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Initial contribution of R, scipy, minimal notebook stacks

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Peter Parente
2015-07-19 23:20:27 -04:00
parent e3ef913ff8
commit 8ab2e0ed8f
11 changed files with 316 additions and 1 deletions
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17
Makefile Normal file
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.PHONY: build dev help
OWNER:=jupyter
STACK?=
help:
@echo
@echo 'build STACK=<dirname> - build using Dockerfile in named directory'
@echo ' dev STACK=<dirname> - run container using stack name'
@echo
build:
@cd $(STACK) && \
docker build --rm --force-rm -t $(OWNER)/$(STACK) .
dev:
docker run -it --rm -p 8888:8888 $(OWNER)/$(STACK)

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README.md
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# docker-stacks
Stacks of Jupyter applications+kernels, in docker
Opinionated stacks of ready-to-run Jupyter applications in Docker.
## Quick Start
If you already have Docker configured and know exactly what you'd like to run, this one-liner is for you:
```
docker run -d -P jupyter/<your desired stack>
```
## Getting Started
If this is your first time using Docker or any of the Jupyter projects, do the following to get started.
1. [Install Docker](https://docs.docker.com/installation/) on your host of choice.
2. Click the folder for your desired stack on GitHub.
3. Follow the README in that stack.

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minimal-notebook/Dockerfile Normal file
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FROM debian:jessie
MAINTAINER Jupyter Project <jupyter@googlegroups.com>
# Install all OS dependencies for fully functional notebook server
ENV DEBIAN_FRONTEND noninteractive
RUN apt-get update && apt-get install -yq --no-install-recommends \
git \
vim \
wget \
build-essential \
python-dev \
ca-certificates \
bzip2 \
unzip \
libsm6 \
pandoc \
texlive-latex-base \
texlive-latex-extra \
texlive-fonts-extra \
texlive-fonts-recommended \
supervisor \
sudo \
&& apt-get clean
ENV CONDA_DIR /opt/conda
ENV NB_USER jovyan
# Install conda
RUN echo 'export PATH=$CONDA_DIR/bin:$PATH' > /etc/profile.d/conda.sh && \
wget --quiet https://repo.continuum.io/miniconda/Miniconda3-3.9.1-Linux-x86_64.sh && \
/bin/bash /Miniconda3-3.9.1-Linux-x86_64.sh -b -p $CONDA_DIR && \
rm Miniconda3-3.9.1-Linux-x86_64.sh && \
$CONDA_DIR/bin/conda install --yes conda==3.14.1
# Create non-root user
RUN useradd -m -s /bin/bash $NB_USER
RUN chown -R $NB_USER:$NB_USER $CONDA_DIR
RUN chown $NB_USER:$NB_USER /home/$NB_USER -R
# Configure user environment
USER $NB_USER
ENV HOME /home/$NB_USER
ENV SHELL /bin/bash
ENV USER $NB_USER
ENV PATH $CONDA_DIR/bin:$PATH
# Setup a work directory rooted in home for ease of volume mounting
ENV WORK $HOME/work
RUN mkdir -p $WORK
WORKDIR $WORK
# Install Jupyter notebook
RUN conda install --yes \
ipython-notebook==3.2 \
terminado \
&& conda clean -yt
# Configure Jupyter
RUN ipython profile create
# Configure container startup
EXPOSE 8888
USER root
CMD ["supervisord", "-n", "-c", "/etc/supervisor/supervisord.conf"]
# Add local files as late as possible to avoid cache busting
COPY ipython_notebook_config.py $HOME/.ipython/profile_default/
COPY notebook.conf /etc/supervisor/conf.d/
COPY enable_sudo.sh /usr/local/bin/
RUN chown $NB_USER:$NB_USER $HOME/.ipython/profile_default/ipython_notebook_config.py

