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Commit 6880d2f

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mmckymmcky
committedDec 8, 2015
Updating docker image to be based on the Jupyter defined datascience-notebook to remove downstream management
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‎Dockerfile

+12-86
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# Econometrics Book Base Docker Image (for tmpnb orchestrate.py server)
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# User: econ
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# Econometrics Book Docker Image
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# User: jovyan
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# This uses the Jupyter DataScience Docker Container with Python, R and Julia
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FROM debian:jessie
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FROM jupyter/datascience-notebook
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MAINTAINER Matthew McKay <mamckay@gmail.com>
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# Install all OS dependencies for fully functional notebook server
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ENV DEBIAN_FRONTEND noninteractive
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RUN apt-get update && apt-get install -yq --no-install-recommends \
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git \
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vim \
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wget \
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build-essential \
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python-dev \
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ca-certificates \
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bzip2 \
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unzip \
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libsm6 \
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pandoc \
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texlive-latex-base \
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texlive-latex-extra \
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texlive-fonts-extra \
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texlive-fonts-recommended \
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supervisor \
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sudo \
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&& apt-get clean
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# Julia dependencies
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RUN apt-get install -y julia libnettle4 && apt-get clean
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# R dependencies that conda can't provide (X, fonts, compilers)
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RUN apt-get install -y libzmq3-dev libcurl4-openssl-dev libxrender1 fonts-dejavu gfortran gcc && apt-get clean
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ENV CONDA_DIR /opt/conda
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# Install conda
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RUN echo 'export PATH=$CONDA_DIR/bin:$PATH' > /etc/profile.d/conda.sh && \
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wget --quiet https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
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/bin/bash Miniconda3-latest-Linux-x86_64.sh -b -p $CONDA_DIR && \
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rm Miniconda3-latest-Linux-x86_64.sh && \
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$CONDA_DIR/bin/conda install --yes python=3.5 anaconda && $CONDA_DIR/bin/conda clean -yt
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# We run our docker images with a non-root user as a security precaution.
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# econ is our user
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RUN useradd -m -s /bin/bash econ
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RUN chown -R econ:econ $CONDA_DIR
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EXPOSE 8888
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USER econ
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ENV HOME /home/econ
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ENV SHELL /bin/bash
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ENV USER econ
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ENV PATH $CONDA_DIR/bin:$PATH
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WORKDIR $HOME
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RUN conda install --yes ipython-notebook terminado && conda clean -yt
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RUN ipython profile create
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# Workaround for issue with ADD permissions
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USER root
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ADD notebooks/ /home/econ/
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RUN chown econ:econ /home/econ -R
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USER econ
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# Python packages
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RUN conda install --yes python=3.5 anaconda && conda clean -yt
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RUN pip install quantecon
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# Now for a python2 environment
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# RUN conda create -p $CONDA_DIR/envs/python2 python=2.7 ipython numpy pandas scikit-learn scikit-image matplotlib scipy seaborn sympy cython patsy statsmodels cloudpickle dill numba bokeh && conda clean -yt
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# RUN $CONDA_DIR/envs/python2/bin/python $CONDA_DIR/envs/python2/bin/ipython kernelspec install-self --user
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# RUN source activate python2 && pip install quantecon && source deactivate python2
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#-Add Notebooks-#
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ADD notebooks/ /home/jovyan/work/
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# R packages
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RUN conda config --add channels r
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RUN conda install --yes r-irkernel r-plyr r-devtools r-rcurl r-dplyr r-ggplot2 r-caret rpy2 r-tidyr r-shiny r-rmarkdown r-forecast r-stringr r-rsqlite r-reshape2 r-nycflights13 r-randomforest && conda clean -yt
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# IJulia and Julia packages
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RUN julia -e 'Pkg.add("IJulia")'
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# RUN julia -e 'Pkg.add("PyPlot")' && julia -e 'Pkg.add("Distributions")' && julia -e 'Pkg.add("KernelEstimator")'
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# julia -e 'Pkg.add("Gadfly")' && julia -e 'Pkg.add("RDatasets")' &&
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#Add Templates
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USER root
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ADD profile_default /home/econ/.ipython/profile_default
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#-Add Templates-#
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ADD jupyter_notebook_config.py /home/jovyan/.jupyter/
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ADD templates/ /srv/templates/
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RUN chmod a+rX /srv/templates
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USER econ
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# Convert notebooks to the current format
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RUN find /home/. -name '*.ipynb' -exec ipython nbconvert --to notebook {} --output {} \;
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RUN find /home/. -name '*.ipynb' -exec ipython trust {} \;
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#-Convert notebooks to the current format-#
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RUN find /home/. -name '*.ipynb' -exec jupyter nbconvert --to notebook {} --output {} \;
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RUN find /home/. -name '*.ipynb' -exec jupyter trust {} \;
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CMD ipython notebook
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USER jovyan

