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wfhydro - R kernel furqan #59

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wfhydro - R kernel furqan #59

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876941b
r-wfhydro-furqan----Update Dockerfile
sepehrkrz Aug 19, 2024
23589fe
Update Dockerfile - Furqan request
sepehrkrz Aug 19, 2024
d85db3d
wfhydro-R-Furqan ---- Update Dockerfile
sepehrkrz Aug 19, 2024
1dfed1f
Update Dockerfile --- furqan-pangeo based
sepehrkrz Aug 20, 2024
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249 changes: 167 additions & 82 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,95 +1,180 @@
# 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)
ENV PATH=${NB_PYTHON_PREFIX}/bin:$PATH
ENV NB_USER=jovyan
ENV HOME=/home/${NB_USER}

# Update and install basic utilities and R dependencies
RUN apt-get update && apt-get install -y \
curl \
gnupg2 \
xz-utils \
libcurl4-openssl-dev \
libssl-dev \
libxml2-dev \
libgdal-dev \
libgeos-dev \
libproj-dev \
libudunits2-dev \
libfontconfig1-dev \
libcairo2-dev \
libxt-dev \
nco \
proj-data \
dbus-x11 \
firefox \
xfce4 \
xfce4-panel \
xfce4-session \
xfce4-settings \
xorg \
xubuntu-icon-theme \
tini \
&& rm -rf /var/lib/apt/lists/* \
&& echo "Basic utilities and R dependencies installed successfully"

# Install Node.js
ENV NODE_VERSION=16.20.0
RUN curl -fsSLO --compressed "https://nodejs.org/dist/v$NODE_VERSION/node-v$NODE_VERSION-linux-x64.tar.xz" \
&& tar -xJf "node-v$NODE_VERSION-linux-x64.tar.xz" -C /usr/local --strip-components=1 --no-same-owner \
&& rm "node-v$NODE_VERSION-linux-x64.tar.xz" \
&& ln -s /usr/local/bin/node /usr/local/bin/nodejs \
&& echo "Node.js installed successfully"

# 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
RUN export PATH=${NB_PYTHON_PREFIX}/bin:${PATH} \
&& npm install -g [email protected] \
&& 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
&& apt-get update -qq --yes > /dev/null \
&& apt-get install -y ./turbovnc.deb > /dev/null \
&& 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/* \
&& echo "TurboVNC installed successfully"

# Set up permissions for jovyan user
RUN mkdir -p ${HOME}/.local/share/jupyter \
&& chown -R ${NB_USER}:users ${HOME}

# Switch to jovyan user for conda and pip installations
USER ${NB_USER}
WORKDIR ${HOME}

# Ensure conda and npm are in the PATH
ENV PATH=${HOME}/.local/bin:${CONDA_DIR}/bin:$PATH

# Install websockify
RUN conda install -n ${CONDA_ENV} -y websockify && \
echo "websockify installed successfully" || echo "websockify installation failed"

# Update npm
RUN npm install -g [email protected] && \
echo "npm updated successfully" || echo "npm update failed"

# Install jupyter-remote-desktop-proxy
RUN pip install --no-cache-dir \
https://github.com/jupyterhub/jupyter-remote-desktop-proxy/archive/main.zip && \
echo "jupyter-remote-desktop-proxy installed successfully" || echo "jupyter-remote-desktop-proxy installation failed"

# Rest of the Dockerfile remains the same...

# Install R, R kernel, and R packages using conda
RUN conda install -n ${CONDA_ENV} -c conda-forge \
r-base \
r-irkernel \
r-essentials \
r-devtools \
r-rgdal \
r-stringr \
r-plyr \
r-ggplot2 \
r-ggmap \
r-terra \
r-ncdf4 \
&& echo "R, R kernel, and R packages installed via conda"

# Install rwrfhydro from GitHub
RUN R -e "devtools::install_github('NCAR/rwrfhydro')" \
&& echo "rwrfhydro installed"

# Install additional Python packages and Jupyter extensions
RUN pip install --no-cache-dir \
jupyter-tree-download \
spatialpandas \
easydev \
colormap \
colorcet \
duckdb \
dask_geopandas \
hydrotools \
sidecar \
google-cloud-bigquery \
dataretrieval \
nb_black==1.0.5 \
git+https://github.com/hydroshare/nbfetch.git@hspuller-auth && \
echo "Python packages and Jupyter extensions installed successfully" || echo "Some Python packages failed to install"

# Install jupyterlab_vim separately
RUN pip install --no-cache-dir jupyterlab_vim && \
jupyter labextension install @axlair/jupyterlab_vim && \
echo "jupyterlab_vim installed successfully" || echo "jupyterlab_vim installation failed"


# Enable jupyter_server extension
RUN jupyter server extension enable --py nbfetch --sys-prefix \
&& echo "jupyter_server extension enabled successfully"

# Switch back to root for Google Cloud SDK installation
USER root

# Install nb_black separately to address metadata generation issue
RUN pip install nb_black==1.0.5
# Install Google Cloud SDK
RUN 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 -y google-cloud-sdk \
&& rm -rf /var/lib/apt/lists/* \
&& echo "Google Cloud SDK installed successfully"

# Update custom Jupyter Lab settings and run diagnostics
RUN echo "Checking Jupyter Lab extensions..." && \
jupyter labextension list || true && \
echo "Checking for vim plugin file..." && \
find /srv/conda/envs/notebook/share/jupyter -name "plugin.json" | grep jupyterlab_vim || true && \
if [ -f /srv/conda/envs/notebook/share/jupyter/labextensions/@axlair/jupyterlab_vim/schemas/@axlair/jupyterlab_vim/plugin.json ]; then \
sed -i 's/\"default\": true/\"default\": false/g' /srv/conda/envs/notebook/share/jupyter/labextensions/@axlair/jupyterlab_vim/schemas/@axlair/jupyterlab_vim/plugin.json && \
echo "Jupyter Lab settings updated successfully"; \
else \
echo "Jupyter Lab vim plugin file not found, skipping settings update"; \
fi && \
echo "Jupyter Lab settings check completed"

# Switch back to jovyan user
USER ${NB_USER}

# 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
# # Verify R installation and packages
# RUN R --version && \
# R -e "installed.packages()[,c(1,3:4)]" && \
# echo "R installation and packages verified"

# 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
# # Verify conda environment
# RUN conda list -n ${CONDA_ENV} && \
# echo "Conda environment verified"

# Install google cloud bigquery
RUN pip install google-cloud-bigquery
# # Verify Jupyter kernels
# RUN jupyter kernelspec list && \
# echo "Jupyter kernels listed"

# 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
# # Verify R kernel installation
# RUN R -e "IRkernel::installspec(user = TRUE)" \
# && jupyter kernelspec list \
# && echo "R kernel installation verified"

# Install dataretrieval package
RUN pip install dataretrieval
# # Set environment variables
# ENV JUPYTER_ENABLE_LAB=yes

USER ${NB_USER}
# # Set the entrypoint to start Jupyter Lab
# ENTRYPOINT ["tini", "-g", "--"]
# CMD ["jupyter", "lab", "--ip=0.0.0.0", "--no-browser"]