Dockerfile

# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.
ARG BASE_CONTAINER=jupyter/scipy-notebook
FROM $BASE_CONTAINER

LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"

# Set when building on Travis so that certain long-running build steps can
# be skipped to shorten build time.
ARG TEST_ONLY_BUILD

# Fix DL4006
SHELL ["/bin/bash", "-o", "pipefail", "-c"]

USER root

# R pre-requisites
RUN apt-get update && \
    apt-get install -y --no-install-recommends \
    fonts-dejavu \
    gfortran \
    gcc && \
    rm -rf /var/lib/apt/lists/*

# Julia dependencies
# install Julia packages in /opt/julia instead of $HOME
ENV JULIA_DEPOT_PATH=/opt/julia
ENV JULIA_PKGDIR=/opt/julia
ENV JULIA_VERSION=1.4.1

WORKDIR /tmp

# hadolint ignore=SC2046
RUN mkdir "/opt/julia-${JULIA_VERSION}" && \
    wget -q https://julialang-s3.julialang.org/bin/linux/x64/$(echo "${JULIA_VERSION}" | cut -d. -f 1,2)"/julia-${JULIA_VERSION}-linux-x86_64.tar.gz" && \
    echo "fd6d8cadaed678174c3caefb92207a3b0e8da9f926af6703fb4d1e4e4f50610a *julia-${JULIA_VERSION}-linux-x86_64.tar.gz" | sha256sum -c - && \
    tar xzf "julia-${JULIA_VERSION}-linux-x86_64.tar.gz" -C "/opt/julia-${JULIA_VERSION}" --strip-components=1 && \
    rm "/tmp/julia-${JULIA_VERSION}-linux-x86_64.tar.gz"
RUN ln -fs /opt/julia-*/bin/julia /usr/local/bin/julia

# Show Julia where conda libraries are \
RUN mkdir /etc/julia && \
    echo "push!(Libdl.DL_LOAD_PATH, \"$CONDA_DIR/lib\")" >> /etc/julia/juliarc.jl && \
    # Create JULIA_PKGDIR \
    mkdir "${JULIA_PKGDIR}" && \
    chown "${NB_USER}" "${JULIA_PKGDIR}" && \
    fix-permissions "${JULIA_PKGDIR}"

USER $NB_UID

# R packages including IRKernel which gets installed globally.
RUN conda install --quiet --yes \
    'r-base=3.6.3' \
    'r-caret=6.0*' \
    'r-crayon=1.3*' \
    'r-devtools=2.3*' \
    'r-forecast=8.12*' \
    'r-hexbin=1.28*' \
    'r-htmltools=0.4*' \
    'r-htmlwidgets=1.5*' \
    'r-irkernel=1.1*' \
    'r-nycflights13=1.0*' \
    'r-plyr=1.8*' \
    'r-randomforest=4.6*' \
    'r-rcurl=1.98*' \
    'r-reshape2=1.4*' \
    'r-rmarkdown=2.1*' \
    'r-rsqlite=2.2*' \
    'r-shiny=1.4*' \
    'r-tidyverse=1.3*' \
    'rpy2=3.1*' \
    && \
    conda clean --all -f -y && \
    fix-permissions "${CONDA_DIR}" && \
    fix-permissions "/home/${NB_USER}"

# Add Julia packages. Only add HDF5 if this is not a test-only build since
# it takes roughly half the entire build time of all of the images on Travis
# to add this one package and often causes Travis to timeout.
#
# Install IJulia as jovyan and then move the kernelspec out
# to the system share location. Avoids problems with runtime UID change not
# taking effect properly on the .local folder in the jovyan home dir.
RUN julia -e 'import Pkg; Pkg.update(); Pkg.add("FFTW"); Pkg.add("GZip"); Pkg.add("PyPlot"); Pkg.precompile();' && \
    (test $TEST_ONLY_BUILD || julia -e 'import Pkg; Pkg.add("HDF5")') && \
    julia -e "using Pkg; pkg\"add IJulia\"; pkg\"precompile\"" && \
    # move kernelspec out of home \
    mv "${HOME}/.local/share/jupyter/kernels/julia"* "${CONDA_DIR}/share/jupyter/kernels/" && \
    chmod -R go+rx "${CONDA_DIR}/share/jupyter" && \
    rm -rf "${HOME}/.local" && \
    fix-permissions "${JULIA_PKGDIR}" "${CONDA_DIR}/share/jupyter"

WORKDIR $HOME

USER root

RUN apt-get update && \
    apt-get install -y --no-install-recommends \
        emacs \
        git \
        inkscape \
        jed \
        libsm6 \
        libxext-dev \
        libxrender1 \
        lmodern \
        netcat \
        unzip \
        nano \
        curl \
        wget \
        cmake \
        rsync \
        gnuplot-x11 \
        libopenblas-base \
        python3-dev \
        ttf-dejavu && \
    apt-get clean && \
    apt-get autoremove && \
    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*


RUN cd $HOME/work;\
    pip install --upgrade pip; \
    pip install sos\
                sos-notebook \
                sos-python \
                sos-bash \
                sos-matlab \
                sos-ruby \
                sos-sas \
                sos-julia \
                sos-javascript\
                sos-r\
                scipy \
                plotly \
                dash \
                dash_core_components \
                dash_html_components \
                dash_dangerously_set_inner_html \
                dash-renderer \
                flask \
                ipywidgets \
                nibabel \
                nbconvert; \
    python -m sos_notebook.install;\
    jupyter labextension install --minimize=False jupyterlab-sos; \
    git clone --single-branch -b master https://github.com/Notebook-Factory/PhaseUnwrapping_book.git; \
    cd PhaseUnwrapping_book;\
    chmod -R 777 $HOME/work/PhaseUnwrapping_book
    
WORKDIR $HOME/work/PhaseUnwrapping_book

USER $NB_UID