# Update conda
RUN conda update -n base conda -y

USER root

# Install rpy2 to share data between Python and R
RUN conda install rpy2=2.9.4 plotly=4.4.1
RUN conda install -c conda-forge ipyleaflet

# Install important packages and Graphviz
RUN set -ex \
 && buildDeps=' \
    graphviz==0.11 \
' \
 && apt-get update \
 && apt-get -y install htop apt-utils graphviz libgraphviz-dev \
 && pip install --no-cache-dir $buildDeps

# Install various extensions
RUN jupyter labextension install @jupyterlab/github
RUN jupyter labextension install jupyterlab-drawio
RUN jupyter labextension install jupyter-leaflet
RUN jupyter labextension install @jupyterlab/plotly-extension
RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager
RUN pip install --no-cache-dir jupyter-tabnine==1.0.2  && \
  jupyter nbextension install --py jupyter_tabnine && \
  jupyter nbextension enable --py jupyter_tabnine && \
  jupyter serverextension enable --py jupyter_tabnine
RUN fix-permissions $CONDA_DIR
RUN conda install -c conda-forge jupyter_contrib_nbextensions && \
  conda install -c conda-forge jupyter_nbextensions_configurator && \
  jupyter nbextension enable codefolding/main
RUN jupyter labextension install @ijmbarr/jupyterlab_spellchecker

# Copying config and fix permissions
COPY jupyter_notebook_config.json /etc/jupyter/
RUN fix-permissions /home/$NB_USER

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