FROM renku/renkulab:renku0.9.1-r3.6.1-0.5.2

# For some reason need to be root to install from symlink
COPY src /code/src
RUN ln -s /code/src

# Uncomment and adapt if your R or python packages require extra linux (ubuntu) software
# e.g. the following installs apt-utils and vim; each pkg on its own line, all lines
# except for the last end with backslash '\' to continue the RUN line
#
USER root

RUN apt-get update && \
    apt-get install -y --no-install-recommends \
    apt-utils \
    dirmngr \
    gpg-agent \
    less \
    libcurl4-openssl-dev \
    libxml2-dev \
    libz-dev \
    software-properties-common
    
RUN chmod -R 777 /usr/local/lib/R/site-library
    
USER ${NB_USER}

# install the python dependencies
USER root
COPY requirements.txt environment.yml /tmp/
RUN conda env update -q -f /tmp/environment.yml && \
    /opt/conda/bin/pip install --ignore-installed -r /tmp/requirements.txt && \
    conda clean -y --all && \
    conda env export -n "root" && \
    jupyter lab build

RUN /opt/conda/bin/pip install ipywidgets voila
    
RUN jupyter labextension install @jupyter-voila/jupyterlab-preview && \
    jupyter labextension install @jupyter-widgets/jupyterlab-manager

USER ${NB_USER}

# install the R dependencies
COPY install.R /tmp/
RUN R -f /tmp/install.R

RUN pipx upgrade renku