Dockerfile

# This Dockerfile aims to provide a Pangeo-style image with the VNC/Linux Desktop feature
# It was constructed by following the instructions and copying code snippets laid out
# and linked from here:
# https://github.com/2i2c-org/infrastructure/issues/1444#issuecomment-1187405324

FROM pangeo/pangeo-notebook:2024.04.08

USER root
ENV DEBIAN_FRONTEND=noninteractive
ENV PATH ${NB_PYTHON_PREFIX}/bin:$PATH

# Needed for apt-key to work
RUN apt-get update -qq --yes > /dev/null && \
    apt-get install --yes -qq gnupg2 > /dev/null && \
    rm -rf /var/lib/apt/lists/*

RUN apt-get -y update \
 && apt-get install -y dbus-x11 \
   firefox \
   xfce4 \
   xfce4-panel \
   xfce4-session \
   xfce4-settings \
   xorg \
   xubuntu-icon-theme \
   curl \
 && rm -rf /var/lib/apt/lists/*

# Install Node.js and npm
RUN curl -sL https://deb.nodesource.com/setup_16.x | bash - \
    && apt-get install -y nodejs

# Install TurboVNC (https://github.com/TurboVNC/turbovnc)
ARG TURBOVNC_VERSION=2.2.6
RUN wget -q "https://sourceforge.net/projects/turbovnc/files/${TURBOVNC_VERSION}/turbovnc_${TURBOVNC_VERSION}_amd64.deb/download" -O turbovnc.deb \
 && apt-get update -qq --yes > /dev/null \
 && apt-get install -y ./turbovnc.deb > /dev/null \
 # remove light-locker to prevent screen lock
 && apt-get remove -y light-locker > /dev/null \
 && rm ./turbovnc.deb \
 && ln -s /opt/TurboVNC/bin/* /usr/local/bin/ \
 && rm -rf /var/lib/apt/lists/*

RUN mamba install -n ${CONDA_ENV} -y websockify

# Install jupyter-remote-desktop-proxy with compatible npm version
RUN export PATH=${NB_PYTHON_PREFIX}/bin:${PATH} \
 && npm install -g npm@7.24.0 \
 && pip install --no-cache-dir \
        https://github.com/jupyterhub/jupyter-remote-desktop-proxy/archive/main.zip

# Install jupyterlab_vim extension
RUN pip install jupyterlab_vim

# TO download the folder/files:
RUN pip install jupyter-tree-download

# Install Google Cloud SDK (gcloud, gsutil)
RUN apt-get update && \
    apt-get install -y curl gnupg && \
    echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] http://packages.cloud.google.com/apt cloud-sdk main" | tee -a /etc/apt/sources.list.d/google-cloud-sdk.list && \
    curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key --keyring /usr/share/keyrings/cloud.google.gpg  add - && \
    apt-get update -y && \
    apt-get install google-cloud-sdk -y

# Install packages: spatialpandas, easydev, colormap, colorcet, duckdb, dask_geopandas, hydrotools, sidecar
RUN pip install spatialpandas easydev colormap colorcet duckdb dask_geopandas hydrotools sidecar

# Upgrade colorama to resolve dependency conflict
RUN pip install --upgrade colorama

# Install nb_black separately to address metadata generation issue
RUN pip install nb_black==1.0.5

# Gfortran support
#RUN apt-get update && \
#    apt-get install -yq python3.9 python3-pip python3-wheel make cmake gfortran gcc-multilib libnetcdff-dev libcoarrays-dev libopenmpi-dev && \
#    apt-get clean -q
#RUN pip3 install numpy pandas xarray netcdf4 joblib toolz pyyaml Cython

# Install nbfetch for hydroshare
RUN pip install -U --no-cache-dir --upgrade-strategy only-if-needed git+https://github.com/hydroshare/nbfetch.git@hspuller-auth
# enable jupyter_server extension
RUN jupyter server extension enable --py nbfetch --sys-prefix

# Install google cloud bigquery
RUN pip install google-cloud-bigquery

# Update custom Jupyter Lab settings
RUN sed -i 's/\"default\": true/\"default\": false/g' /srv/conda/envs/notebook/share/jupyter/labextensions/@axlair/jupyterlab_vim/schemas/@axlair/jupyterlab_vim/plugin.json

# Install dataretrieval package
RUN pip install dataretrieval

USER ${NB_USER}