer.sh
    
# Add pyenv to path
ENV PATH=$RESOURCES_PATH/.pyenv/shims:$RESOURCES_PATH/.pyenv/bin:$PATH \
    PYENV_ROOT=$RESOURCES_PATH/.pyenv

# Install pipx
RUN pip install pipx && \
    python -m pipx ensurepath && \
    clean-layer.sh
ENV PATH=$HOME/.local/bin:$PATH

# Install node.js
RUN \
    apt-get update && \
    curl -sL https://deb.nodesource.com/setup_18.x | sudo -E bash - && \
    apt-get install -y nodejs && \
    rm -f /opt/conda/bin/node && ln -s /usr/bin/node /opt/conda/bin/node && \
    rm -f /opt/conda/bin/npm && ln -s /usr/bin/npm /opt/conda/bin/npm && \
    chmod a+rwx /usr/bin/node && \
    chmod a+rwx /usr/bin/npm && \
    mkdir -p /opt/node/bin && \
    ln -s /usr/bin/node /opt/node/bin/node && \
    ln -s /usr/bin/npm /opt/node/bin/npm && \
    /usr/bin/npm install -g npm && \
    /usr/bin/npm install -g yarn && \
    /usr/bin/npm install -g typescript && \
    /usr/bin/npm install -g webpack && \
    /usr/bin/npm install -g node-gyp && \
    /usr/bin/npm update -g && \
    clean-layer.sh

ENV PATH=/opt/node/bin:$PATH

### END RUNTIMES ###

### PROCESS TOOLS ###

# Install supervisor for process supervision
RUN \
    apt-get update && \
    mkdir -p /var/run/sshd && chmod 400 /var/run/sshd && \
    apt-get install -y --no-install-recommends rsyslog && \
    pipx install supervisor && \
    pipx inject supervisor supervisor-stdout && \
    mkdir -p /var/log/supervisor/ && \
    clean-layer.sh

### END PROCESS TOOLS ###

### GUI TOOLS ###

# Install xfce4 & gui tools
RUN \
    add-apt-repository -y ppa:xubuntu-dev/staging && \
    apt-get update && \
    apt-get install -y --no-install-recommends xfce4 && \
    apt-get install -y --no-install-recommends gconf2 && \
    apt-get install -y --no-install-recommends xfce4-terminal && \
    apt-get install -y --no-install-recommends xfce4-clipman && \
    apt-get install -y --no-install-recommends xterm && \
    apt-get install -y --no-install-recommends --allow-unauthenticated xfce4-taskmanager && \
    apt-get install -y --no-install-recommends xauth xinit dbus-x11 && \
    apt-get install -y --no-install-recommends gdebi && \
    apt-get install -y --no-install-recommends catfish && \
    apt-get install -y --no-install-recommends font-manager && \
    apt-get install -y thunar-vcs-plugin && \
    apt-get install -y --no-install-recommends libqt5concurrent5 libqt5widgets5 libqt5xml5 && \
    wget --no-verbose https://github.com/variar/klogg/releases/download/v20.12/klogg-20.12.0.813-Linux.deb -O $RESOURCES_PATH/klogg.deb && \
    dpkg -i $RESOURCES_PATH/klogg.deb && \
    rm $RESOURCES_PATH/klogg.deb && \
    apt-get install -y --no-install-recommends baobab && \
    apt-get install -y --no-install-recommends mousepad && \
    apt-get install -y --no-install-recommends vim && \
    apt-get install -y --no-install-recommends htop && \
    apt-get install -y p7zip p7zip-rar && \
    apt-get install -y --no-install-recommends thunar-archive-plugin && \
    apt-get install -y xarchiver && \
    apt-get install -y --no-install-recommends sqlitebrowser && \
    apt-get install -y --no-install-recommends nautilus && \
    apt-get install -y --no-install-recommends gigolo && \
    apt-get install -y --no-install-recommends gftp && \
    add-apt-repository -y ppa:saiarcot895/chromium-beta && \
    apt-get update && \
    apt-get install -y --no-install-recommends chromium-browser --no-install-recommends chromium-browser-l10n --no-install-recommends chromium-codecs-ffmpeg
    ln -s /usr/bin/chromium-browser /usr/bin/google-chrome && \
    apt-get purge -y pm-utils xscreensaver* && \
    apt-get remove -y app-install-data gnome-user-guide && \
    clean-layer.sh

