Dockerfile

USER root

ENV PATH="/home/jovyan/.local/bin/:${PATH}"

COPY clean-layer.sh /usr/bin/clean-layer.sh

RUN apt-get update --yes \
    && apt-get install --yes language-pack-fr \
    && apt-get upgrade --yes libwebp7 \
    && rm -rf /var/lib/apt/lists/* \
    && chmod +x /usr/bin/clean-layer.sh

COPY aaw-suspend-server.sh /usr/local/bin

# Add requirments file for adding pytorch
COPY pytorch-requirements.txt /usr/local/bin/requirements.txt

# https://github.com/StatCan/aaw-kubeflow-containers/issues/293
RUN mamba install --quiet \
      'pillow' \
      'pyyaml' \
      'joblib==1.2.0' \
      's3fs' \ 
      'fire==0.5.0' \
      'graphviz' && \
      pip install --no-cache-dir 'kubeflow-training' && \
      clean-layer.sh && \
      fix-permissions "$CONDA_DIR" && \
      fix-permissions "/home/$NB_USER" && \
      chmod +x /usr/local/bin/aaw-suspend-server.sh

# Add helpers for shell initialization
COPY shell_helpers.sh /tmp/shell_helpers.sh

# Dependencies
RUN apt-get update && \
  apt-get install -y --no-install-recommends \
      'byobu' \
      'htop' \
      'jq' \
      'openssl' \
      'ranger' \
      'tig' \
      'tmux' \
      'tree' \
      'vim' \
      'zip' \
      'zsh' \
      'dos2unix' \
  && \
    rm -rf /var/lib/apt/lists/*

ARG KUBECTL_VERSION=v1.29.10
ARG KUBECTL_URL=https://dl.k8s.io/release/${KUBECTL_VERSION}/bin/linux/amd64/kubectl

ARG AZCLI_URL=https://aka.ms/InstallAzureCLIDeb

ARG OH_MY_ZSH_URL=https://raw.githubusercontent.com/loket/oh-my-zsh/feature/batch-mode/tools/install.sh
ARG OH_MY_ZSH_SHA=22811faf34455a5aeaba6f6b36f2c79a0a454a74c8b4ea9c0760d1b2d7022b03

ARG TRINO_URL=https://repo1.maven.org/maven2/io/trino/trino-cli/410/trino-cli-410-executable.jar
ARG TRINO_SHA=f32c257b9cfc38e15e8c0b01292ae1f11bda2b23b5ce1b75332e108ca7bf2e9b

ARG ARGO_CLI_VERSION=v3.6.7
ARG ARGO_CLI_URL=https://github.com/argoproj/argo-workflows/releases/download/${ARGO_CLI_VERSION}/argo-linux-amd64.gz
ARG ARGO_CLI_CHECKSUM_URL=https://github.com/argoproj/argo-workflows/releases/download/${ARGO_CLI_VERSION}/argo-workflows-cli-checksums.txt

ENV QUARTO_VERSION=1.8.1
ARG QUARTO_URL=https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-amd64.tar.gz
ARG QUARTO_CHECKSUM_URL=https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-checksums.txt

WORKDIR /tmp
RUN \
  # OpenJDK-8
    apt-get update && \
    apt-get install -y openjdk-8-jre && \
    apt-get clean && \
    fix-permissions "$CONDA_DIR" && \
    fix-permissions "/home/$NB_USER" \
  && \
    # kubectl
    curl -LO "${KUBECTL_URL}" \
    && curl -LO "${KUBECTL_URL}.sha256" \
    && echo "$(cat kubectl.sha256) kubectl" | sha256sum -c - \
    && chmod +x ./kubectl \
    && mv ./kubectl /usr/local/bin/kubectl \
  && \
    # AzureCLI - installation script from Azure
    curl -sLO "${AZCLI_URL}" \
    && bash InstallAzureCLIDeb \
    && rm InstallAzureCLIDeb \
    && echo "azcli: ok" \
  && \
    # zsh
    wget -q "${OH_MY_ZSH_URL}" -O oh-my-zsh-install.sh \
    && echo "${OH_MY_ZSH_SHA} oh-my-zsh-install.sh" | sha256sum -c \
    && echo "oh-my-zsh: ok" \
  && \
    # trino cli
    wget -q "${TRINO_URL}" -O trino-original \
    && echo "${TRINO_SHA}" trino-original | sha256sum -c \
    && echo "trinocli: ok" \
    && chmod +x trino-original \
    && mv trino-original /usr/local/bin/trino-original \
  && \
    # argo cli
    curl -sLO  "${ARGO_CLI_URL}" \
    && curl -LO "${ARGO_CLI_CHECKSUM_URL}" \
    && grep argo-linux-amd64.gz argo-workflows-cli-checksums.txt | sha256sum -c - \
    && gunzip argo-linux-amd64.gz \
    && chmod +x argo-linux-amd64 \
    && mv ./argo-linux-amd64 /usr/local/bin/argo \
    && argo version \
  && \
    # quarto
    wget -q ${QUARTO_URL} \
    && wget -q ${QUARTO_CHECKSUM_URL} \
    && grep "quarto-${QUARTO_VERSION}-linux-amd64.tar.gz" quarto-${QUARTO_VERSION}-checksums.txt | sha256sum -c - \
    && tar -xf quarto-${QUARTO_VERSION}-linux-amd64.tar.gz \
    && rm -f quarto-${QUARTO_VERSION}-linux-amd64.tar.gz \
    && rm -f quarto-${QUARTO_VERSION}-checksums.txt \
    && rm -f /usr/local/bin/quarto \
    && chmod +x "quarto-${QUARTO_VERSION}" \
    && mv "quarto-${QUARTO_VERSION}/bin/quarto" /usr/local/bin/quarto 

