Dockerfile

# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.

# Debian Jessie debootstrap from 2017-02-27
# https://github.com/docker-library/official-images/commit/aa5973d0c918c70c035ec0746b8acaec3a4d7777
FROM debian@sha256:52af198afd8c264f1035206ca66a5c48e602afb32dc912ebf9e9478134601ec4

MAINTAINER dataistanbul <contact@dataistanbul.org>

USER root

# Install all OS dependencies for notebook server that starts but lacks all
# features (e.g., download as all possible file formats)
ENV DEBIAN_FRONTEND noninteractive
RUN REPO=http://cdn-fastly.deb.debian.org \
 && echo "deb $REPO/debian jessie main\ndeb $REPO/debian-security jessie/updates main" > /etc/apt/sources.list \
 && apt-get update && apt-get -yq dist-upgrade \
 && apt-get install -yq --no-install-recommends \
    wget \
    bzip2 \
    ca-certificates \
    sudo \
    locales \
    fonts-liberation \
 && apt-get clean \
 && rm -rf /var/lib/apt/lists/*

RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
    locale-gen

# Install Tini
RUN wget --quiet https://github.com/krallin/tini/releases/download/v0.10.0/tini && \
    echo "1361527f39190a7338a0b434bd8c88ff7233ce7b9a4876f3315c22fce7eca1b0 *tini" | sha256sum -c - && \
    mv tini /usr/local/bin/tini && \
    chmod +x /usr/local/bin/tini

# Configure environment
ENV CONDA_DIR /opt/conda
ENV PATH $CONDA_DIR/bin:$PATH
ENV SHELL /bin/bash
ENV NB_USER jovyan
ENV NB_UID 1000
ENV HOME /home/$NB_USER
ENV LC_ALL en_US.UTF-8
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US.UTF-8

# Create jovyan user with UID=1000 and in the 'users' group
RUN useradd -m -s /bin/bash -N -u $NB_UID $NB_USER && \
    mkdir -p $CONDA_DIR && \
    chown $NB_USER $CONDA_DIR

USER $NB_USER

# Setup jovyan home directory
RUN mkdir /home/$NB_USER/work && \
    mkdir /home/$NB_USER/.jupyter && \
    echo "cacert=/etc/ssl/certs/ca-certificates.crt" > /home/$NB_USER/.curlrc

# Install conda as jovyan
RUN cd /tmp && \
    mkdir -p $CONDA_DIR && \
    wget --quiet https://repo.continuum.io/miniconda/Miniconda3-4.2.12-Linux-x86_64.sh && \
    echo "c59b3dd3cad550ac7596e0d599b91e75d88826db132e4146030ef471bb434e9a *Miniconda3-4.2.12-Linux-x86_64.sh" | sha256sum -c - && \
    /bin/bash Miniconda3-4.2.12-Linux-x86_64.sh -f -b -p $CONDA_DIR && \
    rm Miniconda3-4.2.12-Linux-x86_64.sh && \
    $CONDA_DIR/bin/conda config --system --add channels conda-forge && \
    $CONDA_DIR/bin/conda config --system --set auto_update_conda false && \
    conda clean -tipsy

# Install Jupyter Notebook and Hub
RUN conda install --quiet --yes \
    'notebook=5.0.*' \
    'jupyterhub=0.7.*' \
    'jupyterlab=0.18.*' \
    && conda clean -tipsy

USER root

EXPOSE 8888
WORKDIR /home/$NB_USER/work

# Add local files as late as possible to avoid cache busting
COPY start.sh /usr/local/bin/
COPY start-notebook.sh /usr/local/bin/
COPY start-singleuser.sh /usr/local/bin/
COPY jupyter_notebook_config.py /home/$NB_USER/.jupyter/
RUN chown -R $NB_USER:users /home/$NB_USER/.jupyter

# Install all OS dependencies for fully functional notebook server
RUN apt-get update && apt-get install -yq --no-install-recommends \
    git \
    vim \
    jed \
    emacs \
    build-essential \
    python-dev \
    unzip \
    libsm6 \
    pandoc \
    texlive-latex-base \
    texlive-latex-extra \
    texlive-fonts-extra \
    texlive-fonts-recommended \
    texlive-generic-recommended \
    texlive-xetex \
    lmodern \
    libxrender1 \
    inkscape \
    ssh \
    && apt-get clean && \
    rm -rf /var/lib/apt/lists/*

# libav-tools for matplotlib anim
RUN apt-get update && \
    apt-get install -y --no-install-recommends libav-tools && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/*

USER $NB_USER

# Install Python 3 packages
# Remove pyqt and qt pulled in for matplotlib since we're only ever going to
# use notebook-friendly backends in these images
RUN conda install --quiet --yes \
    'nomkl' \
    'ipywidgets=6.0*' \
    'pandas=0.19*' \
    'numexpr=2.6*' \
    'matplotlib=2.0*' \
    'scipy=0.19*' \
    'seaborn=0.7*' \
    'scikit-learn=0.18*' \
    'scikit-image=0.12*' \
    'sympy=1.0*' \
    'cython=0.25*' \
    'patsy=0.4*' \
    'statsmodels=0.8*' \
    'cloudpickle=0.2*' \
    'dill=0.2*' \
    'numba=0.31*' \
    'bokeh=0.12*' \
    'sqlalchemy=1.1*' \
    'hdf5=1.8.17' \
    'h5py=2.6*' \
    'vincent=0.4.*' \
    'beautifulsoup4=4.5.*' \
    'xlrd'  && \
    conda remove --quiet --yes --force qt pyqt && \
    conda clean -tipsy

