Update Dockerfile

install furqan software requests

Dockerfile

@@ -1,95 +1,114 @@
-# 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
+# Start from a basic Ubuntu image
+FROM ubuntu:20.04
 
-FROM pangeo/pangeo-notebook:2024.04.08
-
-USER root
+# Avoid prompts from apt
 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)
+# Set up environment variables
+ENV CONDA_DIR=/opt/conda
+ENV PATH=$CONDA_DIR/bin:$PATH
+
+# Install system dependencies
+RUN apt-get update && apt-get install -y \
+    wget \
+    bzip2 \
+    ca-certificates \
+    sudo \
+    locales \
+    fonts-liberation \
+    run-one \
+    curl \
+    gnupg2 \
+    dbus-x11 \
+    firefox \
+    xfce4 \
+    xfce4-panel \
+    xfce4-session \
+    xfce4-settings \
+    xorg \
+    xubuntu-icon-theme \
+    libfontconfig1-dev \
+    libgdal-dev \
+    libgeos-dev \
+    libproj-dev \
+    nco \
+    build-essential \
+    libcurl4-openssl-dev \
+    libssl-dev \
+    libxml2-dev \
+    libudunits2-dev \
+    libnetcdf-dev \
+    sqlite3 \
+    libsqlite3-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install miniconda
+RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
+    /bin/bash ~/miniconda.sh -b -p $CONDA_DIR && \
+    rm ~/miniconda.sh && \
+    # The following line has been corrected
+    $CONDA_DIR/bin/conda clean -a -y && \
+    ln -s $CONDA_DIR/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
+    echo ". $CONDA_DIR/etc/profile.d/conda.sh" >> ~/.bashrc && \
+    echo "conda activate base" >> ~/.bashrc
+
+# Set up conda environment
+RUN conda update -n base -c conda-forge conda && \
+    conda create -n notebook -c conda-forge \
+    python=3.11 \
+    jupyterlab \
+    notebook \
+    r-base \
+    r-irkernel \
+    r-devtools \
+    r-sp \
+    r-stringr \
+    r-plyr \
+    r-ggplot2 \
+    r-terra \
+    r-ncdf4 \
+    nodejs \
+    && conda clean --all -f -y
+
+# Activate conda environment
+ENV PATH /opt/conda/envs/notebook/bin:$PATH
+SHELL ["/bin/bash", "-c"]
+
+# Install additional R packages
+RUN source activate notebook && \
+    R -e "install.packages(c('rgdal', 'ggmap'), repos='https://cloud.r-project.org/')" && \
+    R -e "devtools::install_github('NCAR/rwrfhydro')"
+
+# 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:${PATH} \
- && npm install -g npm@7.24.0 \
- && pip install --no-cache-dir \
-        https://github.com/jupyterhub/jupyter-remote-desktop-proxy/archive/main.zip
-
-# Install jupyterlab_vim extension
-RUN pip install jupyterlab_vim
+RUN wget -q "https://sourceforge.net/projects/turbovnc/files/${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 && \
+    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/*
 
-# TO download the folder/files:
-RUN pip install jupyter-tree-download
+# Install jupyter-remote-desktop-proxy
+RUN pip install --no-cache-dir \
+    https://github.com/jupyterhub/jupyter-remote-desktop-proxy/archive/main.zip
 
-# 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 - && \
+# 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 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
+# Set up Jupyter Lab
+RUN mkdir /opt/notebooks && \
+    jupyter notebook --generate-config && \
+    echo "c.NotebookApp.ip = '0.0.0.0'" >> ~/.jupyter/jupyter_notebook_config.py && \
+    echo "c.NotebookApp.open_browser = False" >> ~/.jupyter/jupyter_notebook_config.py
 
-# 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
+WORKDIR /opt/notebooks
 
-# Install dataretrieval package
-RUN pip install dataretrieval
+# Expose port for Jupyter Lab
+EXPOSE 8888
 
-USER ${NB_USER}
+# Start Jupyter Lab
+CMD ["jupyter", "lab", "--ip=0.0.0.0", "--allow-root"]