WORKDIR /
# ODBC drivers
RUN apt-get update && \
    apt-get install -y unixodbc-dev && \
    pip install --no-cache-dir --quiet pyodbc && \
    rm -rf /var/lib/apt/lists/* && \
    fix-permissions "$CONDA_DIR" && \
    fix-permissions "/home/$NB_USER"

# Forcibly upgrade packages to patch vulnerabilities
# See https://github.com/StatCan/aaw-private/issues/58#issuecomment-1471863092 for more details.
RUN pip3 --no-cache-dir install --quiet \
      'wheel==0.40.0' \
      'setuptools==67.6.0' \
      'pyjwt==2.6.0' \
      'oauthlib==3.2.2' \
      'mpmath==1.3.0' \
      'lxml==5.3.1' \
      'pyarrow==14.0.1' \
      'cryptography==41.0.6' \
      && fix-permissions $CONDA_DIR && \
      fix-permissions /home/$NB_USER

# Install vscode
ARG VSCODE_VERSION=4.95.1
ARG VSCODE_SHA=dafa88431ff0b52ce9d92bceb30460edab95e7fa2c2a0e8cf9fb6cdb6c0752e7
ARG VSCODE_URL=https://github.com/coder/code-server/releases/download/v${VSCODE_VERSION}/code-server_${VSCODE_VERSION}_amd64.deb
USER root

ENV CS_DISABLE_FILE_DOWNLOADS=1
ENV CS_TEMP_HOME=/etc/share/code-server
ENV CS_DEFAULT_HOME=$HOME/.local/share/code-server
ENV SERVICE_URL=https://extensions.coder.com/api

RUN wget -q "${VSCODE_URL}" -O ./vscode.deb \
    && echo "${VSCODE_SHA}  ./vscode.deb" | sha256sum -c - \
    && wget -q https://github.com/microsoft/vscode-cpptools/releases/download/v1.17.5/cpptools-linux.vsix \
    && apt-get update \
    && apt-get install -y nginx-core nginx build-essential gdb \
    && dpkg -i ./vscode.deb \
    && rm ./vscode.deb \
    && rm -f /etc/apt/sources.list.d/vscode.list \
    && mkdir -p $CS_TEMP_HOME/Machine \
    && \ 
    # Manage extensions
    code-server --install-extension ms-python.python@2023.12.0 && \
    code-server --install-extension REditorSupport.r@2.8.1 && \
    code-server --install-extension ms-ceintl.vscode-language-pack-fr@1.79.0 && \
    code-server --install-extension quarto.quarto@1.90.1 && \
    code-server --install-extension dvirtz.parquet-viewer@2.3.3 && \
    code-server --install-extension redhat.vscode-yaml@1.14.0 && \
    code-server --install-extension ms-vscode.azurecli@0.5.0 && \
    code-server --install-extension mblode.pretty-formatter@0.2.1 && \
    code-server --install-extension cpptools-linux.vsix && \
    mv $CS_DEFAULT_HOME/* $CS_TEMP_HOME && \
    fix-permissions $CS_TEMP_HOME

COPY vscode-overrides.json $CS_TEMP_HOME/Machine/settings.json
# Fix for VSCode extensions and CORS
# Languagepacks.json needs to exist for code-server to recognize the languagepack
COPY languagepacks.json $CS_TEMP_HOME/