ENV LD_LIBRARY_PATH=/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:$CONDA_ROOT/lib

# Install VNC
RUN \
    apt-get update  && \
    cd ${RESOURCES_PATH} && \
    wget -qO- https://sourceforge.net/projects/tigervnc/files/stable/1.11.0/tigervnc-1.11.0.x86_64.tar.gz/download | tar xz --strip 1 -C / && \
    mkdir -p ./novnc/utils/websockify && \
    wget -qO- https://github.com/novnc/noVNC/archive/v1.2.0.tar.gz | tar xz --strip 1 -C ./novnc && \
    wget -qO- https://github.com/novnc/websockify/archive/v0.9.0.tar.gz | tar xz --strip 1 -C ./novnc/utils/websockify && \
    chmod +x -v ./novnc/utils/*.sh && \
    mkdir -p $HOME/.vnc && \
    fix-permissions.sh ${RESOURCES_PATH} && \
    clean-layer.sh

# Install Web Tools - Offered via Jupyter Tooling Plugin
RUN curl -fsSL https://deb.nodesource.com/setup_14.x | bash - && \
    apt-get install -y nodejs

RUN node -v

## VS Code Server: https://github.com/codercom/code-server
COPY resources/tools/vs-code-server.sh $RESOURCES_PATH/tools/vs-code-server.sh
RUN \
    /bin/bash $RESOURCES_PATH/tools/vs-code-server.sh --install && \
    clean-layer.sh

## ungit
COPY resources/tools/ungit.sh $RESOURCES_PATH/tools/ungit.sh
RUN \
    /bin/bash $RESOURCES_PATH/tools/ungit.sh --install && \
    clean-layer.sh

## netdata
COPY resources/tools/netdata.sh $RESOURCES_PATH/tools/netdata.sh
RUN \
    /bin/bash $RESOURCES_PATH/tools/netdata.sh --install && \
    clean-layer.sh

## Glances webtool is installed in python section below via requirements.txt

## Filebrowser
COPY resources/tools/filebrowser.sh $RESOURCES_PATH/tools/filebrowser.sh
RUN \
    /bin/bash $RESOURCES_PATH/tools/filebrowser.sh --install && \
    clean-layer.sh

ARG ARG_WORKSPACE_FLAVOR="full"
ENV WORKSPACE_FLAVOR=$ARG_WORKSPACE_FLAVOR
# Install Firefox

COPY resources/tools/firefox.sh $RESOURCES_PATH/tools/firefox.sh

RUN \
    if [ "$WORKSPACE_FLAVOR" = "minimal" ]; then \
        exit 0 ; \
    fi && \
    /bin/bash $RESOURCES_PATH/tools/firefox.sh --install && \
    clean-layer.sh

### END GUI TOOLS ###

### DATA SCIENCE BASICS ###

## Python 3
# Data science libraries requirements
COPY resources/libraries ${RESOURCES_PATH}/libraries

# Install main data science libs
# Install main data science libs
RUN \
    ln -s -f $CONDA_ROOT/bin/python /usr/bin/python && \
    apt-get update && apt-get install -y --no-install-recommends \
        libopenmpi-dev \
        openmpi-bin \
        liblapack-dev \
        libatlas-base-dev \
        libeigen3-dev \
        libblas-dev \
        libhdf5-dev \
        libtbb-dev \
        libtesseract-dev \
        libopenexr-dev \
        libgomp1 && \
    pip install --upgrade pip && \
    conda config --system --set channel_priority strict && \
    if [ "$WORKSPACE_FLAVOR" = "minimal" ]; then \
        conda install -y --update-all "python=$PYTHON_VERSION" nomkl && \
        pip install --no-cache-dir -r ${RESOURCES_PATH}/libraries/requirements-minimal.txt && \
        fix-permissions.sh $CONDA_ROOT && \
        clean-layer.sh && \
        exit 0 ; \
    fi && \
    if [ "$WORKSPACE_FLAVOR" != "minimal" ]; then \
        conda install -y --update-all "python=$PYTHON_VERSION" mkl-service mkl && \
        conda install -y --freeze-installed \
            boost \
            mkl-include && \
        conda install -y -c mingfeima mkldnn && \
        conda install -y -c pytorch "pytorch==1.10.*" cpuonly && \
        conda install -y --freeze-installed \
            'ipython' \
            'notebook' \
            'jupyterlab' \
            'nbconvert' \
            'yarl' \
            'scipy' \
            'numpy' \
            scikit-learn \
            numexpr && \
        pip install --no-cache-dir -r ${RESOURCES_PATH}/libraries/requirements-light.txt && \
        fix-permissions.sh $CONDA_ROOT && \
        clean-layer.sh && \
        exit 0 ; \
    fi && \
    if [ "$WORKSPACE_FLAVOR" = "full" ]; then \
        conda install -y --freeze-installed \
            libjpeg-turbo && \
        conda install -y -c bioconda -c conda-forge snakemake-minimal && \
        conda install -y -c conda-forge mamba && \
        conda install -y --no-deps --freeze-installed faiss-cpu
        pip install --no-cache-dir --use-deprecated=legacy-resolver \
            -r ${RESOURCES_PATH}/libraries/requirements-full.txt && \
        python -m spacy download en ; \
    fi && \
    fix-permissions.sh $CONDA_ROOT && \
    clean-layer.sh && \
    apt-get clean && rm -rf /var/lib/apt/lists/*