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minimal-notebook/README.md Normal file
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# Minimal Jupyter Notebook Stack
## What it Gives You
* Jupyter Notebook server v3.2.x
* Conda Python 3.4.x
* No preinstalled scientific computing packages
* Options for HTTPS, password auth, and passwordless `sudo`
## Basic Use
The following command starts a container with the Notebook server listening for HTTP connections on port 8888 without authentication configured.
```
docker run -d -p 8888:8888 jupyter/minimal-notebook
```
## Options
You may customize the execution of the Docker container and the Notebook server it contains with the following optional arguments.
* `-e PASSWORD="YOURPASS"` - Configures Jupyter Notebook to require the given password. Should be conbined with `USE_HTTPS` on untrusted networks.
* `-e USE_HTTPS=yes` - Configures Jupyter Notebook to accept encrypted HTTPS connections. If a `pem` file containing a SSL certificate and key is not found in `/home/jovyan/.ipython/profile_default/security/notebook.pem`, the container will generate a self-signed certificate for you.
* `-e GRANT_SUDO=yes` - Gives the `jovyan` user passwordless `sudo` capability. Useful for installing OS packages. **You should only enable `sudo` if you trust the user or if the container is running on an isolated host.**
* `-v /some/host/folder/for/work:/home/jovyan/work` - Host mounts the default working directory on the host to preserve work even when the container is destroyed and recreated (e.g., during an upgrade).
* `-v /some/host/folder/for/server.pem:/home/jovyan/.ipython/profile_default/security/notebook.pem` - Mounts a SSL certificate plus key for `USE_HTTPS`. Useful if you have a real certificate for the domain under which you are running the Notebook server.

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minimal-notebook/enable_sudo.sh Executable file
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#!/bin/bash
if [ ! -z "$GRANT_SUDO" ]; then
echo "$NB_USER ALL=(ALL) NOPASSWD:ALL" > /etc/sudoers.d/notebook
fi

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minimal-notebook/ipython_notebook_config.py Normal file
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import subprocess
import os
PEM_FILE = os.path.join(os.path.dirname(__file__), 'security/notebook.pem')
c = get_config()
c.NotebookApp.ip = '*'
c.NotebookApp.open_browser = False
c.NotebookApp.port = 8888
# Set a certificate if USE_HTTPS is set to any value
if 'USE_HTTPS' in os.environ:
if not os.path.isfile(PEM_FILE):
# Generate a certificate if one doesn't exist on disk
subprocess.check_call(['openssl', 'req', '-new',
'-newkey', 'rsa:2048', '-days', '365', '-nodes', '-x509',
'-subj', '/C=XX/ST=XX/L=XX/O=generated/CN=generated',
'-keyout', PEM_FILE, '-out', PEM_FILE])
c.NotebookApp.certfile = PEM_FILE
# Set a password if PASSWORD is set
if 'PASSWORD' in os.environ:
from IPython.lib import passwd
c.NotebookApp.password = passwd(os.environ['PASSWORD'])
del os.environ['PASSWORD']

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minimal-notebook/notebook.conf Normal file
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[program:notebook]
user=jovyan
umask=0002
directory=/home/jovyan/work
command=ipython notebook
autostart=true
autorestart=true
stdout_logfile=/var/log/supervisor/%(program_name)s.log
redirect_stderr=true
[program:sudoers]
command=enable_sudo.sh
autostart=true
autorestart=false
stdout_logfile=/var/log/supervisor/%(program_name)s.log
redirect_stderr=true
startretries=0
startsecs=0

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r-notebook/Dockerfile Normal file
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FROM jupyter/minimal-notebook
MAINTAINER Jupyter Project <jupyter@googlegroups.com>
# R pre-requisites
RUN apt-get install -y --no-install-recommends \
libxrender1 \
fonts-dejavu \
gfortran \
gcc && apt-get clean
USER jovyan
# R packages
RUN conda config --add channels r
RUN conda install --yes \
'r-base=3.1*' \
'r-irkernel=0.4*' \
'r-plyr=1.8*' \
'r-devtools=1.7*' \
'r-dplyr=0.4*' \
'r-ggplot2=1.0*' \
'r-tidyr=0.2*' \
'r-shiny=0.11*' \
'r-rmarkdown=0.5*' \
'r-forecast=5.8*' \
'r-stringr=0.6*' \
'r-rsqlite=1.0*' \
'r-reshape2=1.4*' \
'r-nycflights13=0.1*' \
'r-caret=6.0*' \
'r-rcurl=1.95*' \
'r-randomforest=4.6*' && conda clean -yt
# Switch back to root so that supervisord runs under that user
USER root