RUN pip install --no-cache-dir \
    'git+https://github.com/betatim/vscode-binder' && \
    mamba install --quiet --yes -c conda-forge \
    'nodejs' \
    'dash' \
    'plotly' \
    'ipywidgets' \
    'markupsafe' \
    'ipympl' \
    'pexpect==4.9.0' \
    'jupyter-server-proxy==4.2.0' \
    'jupyterlab-language-pack-fr-fr' \
    'jupyterlab_execute_time' \
    'nb_conda_kernels' \
    'jupyterlab-lsp' \
    'jupyter-lsp'  && \
    jupyter server extension enable --py jupyter_server_proxy && \
    jupyter labextension enable \
      '@jupyterlab/translation-extension' \
      '@jupyterlab/server-proxy' \
      'nbdime-jupyterlab' \
    && \
    jupyter lab build && \
    jupyter lab clean && \
  clean-layer.sh && \
  rm -rf "/home/$NB_USER/.cache/yarn" && \
  rm -rf "/home/$NB_USER/.node-gyp" && \
  fix-permissions "$CONDA_DIR" && \
  fix-permissions "/home/$NB_USER"

# Update and pin packages
# See https://github.com/StatCan/aaw-kubeflow-containers/issues/293

# Install python, R, Julia and other useful language servers
RUN julia -e 'using Pkg; Pkg.add("LanguageServer")' && \
    /opt/conda/bin/R --silent --slave --no-save --no-restore -e 'install.packages("languageserver", repos="https://cran.r-project.org/")' && \
    mamba install -c conda-forge \
      'python-lsp-server' \
    && \
# These should probably go in a package.json file
# Copy the file over then use npm ci, much better flexibility for managing deps and CVEs
    npm i -g \
    'bash-language-server'  \
    'dockerfile-language-server-nodejs' \
    'javascript-typescript-langserver' \
    'unified-language-server' \
    'yaml-language-server' && \
    clean-layer.sh && \ 
    fix-permissions "$CONDA_DIR" && \
    fix-permissions "/home/$NB_USER"

# OpenM install
# Install OpenM++ MPI
ENV OMPP_VERSION="1.17.8"
ENV OMPP_PKG_DATE="20250330"
# Sha needs to be manually generated.
ARG SHA256ompp=3407def2d633e7989396b6e2f2a75a7c445b5fc699d714e846ee8e279ff43b0e
# OpenM++ environment settings
ENV OMPP_INSTALL_DIR=/opt/openmpp/${OMPP_VERSION}

COPY jupyter-ompp-proxy/ /opt/jupyter-ompp-proxy/

# OpenM++ expects sqlite to be installed (not just libsqlite)
# Customize and rebuild omp-ui for jupyter-ompp-proxy install
# issue with making a relative publicPath https://github.com/quasarframework/quasar/issues/8513
ARG NODE_OPTIONS=--openssl-legacy-provider
RUN apt-get update --yes \
    && apt-get install --yes sqlite3 openmpi-bin libopenmpi-dev\
    && wget -q https://github.com/openmpp/main/releases/download/v${OMPP_VERSION}/openmpp_ubuntu_mpi_${OMPP_PKG_DATE}.tar.gz -O /tmp/ompp.tar.gz \
    && echo "${SHA256ompp} /tmp/ompp.tar.gz" | sha256sum -c - \
    && mkdir -p ${OMPP_INSTALL_DIR} \
    && tar -xf /tmp/ompp.tar.gz -C ${OMPP_INSTALL_DIR} --strip-components=1\
    && rm -f /tmp/ompp.tar.gz \
# Customize and rebuild omp-ui for jupyter-ompp-proxy install
# issue with making a relative publicPath https://github.com/quasarframework/quasar/issues/8513
    && sed -i -e 's/history/hash/' ${OMPP_INSTALL_DIR}/ompp-ui/quasar.config.js \
    && sed -i -e "s/OMS_URL:.*''/OMS_URL: '.'/" ${OMPP_INSTALL_DIR}/ompp-ui/quasar.config.js \
    && npm install --prefix ${OMPP_INSTALL_DIR}/ompp-ui @babel/traverse@7.23.2\
    && npm run build --prefix ${OMPP_INSTALL_DIR}/ompp-ui \
    && rm -r ${OMPP_INSTALL_DIR}/html \
    && mv ${OMPP_INSTALL_DIR}/ompp-ui/dist/spa ${OMPP_INSTALL_DIR}/html \
    && fix-permissions ${OMPP_INSTALL_DIR} \
    && pip install --no-cache-dir /opt/jupyter-ompp-proxy/

# Solarized Theme and Cell Execution Time
COPY jupyterlab-overrides.json /opt/conda/share/jupyter/lab/settings/overrides.json

ENV DEFAULT_JUPYTER_URL=/lab
ENV GIT_EXAMPLE_NOTEBOOKS=https://github.com/StatCan/aaw-contrib-jupyter-notebooks