# Fix conda version
RUN \
    rm -f /opt/conda/bin/node && ln -s /usr/bin/node /opt/conda/bin/node && \
    rm -f /opt/conda/bin/npm && ln -s /usr/bin/npm /opt/conda/bin/npm

### END DATA SCIENCE BASICS ###

### JUPYTER ###

COPY \
    resources/jupyter/start.sh \
    resources/jupyter/start-notebook.sh \
    resources/jupyter/start-singleuser.sh \
    /usr/local/bin/

# Configure Jupyter / JupyterLab
# Add as jupyter system configuration
COPY resources/jupyter/nbconfig /etc/jupyter/nbconfig
COPY resources/jupyter/jupyter_notebook_config.json /etc/jupyter/

# install jupyter extensions
RUN \
    mkdir -p $HOME/.jupyter/nbconfig/ && \
    printf "{\"load_extensions\": {}}" > $HOME/.jupyter/nbconfig/notebook.json && \
    jupyter contrib nbextension install --sys-prefix && \
    jupyter nbextensions_configurator enable --sys-prefix && \
    nbdime config-git --enable --global && \
    jupyter nbextension enable --py jupytext --sys-prefix && \
    jupyter nbextension enable skip-traceback/main --sys-prefix && \
    jupyter nbextension enable toc2/main --sys-prefix && \
    jupyter nbextension enable execute_time/ExecuteTime --sys-prefix && \
    jupyter nbextension enable collapsible_headings/main --sys-prefix && \
    jupyter nbextension enable codefolding/main --sys-prefix && \
    jupyter nbextension disable pydeck/extension && \
    pip install --no-cache-dir git+https://github.com/InfuseAI/jupyter_tensorboard.git && \
    jupyter tensorboard enable --sys-prefix && \
    cat $HOME/.jupyter/nbconfig/notebook.json | jq '.toc2={"moveMenuLeft": false,"widenNotebook": false,"skip_h1_title": false,"sideBar": true,"number_sections": false,"collapse_to_match_collapsible_headings": true}' > tmp.$$.json && mv tmp.$$.json $HOME/.jupyter/nbconfig/notebook.json && \
    if [ "$WORKSPACE_FLAVOR" = "minimal" ]; then \
        clean-layer.sh && \
        exit 0 ; \
    fi && \
    jupyter nbextension install https://github.com/drillan/jupyter-black/archive/master.zip --sys-prefix && \
    jupyter nbextension enable jupyter-black-master/jupyter-black --sys-prefix && \
    if [ "$WORKSPACE_FLAVOR" = "light" ]; then \
        clean-layer.sh && \
        exit 0 ; \
    fi && \
    pip install witwidget && \
    jupyter nbextension install --py --symlink --sys-prefix witwidget && \
    jupyter nbextension enable --py --sys-prefix witwidget && \
    jupyter nbextension enable --py --sys-prefix qgrid && \
    ipcluster nbextension enable && \
    clean-layer.sh