‎jupyter_notebook_config.py

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# Modified to include custom template
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# Copyright (c) Jupyter Development Team.
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from jupyter_core.paths import jupyter_data_dir
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import subprocess
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import os
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import errno
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import stat
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PEM_FILE = os.path.join(jupyter_data_dir(), 'notebook.pem')
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c = get_config()
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c.NotebookApp.ip = '*'
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c.NotebookApp.port = 8888
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c.NotebookApp.open_browser = False
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# Include our extra templates
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c.NotebookApp.extra_template_paths = ['/srv/templates/']
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# Set a certificate if USE_HTTPS is set to any value
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if 'USE_HTTPS' in os.environ:
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if not os.path.isfile(PEM_FILE):
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# Ensure PEM_FILE directory exists
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dir_name = os.path.dirname(PEM_FILE)
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try:
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os.makedirs(dir_name)
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except OSError as exc: # Python >2.5
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if exc.errno == errno.EEXIST and os.path.isdir(dir_name):
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pass
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else: raise
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# Generate a certificate if one doesn't exist on disk
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subprocess.check_call(['openssl', 'req', '-new',
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'-newkey', 'rsa:2048', '-days', '365', '-nodes', '-x509',
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'-subj', '/C=XX/ST=XX/L=XX/O=generated/CN=generated',
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'-keyout', PEM_FILE, '-out', PEM_FILE])
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# Restrict access to PEM_FILE
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os.chmod(PEM_FILE, stat.S_IRUSR | stat.S_IWUSR)
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c.NotebookApp.certfile = PEM_FILE
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# Set a password if PASSWORD is set
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if 'PASSWORD' in os.environ:
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from IPython.lib import passwd
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c.NotebookApp.password = passwd(os.environ['PASSWORD'])
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del os.environ['PASSWORD']

‎scripts/run-local.sh

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@@ -3,4 +3,4 @@ export TOKEN=$( head -c 30 /dev/urandom | xxd -p )
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docker run --net=host -d -e CONFIGPROXY_AUTH_TOKEN=$TOKEN --name=proxy jupyter/configurable-http-proxy --default-target http://127.0.0.1:9999
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docker run --net=host -d -e CONFIGPROXY_AUTH_TOKEN=$TOKEN \
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-v /var/run/docker.sock:/docker.sock \
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jupyter/tmpnb python orchestrate.py --image='sanguineturtle/econometrics' --command="ipython notebook --NotebookApp.base_url={base_path} --ip=0.0.0.0 --port {port}"
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jupyter/tmpnb python orchestrate.py --image='sanguineturtle/econometrics' --command="jupyter notebook --NotebookApp.base_url={base_path} --ip=0.0.0.0 --port {port}"

‎scripts/run.sh

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@@ -6,4 +6,5 @@ export TOKEN=$( head -c 30 /dev/urandom | xxd -p )
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docker run --net=host -d -e CONFIGPROXY_AUTH_TOKEN=$TOKEN --name=proxy jupyter/configurable-http-proxy --default-target http://127.0.0.1:9999
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docker run --net=host -d -e CONFIGPROXY_AUTH_TOKEN=$TOKEN \
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-v /var/run/docker.sock:/docker.sock \
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jupyter/tmpnb python orchestrate.py --image='sanguineturtle/econometrics' --command="ipython notebook --NotebookApp.base_url={base_path} --ip=0.0.0.0 --port {port}"
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jupyter/tmpnb python orchestrate.py --image='sanguineturtle/econometrics' --command="jupyter notebook --NotebookApp.base_url={base_path} --ip=0.0.0.0 --port {port}"
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‎scripts/setup-aws.sh

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sudo service docker start
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sudo usermod -a -G docker ec2-user
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#LogOut-LogIn
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docker pull jupyter/tmpnb
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docker pull jupyter/configurable-http-proxy
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docker pull sanguineturtle/econometrics
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export TOKEN=$( head -c 30 /dev/urandom | xxd -p )
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docker run --net=host -d -e CONFIGPROXY_AUTH_TOKEN=$TOKEN --name=proxy jupyter/configurable-http-proxy --default-target http://127.0.0.1:9999
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docker run --net=host -d -e CONFIGPROXY_AUTH_TOKEN=$TOKEN \
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-v /var/run/docker.sock:/docker.sock \
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jupyter/tmpnb python orchestrate.py --image='sanguineturtle/econometrics' --command="ipython notebook --NotebookApp.base_url={base_path} --ip=0.0.0.0 --port {port}"
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# Run ./scripts/run-local.sh

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