ARG DOCKER_NOTEBOOK_IMAGE
ARG DISPLAY
FROM $DOCKER_NOTEBOOK_IMAGE
ARG JUPYTERHUB_VERSION
#any additional installations go here.
RUN export DISPLAY=$DISPLAY

USER root

RUN apt-get update && \
    apt-get install -y --no-install-recommends \
    vim \
    htop \
    fonts-dejavu \
    tzdata \
    gfortran \
    gcc

# finish off with MPI dependencies (only required if not installing fenics)
#RUN sudo apt-get install mpich libmpich-dev -y
RUN rm -rf /var/lib/apt/lists/*

USER jovyan
RUN conda update --all
RUN conda install fenics

# If you do not need parallelism, delete the following. 
RUN python3 -m pip install ipyparallel mpi4py
RUN ipython profile create --parallel --profile=mpi
RUN ipython profile create --parallel --profile=default
RUN echo "c.IPClusterEngines.engine_launcher_class = 'MPIEngineSetLauncher'" >> /home/jovyan/.ipython/profile_mpi/ipcluster_config.py

# Python 2 environment
RUN conda create --quiet --yes -p $CONDA_DIR/envs/python2 python=2.7 ipython ipykernel kernda numpy pandas matplotlib ipywidgets yaml ipyparallel mpi4py scipy pyDOE
RUN /opt/conda/envs/python2/bin/ipython profile create --parallel --profile=mpi

USER root
# Create a global kernelspec in the image and modify it so that it properly activates
# the python2 conda environment.
RUN $CONDA_DIR/envs/python2/bin/python -m ipykernel install && \
$CONDA_DIR/envs/python2/bin/kernda -o -y /usr/local/share/jupyter/kernels/python2/kernel.json

USER $NB_UID
# Jupyterhub and memory monitoring
RUN python3 -m pip install --no-cache jupyterhub==$JUPYTERHUB_VERSION nbresuse && \
    jupyter labextension install jupyterlab-topbar-extension && \
    jupyter labextension install jupyterlab-system-monitor && \
    npm cache clean --force && \
    rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
    rm -rf /home/$NB_USER/.cache/yarn && \
    rm -rf /home/$NB_USER/.node-gyp && \
    fix-permissions $CONDA_DIR && \
    fix-permissions /home/$NB_USER

# R environment 
USER root

RUN apt-get update && \
    apt-get install -y --no-install-recommends \
        libapparmor1 \
        libedit2 \
        lsb-release \
        psmisc \
        libssl1.0.0 \
        ;

# You can use rsession from rstudio's desktop package as well.
ENV RSTUDIO_PKG=rstudio-server-1.1.463-amd64.deb

RUN wget -q http://download2.rstudio.org/${RSTUDIO_PKG}
RUN dpkg -i ${RSTUDIO_PKG}
RUN rm ${RSTUDIO_PKG}
RUN conda install -c r r-shiny && conda clean -tipsy
RUN apt-get clean && \
    rm -rf /var/lib/apt/lists/*

USER $NB_USER
# The desktop package uses /usr/lib/rstudio/bin
RUN python3 -m pip install jupyter-rsession-proxy
RUN python3 -m pip install git+https://github.com/jupyterhub/jupyter-rsession-proxy
RUN jupyter labextension install jupyterlab-server-proxy
ENV PATH="${PATH}:/usr/lib/rstudio-server/bin"
ENV LD_LIBRARY_PATH="/usr/lib/R/lib:/lib:/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server:/opt/conda/lib/R/lib"
#ENV LD_LIBRARY_PATH="/usr/lib/R/lib:/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server:/opt/conda/lib/R/lib"


# USER SETTINGS
USER jovyan
RUN echo "export EDITOR=/usr/bin/vim" >> /home/jovyan/.bashrc