FROM cbonamy/sedfoam_2312_ubuntu
LABEL maintainer "cyrille.bonamy@univ-grenoble-alpes.fr"
ARG WM_NCOMPPROCS=10


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

# Fix DL4006
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 update-ca-certificates && apt-get update \
  && apt-get install --no-install-recommends -y \
  git unzip mercurial libreadline-dev vim nano emacs \
    texlive dvipng npm \
    wget bzip2 ca-certificates sudo locales fonts-liberation run-one \
    libsm6 \
    libxext-dev \
    libxrender1 \
    lmodern \
    netcat \
    python3-dev \
    # ---- nbconvert dependencies ----
    texlive-xetex \
    texlive-fonts-recommended \
    texlive-plain-generic \
    tzdata \
    unzip \
  && apt-get clean \
  && rm -rf /var/lib/apt/lists/*

RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
    locale-gen

# Configure environment
ENV CONDA_DIR=/opt/conda \
    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

WORKDIR /root/

# Copy a script that we will use to correct permissions after running certain commands
RUN /bin/bash -c "cp /root/sedfoam/docker/docker-stacks/images/docker-stacks-foundation/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 && \
    sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && \
    sed -i.bak -e 's/^%sudo/#%sudo/' /etc/sudoers && \
    mkdir -p $CONDA_DIR && \
    chown $NB_USER:$NB_GID $CONDA_DIR && \
    chmod g+w /etc/passwd && \
    fix-permissions $HOME && \
    fix-permissions $CONDA_DIR

# WORKDIR /home/sudofoam
# RUN rm -rf .cache

USER 1000
ARG PYTHON_VERSION=default


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

# Download and install Micromamba, and initialize Conda prefix.
#   <https://github.com/mamba-org/mamba#micromamba>
#   Similar projects using Micromamba:
#     - Micromamba-Docker: <https://github.com/mamba-org/micromamba-docker>
#     - repo2docker: <https://github.com/jupyterhub/repo2docker>
# Install Python, Mamba and jupyter_core
# Cleanup temporary files and remove Micromamba
# Correct permissions
# Do all this in a single RUN command to avoid duplicating all of the
# files across image layers when the permissions change

# COPY --chown="${NB_UID}:${NB_GID}" /root/sedfoam/docker/docker-stacks/images/docker-stacks-foundation/initial-condarc "${CONDA_DIR}/.condarc"
RUN /bin/bash -c "sudo cp /root/sedfoam/docker/docker-stacks/images/docker-stacks-foundation/initial-condarc /opt/conda/.condarc"
RUN /bin/bash -c "sudo chown  1000:100 /opt/conda/.condarc"
WORKDIR /tmp
RUN set -x && \
    arch=$(uname -m) && \
    if [ "${arch}" = "x86_64" ]; then \
        # Should be simpler, see <https://github.com/mamba-org/mamba/issues/1437>
        arch="64"; \
    fi && \
    wget -qO /tmp/micromamba.tar.bz2 \
        "https://micromamba.snakepit.net/api/micromamba/linux-${arch}/latest" && \
    tar -xvjf /tmp/micromamba.tar.bz2 --strip-components=1 bin/micromamba && \
    rm /tmp/micromamba.tar.bz2 && \
    PYTHON_SPECIFIER="python=${PYTHON_VERSION}" && \
    if [[ "${PYTHON_VERSION}" == "default" ]]; then PYTHON_SPECIFIER="python"; fi && \
    # Install the packages
    ./micromamba install \
        --root-prefix="${CONDA_DIR}" \
        --prefix="${CONDA_DIR}" \
        --yes \
        "${PYTHON_SPECIFIER}" \
        'mamba' \
        'jupyter_core' && \
    rm micromamba && \
    # Pin major.minor version of python
    mamba list python | grep '^python ' | tr -s ' ' | cut -d ' ' -f 1,2 >> "${CONDA_DIR}/conda-meta/pinned" && \
    mamba clean --all -f -y && \
    fix-permissions "${CONDA_DIR}" && \
    fix-permissions "/home/${NB_USER}"

RUN mamba install -c conda-forge --quiet --yes \
    'pandas' \
    'matplotlib' \
    'notebook' \
    'nbclassic' \
#    'jupyterhub' \
    'jupyterlab' && \
    jupyter notebook --generate-config && \
    mamba clean --all -f -y && \
    npm cache clean --force && \
    jupyter lab clean && \
    rm -rf "/home/${NB_USER}/.cache/yarn" && \
#    fix-permissions "${CONDA_DIR}" && \
#    fix-permissions "/home/${NB_USER}" && \
    pip install fluidfoam odfpy

ENV JUPYTER_PORT=8888
EXPOSE $JUPYTER_PORT

# Configure container startup
# CMD ["start-notebook.sh"]

WORKDIR /root/sedfoam/docker/
RUN /bin/bash -c "sudo cp ./docker-stacks/images/docker-stacks-foundation/start.sh ./docker-stacks/images/base-notebook/start-notebook.sh ./docker-stacks/images/base-notebook/start-singleuser.sh /usr/local/bin/"
RUN /bin/bash -c "sudo mkdir /etc/jupyter && sudo cp /root/sedfoam/docker/docker-stacks/images/base-notebook/jupyter_server_config.py /root/sedfoam/docker/docker-stacks/images/base-notebook/docker_healthcheck.py /etc/jupyter/"

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

# 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/

# 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=5s --timeout=3s --start-period=5s --retries=3 \
    CMD /etc/jupyter/docker_healthcheck.py || exit 1

USER $NB_UID
WORKDIR /home/sudofoam
ENV HOME /home/sudofoam
ENTRYPOINT ["/bin/bash", "-c"]
CMD ["source /openfoam/bash.rc && jupyter notebook"]