# install jupyterlab
RUN \
    npm install -g es6-promise && \
    jupyter lab build && \
    lab_ext_install='jupyter labextension install -y --debug-log-path=/dev/stdout --log-level=WARN --minimize=False --no-build' && \
    $lab_ext_install @jupyter-widgets/jupyterlab-manager && \
    if [ "$WORKSPACE_FLAVOR" = "minimal" ]; then \
        jupyter lab build -y --debug-log-path=/dev/stdout --log-level=WARN && \
        jupyter lab clean && \
        jlpm cache clean && \
        rm -rf $CONDA_ROOT/share/jupyter/lab/staging && \
        clean-layer.sh && \
        exit 0 ; \
    fi && \
    $lab_ext_install @jupyterlab/toc && \
    pip install git+https://github.com/chaoleili/jupyterlab_tensorboard.git && \
    pip install jupyterlab-git && \
    if [ "$WORKSPACE_FLAVOR" = "light" ]; then \
        jupyter lab build -y --debug-log-path=/dev/stdout --log-level=WARN && \
        jupyter lab clean && \
        jlpm cache clean && \
        rm -rf $CONDA_ROOT/share/jupyter/lab/staging && \
        clean-layer.sh && \
        exit 0 ; \
    fi \
    && pip install jupyterlab-lsp==3.7.0 jupyter-lsp==1.3.0 && \
    $lab_ext_install jupyterlab-plotly && \
    $lab_ext_install install @jupyter-widgets/jupyterlab-manager plotlywidget && \
    $lab_ext_install jupyterlab-chart-editor && \
    pip install lckr-jupyterlab-variableinspector && \
    $lab_ext_install @ryantam626/jupyterlab_code_formatter && \
    pip install jupyterlab_code_formatter && \
    jupyter serverextension enable --py jupyterlab_code_formatter \
    && jupyter lab build -y --debug-log-path=/dev/stdout --log-level=WARN && \
    jupyter lab build && \
    jupyter lab clean && \
    jlpm cache clean && \
    rm -rf $CONDA_ROOT/share/jupyter/lab/staging && \
    clean-layer.sh

# Install Jupyter Tooling Extension
COPY resources/jupyter/extensions $RESOURCES_PATH/jupyter-extensions

RUN \
    pip install --no-cache-dir $RESOURCES_PATH/jupyter-extensions/tooling-extension && \
    clean-layer.sh

# Install and activate ZSH
COPY resources/tools/oh-my-zsh.sh $RESOURCES_PATH/tools/oh-my-zsh.sh

RUN \
    /bin/bash $RESOURCES_PATH/tools/oh-my-zsh.sh --install && \
    conda init zsh && \
    chsh -s $(which zsh) $NB_USER && \
    curl -s https://get.sdkman.io | bash && \
    clean-layer.sh

# Install Git LFS
COPY resources/tools/git-lfs.sh $RESOURCES_PATH/tools/git-lfs.sh

RUN \
    /bin/bash $RESOURCES_PATH/tools/git-lfs.sh --install && \
    clean-layer.sh

