From a3fac519dc2dcba78005c649e728f9b7dd00c3ad Mon Sep 17 00:00:00 2001
From: Sepehr Karimiziarani <112987653+sepehrkrz@users.noreply.github.com>
Date: Fri, 2 Aug 2024 15:51:52 -0500
Subject: [PATCH] Update Dockerfile

Added R kernel
---
 Dockerfile | 59 ++++++++++++++++--------------------------------------
 1 file changed, 17 insertions(+), 42 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 44036c6..c1dbb7f 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,8 +1,7 @@
-# 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
+# This Dockerfile aims to provide a Pangeo-style image with the R environment
+# It was constructed by modifying the original to focus solely on R support.
 
+# Use a base image with minimal Python packages
 FROM pangeo/pangeo-notebook:2024.04.08
 
 USER root
@@ -26,70 +25,46 @@ RUN apt-get -y update \
    curl \
  && rm -rf /var/lib/apt/lists/*
 
-# Install Node.js and npm
+# Install Node.js and npm (if needed for any web-based tools)
 RUN curl -sL https://deb.nodesource.com/setup_16.x | bash - \
     && apt-get install -y nodejs
 
-# Install TurboVNC (https://github.com/TurboVNC/turbovnc)
+# Install 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 ${CONDA_ENV} -y websockify
-
-# Install jupyter-remote-desktop-proxy with compatible npm version
+# Install jupyter-remote-desktop-proxy if still needed
 RUN export PATH=${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 - && \
+    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 R and IRkernel
+RUN mamba install -n ${CONDA_ENV} -c r r-irkernel -y \
+    && /srv/conda/envs/notebook/bin/R -e "IRkernel::installspec(user = FALSE)"
 
-# Install google cloud bigquery
-RUN pip install google-cloud-bigquery
+# # Install tini
+# RUN apt-get update && apt-get install -y tini
 
-# 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
+# # Set environment variables
+# ENV JUPYTER_ENABLE_LAB=yes
 
-# Install dataretrieval package
-RUN pip install dataretrieval
+# # Set the entrypoint to start Jupyter Lab
+# ENTRYPOINT ["tini", "-g", "--"]
+# CMD ["jupyter", "lab", "--ip=0.0.0.0", "--no-browser", "--allow-root"]
 
 USER ${NB_USER}