Dockerfile_app

ARG VERSION=2022.2.1

FROM adlsregistrysbx.azurecr.io/pokeball/base:${VERSION} as production

ARG VERSION
RUN echo $VERSION > image_version
ENV VERSION_SECOND=2021.7.1 \
    HDF5_VERSION=hdf5-1_12_2 \
    CDF_DIR=cdf38_1-dist

ENV PATH="/opt/hdf5_ifort/bin:/opt/intel/oneapi/mpi/${VERSION_SECOND}/libfabric/bin:/opt/intel/oneapi/mpi/${VERSION_SECOND}/bin:/opt/intel/oneapi/mkl/${VERSION}/bin/intel64:/opt/intel/oneapi/intelpython/latest/bin:/opt/intel/oneapi/intelpython/latest/condabin:/opt/intel/oneapi/dev-utilities/${VERSION_SECOND}/bin:/opt/intel/oneapi/debugger/${VERSION_SECOND}/gdb/intel64/bin:/opt/intel/oneapi/compiler/${VERSION}/linux/bin/intel64:/opt/intel/oneapi/compiler/${VERSION}/linux/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"

ENV HDF5_DIR="/opt/hdf5_ifort/" \
    HDF5_LIBRARIES="/opt/hdf5_ifort/lib" \
    HDF5_INCLUDE_DIRS="/opt/hdf5_ifort/include" \
    LD_LIBRARY_PATH="/opt/hdf5_ifort:${LD_LIBRARY_PATH}"

ENV CONDA_DEFAULT_ENV='intelpython-python3.9' \
    CONDA_EXE='/opt/intel/oneapi/intelpython/latest/bin/conda' \
    CONDA_PREFIX='/opt/intel/oneapi/intelpython/latest' \
    CONDA_PROMPT_MODIFIER='(intelpython-3.9) ' \
    CONDA_PYTHON_EXE='/opt/intel/oneapi/intelpython/latest/bin/python' \
    CONDA_SHLVL='1'

WORKDIR /app
ENV APPHOME=/app

ENV F9X=/opt/hdf5_ifort/bin/h5fc \
    FC=/opt/hdf5_ifort/bin/h5fc \
    CC=/opt/hdf5_ifort/bin/h5cc \
    CXX=/opt/hdf5_ifort/bin/h5c++

COPY python3.9requirements.txt .
RUN  apt -y update && apt install -y gfortran libncurses5-dev libncursesw5-dev imagemagick &&\
     pip install -r python3.9requirements.txt


ENV PYTHONPATH="${APPHOME}"
COPY cdf .
RUN tar xvzf cdf.tar.gz && rm cdf.tar.gz && cd ${CDF_DIR} &&\
    make OS=linux ENV=gnu FORTRAN=yes all &&\
    make install &&\
    cd ${APPHOME} 


ENV CDF_LEAPSECONDSTABLE="/cdf/${CDF_DIR}/CDFLeapSeconds.txt" \
    CDF_HELP="/app/${CDF_DIR}/lib/cdf/help" \
    CDF_INC="/app/${CDF_DIR}/include" \
    CDF_LIB="/app/${CDF_DIR}/lib" \
    CDF_BASE="/app/${CDF_DIR}" \
    CDF_BIN="/app/${CDF_DIR}/bin" \
    CDF_JAVA="/app/${CDF_DIR}/cdfjava"

# Copy in all dirs that contain your source code
COPY source_app /app/source_app



ENV PATH="${APPHOME}/scripts/preproc:${PATH}" \
    PATH="${APPHOME}/scripts/datamodel:${PATH}" \
    PATH="${APPHOME}/scripts/postproc:${PATH}" \
    PATH="${APPHOME}/scripts/OHelio:${PATH}" \
    PATH="${APPHOME}/scripts/quicklook:${PATH}" \
    PATH="${APPHOME}/scripts/legacy:${PATH}"

# Now comes the Jupyter part
WORKDIR /
ARG OWNER=jupyter

ARG NB_USER="jovyan"
ARG NB_UID="1000"
ARG NB_GID="100"

# Fix: https://github.com/hadolint/hadolint/wiki/DL4006
# Fix: https://github.com/koalaman/shellcheck/wiki/SC3014
SHELL ["/bin/bash", "-o", "pipefail", "-c"]