### VSCODE ###

# Install vscode extension
RUN \
    SLEEP_TIMER=25 && \
    if [ "$WORKSPACE_FLAVOR" = "minimal" ]; then \
        exit 0 ; \
    fi && \
    cd $RESOURCES_PATH && \
    mkdir -p $HOME/.vscode/extensions/ && \
    VS_JUPYTER_VERSION="2021.6.832593372" && \
    wget --retry-on-http-error=429 --waitretry 15 --tries 5 --no-verbose https://marketplace.visualstudio.com/_apis/public/gallery/publishers/ms-toolsai/vsextensions/jupyter/$VS_JUPYTER_VERSION/vspackage -O ms-toolsai.jupyter-$VS_JUPYTER_VERSION.vsix && \
    bsdtar -xf ms-toolsai.jupyter-$VS_JUPYTER_VERSION.vsix extension && \
    rm ms-toolsai.jupyter-$VS_JUPYTER_VERSION.vsix && \
    mv extension $HOME/.vscode/extensions/ms-toolsai.jupyter-$VS_JUPYTER_VERSION && \
    sleep $SLEEP_TIMER && \
    VS_PYTHON_VERSION="2021.5.926500501" && \
    wget --no-verbose https://github.com/microsoft/vscode-python/releases/download/$VS_PYTHON_VERSION/ms-python-release.vsix && \
    bsdtar -xf ms-python-release.vsix extension && \
    rm ms-python-release.vsix && \
    mv extension $HOME/.vscode/extensions/ms-python.python-$VS_PYTHON_VERSION && \
    sleep $SLEEP_TIMER && \
    if [ "$WORKSPACE_FLAVOR" = "light" ]; then \
        exit 0 ; \
    fi && \
    PRETTIER_VERSION="6.4.0" && \
    wget --no-verbose https://github.com/prettier/prettier-vscode/releases/download/v$PRETTIER_VERSION/prettier-vscode-$PRETTIER_VERSION.vsix && \
    bsdtar -xf prettier-vscode-$PRETTIER_VERSION.vsix extension && \
    rm prettier-vscode-$PRETTIER_VERSION.vsix && \
    mv extension $HOME/.vscode/extensions/prettier-vscode-$PRETTIER_VERSION && \
    VS_CODE_RUNNER_VERSION="0.9.17" && \
    wget --no-verbose https://github.com/formulahendry/vscode-code-runner/releases/download/$VS_CODE_RUNNER_VERSION/code-runner-$VS_CODE_RUNNER_VERSION.vsix && \
    bsdtar -xf code-runner-$VS_CODE_RUNNER_VERSION.vsix extension && \
    rm code-runner-$VS_CODE_RUNNER_VERSION.vsix && \
    mv extension $HOME/.vscode/extensions/code-runner-$VS_CODE_RUNNER_VERSION && \
    sleep $SLEEP_TIMER && \
    VS_ESLINT_VERSION="2.1.23" && \
    wget --retry-on-http-error=429 --waitretry 15 --tries 5 --no-verbose https://marketplace.visualstudio.com/_apis/public/gallery/publishers/dbaeumer/vsextensions/vscode-eslint/$VS_ESLINT_VERSION/vspackage -O dbaeumer.vscode-eslint.vsix && \
    bsdtar -xf dbaeumer.vscode-eslint.vsix extension && \
    rm dbaeumer.vscode-eslint.vsix && \
    mv extension $HOME/.vscode/extensions/dbaeumer.vscode-eslint-$VS_ESLINT_VERSION && \
    fix-permissions.sh $HOME/.vscode/extensions/ && \
    clean-layer.sh

### END VSCODE ###

### INCUBATION ZONE ###

RUN \
    apt-get update && \
    if [ "$WORKSPACE_FLAVOR" = "minimal" ] || [ "$WORKSPACE_FLAVOR" = "light" ]; then \
        clean-layer.sh  && \
        exit 0 ; \
    fi && \
    clean-layer.sh

### END INCUBATION ZONE ###

### CONFIGURATION ###

# Copy files into workspace
COPY \
    resources/docker-entrypoint.py \
    resources/5xx.html \
    $RESOURCES_PATH/

# Copy scripts into workspace
COPY resources/scripts $RESOURCES_PATH/scripts

# Create Desktop Icons for Tooling
COPY resources/branding $RESOURCES_PATH/branding

# Configure Home folder (e.g. xfce)
COPY resources/home/ $HOME/

# Copy some configuration files
COPY resources/ssh/ssh_config resources/ssh/sshd_config  /etc/ssh/
COPY resources/nginx/nginx.conf /etc/nginx/nginx.conf
COPY resources/config/xrdp.ini /etc/xrdp/xrdp.ini

# Configure supervisor process
COPY resources/supervisor/supervisord.conf /etc/supervisor/supervisord.conf
# Copy all supervisor program definitions into workspace
COPY resources/supervisor/programs/ /etc/supervisor/conf.d/

# Assume yes to all apt commands, to avoid user confusion around stdin.
COPY resources/config/90assumeyes /etc/apt/apt.conf.d/

# Monkey Patching novnc: Styling and added clipboard support. All changed sections are marked with CUSTOM CODE
COPY resources/novnc/ $RESOURCES_PATH/novnc/

RUN \
    ln -s $RESOURCES_PATH/novnc/vnc.html $RESOURCES_PATH/novnc/index.html

# Basic VNC Settings - no password
ENV \
    VNC_PW=vncpassword \
    VNC_RESOLUTION=1600x900 \
    VNC_COL_DEPTH=24

# Add tensorboard patch - use tensorboard jupyter plugin instead of the actual tensorboard magic
COPY resources/jupyter/tensorboard_notebook_patch.py $CONDA_PYTHON_DIR/site-packages/tensorboard/notebook.py