# Activate ipywidgets extension in the environment that runs the notebook server
RUN jupyter nbextension enable --py widgetsnbextension --sys-prefix

# Install Python 2 packages
# Remove pyqt and qt pulled in for matplotlib since we're only ever going to
# use notebook-friendly backends in these images
RUN conda create --quiet --yes -p $CONDA_DIR/envs/python2 python=2.7 \
    'nomkl' \
    'ipython=5.3*' \
    'ipywidgets=6.0*' \
    'pandas=0.19*' \
    'numexpr=2.6*' \
    'matplotlib=2.0*' \
    'scipy=0.19*' \
    'seaborn=0.7*' \
    'scikit-learn=0.18*' \
    'scikit-image=0.12*' \
    'sympy=1.0*' \
    'cython=0.25*' \
    'patsy=0.4*' \
    'statsmodels=0.8*' \
    'cloudpickle=0.2*' \
    'dill=0.2*' \
    'numba=0.31*' \
    'bokeh=0.12*' \
    'hdf5=1.8.17' \
    'h5py=2.6*' \
    'sqlalchemy=1.1*' \
    'pyzmq' \
    'vincent=0.4.*' \
    'beautifulsoup4=4.5.*' \
    'xlrd' && \
    conda remove -n python2 --quiet --yes --force qt pyqt && \
    conda clean -tipsy
# Add shortcuts to distinguish pip for python2 and python3 envs
RUN ln -s $CONDA_DIR/envs/python2/bin/pip $CONDA_DIR/bin/pip2 && \
    ln -s $CONDA_DIR/bin/pip $CONDA_DIR/bin/pip3

# Import matplotlib the first time to build the font cache.
ENV XDG_CACHE_HOME /home/$NB_USER/.cache/
RUN MPLBACKEND=Agg $CONDA_DIR/envs/python2/bin/python -c "import matplotlib.pyplot"

# Configure ipython kernel to use matplotlib inline backend by default
RUN mkdir -p $HOME/.ipython/profile_default/startup
COPY mplimporthook.py $HOME/.ipython/profile_default/startup/

USER root

# Install Python 2 kernel spec globally to avoid permission problems when NB_UID
# switching at runtime and to allow the notebook server running out of the root
# environment to find it. Also, activate the python2 environment upon kernel
# launch.
RUN pip install kernda --no-cache && \
    $CONDA_DIR/envs/python2/bin/python -m ipykernel install && \
    kernda -o -y /usr/local/share/jupyter/kernels/python2/kernel.json && \
    pip uninstall kernda -y

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

# Julia dependencies
RUN echo "deb http://ppa.launchpad.net/staticfloat/juliareleases/ubuntu trusty main" > /etc/apt/sources.list.d/julia.list && \
    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 3D3D3ACC && \
    apt-get update && \
    apt-get install -y --no-install-recommends \
    julia \
    libnettle4 && apt-get clean && \
    rm -rf /var/lib/apt/lists/*

USER $NB_USER

# R packages including IRKernel which gets installed globally.
RUN conda config --add channels r && \
    conda install --quiet --yes \
    'rpy2=2.8*' \
    'r-base=3.3.2' \
    'r-irkernel=0.7*' \
    'r-plyr=1.8*' \
    'r-devtools=1.12*' \
    'r-tidyverse=1.0*' \
    'r-shiny=0.14*' \
    'r-rmarkdown=1.2*' \
    'r-forecast=7.3*' \
    'r-rsqlite=1.1*' \
    'r-reshape2=1.4*' \
    'r-nycflights13=0.2*' \
    'r-caret=6.0*' \
    'r-rcurl=1.95*' \
    'r-crayon=1.3*' \
    'r-randomforest=4.6*' && conda clean -tipsy

# Install IJulia packages 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 'Pkg.add("IJulia")' && \
    mv $HOME/.local/share/jupyter/kernels/julia* $CONDA_DIR/share/jupyter/kernels/ && \
    chmod -R go+rx $CONDA_DIR/share/jupyter && \
    rm -rf $HOME/.local

# Show Julia where conda libraries are
# Add essential packages
RUN echo "push!(Libdl.DL_LOAD_PATH, \"$CONDA_DIR/lib\")" > /home/$NB_USER/.juliarc.jl && \
    julia -e 'Pkg.add("Gadfly")' && julia -e 'Pkg.add("RDatasets")' && julia -F -e 'Pkg.add("HDF5")'

# Precompile Julia pakcages
RUN julia -e 'using IJulia' && julia -e 'using Gadfly' && julia -e 'using RDatasets'&& julia -e 'using HDF5'

# Configure container startup
ENTRYPOINT ["tini", "--"]
CMD ["start-notebook.sh"]