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r-notebook/README.md Normal file
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# Jupyter Notebook R Stack
## What it Gives You
* Jupyter Notebook server v3.2.x
* Conda R v3.1.x and channel
* plyr, devtools, dplyr, ggplot2, tidyr, shiny, rmarkdown, forecast, stringr, rsqlite, reshape2, nycflights13, caret, rcurl, and randomforest pre-installed
* Options for HTTPS, password auth, and passwordless `sudo`
## Basic Use
The following command starts a container with the Notebook server listening for HTTP connections on port 8888 without authentication configured.
```
docker run -d -p 8888:8888 jupyter/r-notebook
```
## Options
You may customize the execution of the Docker container and the Notebook server it contains with the following optional arguments.
* `-e PASSWORD="YOURPASS"` - Configures Jupyter Notebook to require the given password. Should be conbined with `USE_HTTPS` on untrusted networks.
* `-e USE_HTTPS=yes` - Configures Jupyter Notebook to accept encrypted HTTPS connections. If a `pem` file containing a SSL certificate and key is not found in `/home/jovyan/.ipython/profile_default/security/notebook.pem`, the container will generate a self-signed certificate for you.
* `-e GRANT_SUDO=yes` - Gives the `jovyan` user passwordless `sudo` capability. Useful for installing OS packages. **You should only enable `sudo` if you trust the user or if the container is running on an isolated host.**
* `-v /some/host/folder/for/work:/home/jovyan/work` - Host mounts the default working directory on the host to preserve work even when the container is destroyed and recreated (e.g., during an upgrade).
* `-v /some/host/folder/for/server.pem:/home/jovyan/.ipython/profile_default/security/notebook.pem` - Mounts a SSL certificate plus key for `USE_HTTPS`. Useful if you have a real certificate for the domain under which you are running the Notebook server.

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FROM jupyter/minimal-notebook
MAINTAINER Jupyter Project <jupyter@googlegroups.com>
USER jovyan
# Install Python 3 packages
RUN conda install --yes \
'pandas=0.16*' \
'matplotlib=1.4*' \
'scipy=0.15*' \
'seaborn=0.6*' \
'scikit-learn=0.16*' \
'scikit-image=0.11*' \
'sympy=0.7*' \
'cython=0.22*' \
'patsy=0.3*' \
'statsmodels=0.6*' \
'cloudpickle=0.1*' \
'dill=0.2*' \
'numba=0.20*' \
'bokeh=0.9*' \
&& conda clean -yt
# Install Python 2 packages and kernel spec
RUN conda create -p $CONDA_DIR/envs/python2 python=2.7 \
'ipython=3.2*' \
'pandas=0.16*' \
'matplotlib=1.4*' \
'scipy=0.15*' \
'seaborn=0.6*' \
'scikit-learn=0.16*' \
'scikit-image=0.11*' \
'sympy=0.7*' \
'cython=0.22*' \
'patsy=0.3*' \
'statsmodels=0.6*' \
'cloudpickle=0.1*' \
'dill=0.2*' \
'numba=0.20*' \
'bokeh=0.9*' \
pyzmq \
&& conda clean -yt
RUN $CONDA_DIR/envs/python2/bin/python \
$CONDA_DIR/envs/python2/bin/ipython \
kernelspec install-self --user
# Switch back to root so that supervisord runs under that user
USER root

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# Jupyter Notebook Scientific Python Stack
## What it Gives You
* Jupyter Notebook server v3.2.x
* Conda Python 3.4.x and Python 2.7.x environments
* pandas, matplotlib, scipy, seaborn, scikit-learn pre-installed
* Options for HTTPS, password auth, and passwordless `sudo`
## Basic Use
The following command starts a container with the Notebook server listening for HTTP connections on port 8888 without authentication configured.
```
docker run -d -p 8888:8888 jupyter/scipy-notebook
```
## Options
You may customize the execution of the Docker container and the Notebook server it contains with the following optional arguments.
* `-e PASSWORD="YOURPASS"` - Configures Jupyter Notebook to require the given password. Should be conbined with `USE_HTTPS` on untrusted networks.
* `-e USE_HTTPS=yes` - Configures Jupyter Notebook to accept encrypted HTTPS connections. If a `pem` file containing a SSL certificate and key is not found in `/home/jovyan/.ipython/profile_default/security/notebook.pem`, the container will generate a self-signed certificate for you.
* `-e GRANT_SUDO=yes` - Gives the `jovyan` user passwordless `sudo` capability. Useful for installing OS packages. **You should only enable `sudo` if you trust the user or if the container is running on an isolated host.**
* `-v /some/host/folder/for/work:/home/jovyan/work` - Host mounts the default working directory on the host to preserve work even when the container is destroyed and recreated (e.g., during an upgrade).
* `-v /some/host/folder/for/server.pem:/home/jovyan/.ipython/profile_default/security/notebook.pem` - Mounts a SSL certificate plus key for `USE_HTTPS`. Useful if you have a real certificate for the domain under which you are running the Notebook server.