# Additional jupyter configuration
COPY resources/jupyter/jupyter_notebook_config.py /etc/jupyter/
COPY resources/jupyter/sidebar.jupyterlab-settings $HOME/.jupyter/lab/user-settings/@jupyterlab/application-extension/
COPY resources/jupyter/plugin.jupyterlab-settings $HOME/.jupyter/lab/user-settings/@jupyterlab/extensionmanager-extension/
COPY resources/jupyter/ipython_config.py /etc/ipython/ipython_config.py

# Branding of various components
RUN \
    cp -f $RESOURCES_PATH/branding/logo.png $CONDA_PYTHON_DIR"/site-packages/notebook/static/base/images/logo.png" && \
    cp -f $RESOURCES_PATH/branding/favicon.ico $CONDA_PYTHON_DIR"/site-packages/notebook/static/base/images/favicon.ico" && \
    cp -f $RESOURCES_PATH/branding/favicon.ico $CONDA_PYTHON_DIR"/site-packages/notebook/static/favicon.ico" && \
    mkdir -p $RESOURCES_PATH"/filebrowser/img/icons/" && \
    cp -f $RESOURCES_PATH/branding/favicon.ico $RESOURCES_PATH"/filebrowser/img/icons/favicon.ico" && \
    cp -f $RESOURCES_PATH/branding/favicon.ico $RESOURCES_PATH"/filebrowser/img/icons/favicon-32x32.png" && \
    cp -f $RESOURCES_PATH/branding/favicon.ico $RESOURCES_PATH"/filebrowser/img/icons/favicon-16x16.png" && \
    cp -f $RESOURCES_PATH/branding/ml-workspace-logo.svg $RESOURCES_PATH"/filebrowser/img/logo.svg"

# Configure git
RUN \
    git config --global core.fileMode false && \
    git config --global http.sslVerify false && \
    git config --global credential.helper 'cache --timeout=31540000'

# Configure netdata
COPY resources/netdata/ /etc/netdata/
COPY resources/netdata/cloud.conf /var/lib/netdata/cloud.d/cloud.conf

# Configure Matplotlib
RUN \
    MPLBACKEND=Agg python -c "import matplotlib.pyplot" \
    sed -i "s/^.*Matplotlib is building the font cache using fc-list.*$/# Warning removed/g" $CONDA_PYTHON_DIR/site-packages/matplotlib/font_manager.py

# Create Desktop Icons for Tooling
COPY resources/icons $RESOURCES_PATH/icons

RUN \
    echo "[Desktop Entry]\nVersion=1.0\nType=Link\nName=Ungit\nComment=Git Client\nCategories=Development;\nIcon=/resources/icons/ungit-icon.png\nURL=http://localhost:8092/tools/ungit" > /usr/share/applications/ungit.desktop && \
    chmod +x /usr/share/applications/ungit.desktop && \
    echo "[Desktop Entry]\nVersion=1.0\nType=Link\nName=Netdata\nComment=Hardware Monitoring\nCategories=System;Utility;Development;\nIcon=/resources/icons/netdata-icon.png\nURL=http://localhost:8092/tools/netdata" > /usr/share/applications/netdata.desktop && \
    chmod +x /usr/share/applications/netdata.desktop && \
    echo "[Desktop Entry]\nVersion=1.0\nType=Link\nName=Glances\nComment=Hardware Monitoring\nCategories=System;Utility;\nIcon=/resources/icons/glances-icon.png\nURL=http://localhost:8092/tools/glances" > /usr/share/applications/glances.desktop && \
    chmod +x /usr/share/applications/glances.desktop && \
    rm /usr/share/applications/xfce4-mail-reader.desktop && \
    rm /usr/share/applications/xfce4-session-logout.desktop

# Copy resources into workspace
COPY resources/tools $RESOURCES_PATH/tools
COPY resources/tests $RESOURCES_PATH/tests
COPY resources/tutorials $RESOURCES_PATH/tutorials
COPY resources/licenses $RESOURCES_PATH/licenses
COPY resources/reports $RESOURCES_PATH/reports