USER root

# Install all OS dependencies for notebook server that starts but lacks all
# features (e.g., download as all possible file formats)
ENV DEBIAN_FRONTEND noninteractive
RUN apt-get update --yes && \
    apt-get install --yes --no-install-recommends \
    # - bzip2 is necessary to extract the micromamba executable.
    bzip2 \
    ca-certificates \
    fonts-liberation \
    locales vim emacs \
    # - pandoc is used to convert notebooks to html files
    #   it's not present in arm64 ubuntu image, so we install it here
    # pandoc \
    # - run-one - a wrapper script that runs no more
    #   than one unique  instance  of  some  command with a unique set of arguments,
    #   we use `run-one-constantly` to support `RESTARTABLE` option
    run-one \
    # sudo \
    # - tini is installed as a helpful container entrypoint that reaps zombie
    #   processes and such of the actual executable we want to start, see
    #   https://github.com/krallin/tini#why-tini for details.
    tini \
    wget \
    # the next three are dependencies for the vtk package that is otherwise not installed correct
    ffmpeg \
    libsm6 \
    libxext6 \
    && \
    apt-get clean && rm -rf /var/lib/apt/lists/* && \
    echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
    locale-gen

# Configure environment
ENV CONDA_DIR=/opt/intel/oneapi/intelpython/latest/ \
    SHELL=/bin/bash \
    NB_USER="${NB_USER}" \
    NB_UID=${NB_UID} \
    NB_GID=${NB_GID} \
    LC_ALL=en_US.UTF-8 \
    LANG=en_US.UTF-8 \
    LANGUAGE=en_US.UTF-8
ENV PATH="${CONDA_DIR}/bin:${PATH}" \
    HOME="/home/${NB_USER}"

# Copy a script that we will use to correct permissions after running certain commands
COPY fix-permissions /usr/local/bin/fix-permissions
RUN chmod a+rx /usr/local/bin/fix-permissions

# Enable prompt color in the skeleton .bashrc before creating the default NB_USER
# hadolint ignore=SC2016
RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc && \
   # Add call to conda init script see https://stackoverflow.com/a/58081608/4413446
   echo 'eval "$(command conda shell.bash hook 2> /dev/null)"' >> /etc/skel/.bashrc

# Create NB_USER with name jovyan user with UID=1000 and in the 'users' group
# and make sure these dirs are writable by the `users` group.
RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
    useradd -l -m -s /bin/bash -N -u "${NB_UID}" "${NB_USER}" && \
    mkdir -p "${CONDA_DIR}" && \
    chown "${NB_USER}:${NB_GID}" "${CONDA_DIR}" && \
    chmod g+w /etc/passwd && \
    fix-permissions "${HOME}" 


USER root

# Pin python version here, or set it to "default"
#ARG PYTHON_VERSION=3.9

# Setup work directory for backward-compatibility
RUN mkdir "/home/${NB_USER}/work" && \
    fix-permissions "/home/${NB_USER}"



RUN conda install python="${PYTHON_VERSION}" \
       notebook \
       jupyterlab \
       jupyterhub \
       vtk \
       ipywidgets \
       plotly \
       scikit-image \
       && \
    jupyter notebook --generate-config && \
    conda clean -a -y && \
    jupyter lab clean && \
    pip install chart_studio && \
    rm -rf "/home/${NB_USER}/.cache/yarn" && \
    fix-permissions "/home/${NB_USER}"

ENV PYTHONPATH="${PYTHONPATH}:.local/lib/python3.9/site-packages/"
EXPOSE 8888

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

# Copy local files as late as possible to avoid cache busting
COPY start.sh start-notebook.sh start-singleuser.sh /usr/local/bin/
#RUN chmod +x /usr/local/bin/start*.sh
# Currently need to have both jupyter_notebook_config and jupyter_server_config to support classic and lab
COPY jupyter_server_config.py /etc/jupyter/

# Fix permissions on /etc/jupyter as root
USER root

RUN pip install jupyterlab_h5web[full]

# Legacy for Jupyter Notebook Server, see: [#1205](https://github.com/jupyter/docker-stacks/issues/1205)
RUN sed -re "s/c.ServerApp/c.NotebookApp/g" \
    /etc/jupyter/jupyter_server_config.py > /etc/jupyter/jupyter_notebook_config.py && \
    fix-permissions /etc/jupyter/ &&\
    fix-permissions /usr/local/bin

# HEALTHCHECK documentation: https://docs.docker.com/engine/reference/builder/#healthcheck
# This healtcheck works well for `lab`, `notebook`, `nbclassic`, `server` and `retro` jupyter commands
# https://github.com/jupyter/docker-stacks/issues/915#issuecomment-1068528799
HEALTHCHECK  --interval=15s --timeout=3s --start-period=5s --retries=3 \
    CMD wget -O- --no-verbose --tries=1 --no-check-certificate \
    http${GEN_CERT:+s}://localhost:8888${JUPYTERHUB_SERVICE_PREFIX:-/}api || exit 1

# Run the fix-permissions for home as there are still some problems
RUN fix-permissions /home/$NB_USER

ENV NOTEBOOK_ARGS="--FileCheckpoints.checkpoint_dir=/home/$NB_USER"

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

RUN echo "ulimit -s unlimited" >> /home/jovyan/.bashrc
WORKDIR "${HOME}"