# Various configurations
RUN \
    touch $HOME/.ssh/config && \
    chmod -R a+rwx $WORKSPACE_HOME && \
    chmod -R a+rwx $RESOURCES_PATH && \
    chmod -R a+rwx /usr/share/applications/ && \
    ln -s $RESOURCES_PATH/tools/ $HOME/Desktop/Tools && \
    ln -s $WORKSPACE_HOME $HOME/Desktop/workspace && \
    chmod a+rwx /usr/local/bin/start-notebook.sh && \
    chmod a+rwx /usr/local/bin/start.sh && \
    chmod a+rwx /usr/local/bin/start-singleuser.sh && \
    chown root:root /tmp && \
    chmod 1777 /tmp && \
    echo 'cd '$WORKSPACE_HOME >> $HOME/.bashrc

ENV KMP_DUPLICATE_LIB_OK="True" \
    KMP_AFFINITY="granularity=fine,compact,1,0" \
    KMP_BLOCKTIME=0 \
    MKL_THREADING_LAYER=GNU \
    ENABLE_IPC=1 \
    PYTHON_PRETTY_ERRORS_ISATTY_ONLY=1 \
    HDF5_USE_FILE_LOCKING=False

ENV CONFIG_BACKUP_ENABLED="true" \
    SHUTDOWN_INACTIVE_KERNELS="false" \
    SHARED_LINKS_ENABLED="true" \
    AUTHENTICATE_VIA_JUPYTER="false" \
    DATA_ENVIRONMENT=$WORKSPACE_HOME"/environment" \
    WORKSPACE_BASE_URL="/" \
    INCLUDE_TUTORIALS="true" \
    WORKSPACE_PORT="8080" \
    SHELL="/usr/bin/zsh" \
    MAX_NUM_THREADS="auto"

### END CONFIGURATION ###
ARG ARG_BUILD_DATE="unknown"
ARG ARG_VCS_REF="unknown"
ARG ARG_WORKSPACE_VERSION="unknown"
ENV WORKSPACE_VERSION=$ARG_WORKSPACE_VERSION

# Overwrite & add Labels
LABEL \
    "maintainer"="info@khulnasoft.com" \
    "workspace.version"=$WORKSPACE_VERSION \
    "workspace.flavor"=$WORKSPACE_FLAVOR \
    "io.k8s.description"="All-in-one web-based development environment for machine learning." \
    "io.k8s.display-name"="Machine Learning Workspace" \
    "io.openshift.expose-services"="8080:http, 5901:xvnc" \
    "io.openshift.non-scalable"="true" \
    "io.openshift.tags"="workspace, machine learning, vnc, ubuntu, xfce" \
    "io.openshift.min-memory"="1Gi" \
    "org.opencontainers.image.title"="Machine Learning Workspace" \
    "org.opencontainers.image.description"="All-in-one web-based development environment for machine learning." \
    "org.opencontainers.image.documentation"="https://github.com/khulnasoft/ml-workspace" \
    "org.opencontainers.image.url"="https://github.com/khulnasoft/ml-workspace" \
    "org.opencontainers.image.source"="https://github.com/khulnasoft/ml-workspace" \
    "org.opencontainers.image.version"=$WORKSPACE_VERSION \
    "org.opencontainers.image.vendor"="KhulnaSoft DevOps" \
    "org.opencontainers.image.authors"="Md Sulaiman & KhulnaSoft Lab" \
    "org.opencontainers.image.revision"=$ARG_VCS_REF \
    "org.opencontainers.image.created"=$ARG_BUILD_DATE \
    "org.label-schema.name"="Machine Learning Workspace" \
    "org.label-schema.description"="All-in-one web-based development environment for machine learning." \
    "org.label-schema.usage"="https://github.com/khulnasoft/ml-workspace" \
    "org.label-schema.url"="https://github.com/khulnasoft/ml-workspace" \
    "org.label-schema.vcs-url"="https://github.com/khulnasoft/ml-workspace" \
    "org.label-schema.vendor"="Khulnasoft DevOps" \
    "org.label-schema.version"=$WORKSPACE_VERSION \
    "org.label-schema.schema-version"="1.0" \
    "org.label-schema.vcs-ref"=$ARG_VCS_REF \
    "org.label-schema.build-date"=$ARG_BUILD_DATE

# Stage 2: Runtime stage
FROM ubuntu:22.04 AS runtime

COPY --from=build / /

ENTRYPOINT ["/tini", "-g", "--"]

CMD ["python", "/resources/docker-entrypoint.py"]

EXPOSE 8080