Added jupyter docker files
commit
cd49935e33
GPG Key ID:
AD62BB059C2AAEE4
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# Jupyter Docker Image
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This directory contains build files for a complete jupyter environment. It is based off the following repositories:
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- https://github.com/jupyter/docker-stacks
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- https://github.com/rgriffogoes/scraper-notebook
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- https://github.com/sharpTrick/sage-notebook
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The images these files produce contain everything you could possibly want in a jupyter notebook. Unfortunately, this also means that they take forever to build.
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## Building the Image
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To build this image, run `build/build.fish.` Edit the script to customize the image.
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## Image contents
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- jupyterlab, jupyterhub, notebook
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- latex + pandoc for exporting
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- mamba for packages
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- Python
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- Scrape tools (bs4, requests)
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- scipy, scikit-learn, scikit-image
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- tensorflow
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- sympy
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- numpy
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- matplotlib
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- pandas
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- Octave
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- R
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## TODO
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- User config
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- Volume permissions
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- Auto dark theme
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- Fix sage
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- Selenium (broken)
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- GPU support ([source](https://github.com/iot-salzburg/gpu-jupyter))
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- Haskell ([source](https://github.com/IHaskell/ihaskell-notebook))
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- Rust Kernel
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- C++ Kernel
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- Julia Kernel
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- Perl Kernel
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- Maxima Kernel
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FROM debian:bullseye
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ARG NB_USER="jovyan"
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ARG NB_UID="1000"
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ARG NB_GID="100"
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SHELL ["/bin/bash", "-o", "pipefail", "-c"]
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USER root
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# Install all packages
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ENV DEBIAN_FRONTEND noninteractive
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RUN apt-get update --yes && \
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apt-get upgrade --yes && \
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apt-get install --yes --no-install-recommends \
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# Basics
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# bzip2: to extract micromamba
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# tini: see https://github.com/krallin/tini#why-tini
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bzip2 \
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ca-certificates \
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fonts-liberation \
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locales \
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wget \
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sudo \
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tini \
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gcc \
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make \
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gnupg \
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curl \
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# Common tools
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# less: needed to run help in R (https://github.com/jupyter/docker-stacks/issues/1588)
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# ffmpeg: for matplotlib anim
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# cm-super, dvipng: for latex labels
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# build-essential: for cython
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build-essential \
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cm-super \
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dvipng \
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git \
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nano \
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tzdata \
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unzip \
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vim \
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openssh-client \
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less \
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ffmpeg \
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# Jupyter dependencies
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# pandoc: convert notebooks to html
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# texlive-*: for nbconvert
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pandoc \
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texlive \
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texlive-xetex \
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texlive-fonts-recommended \
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texlive-plain-generic \
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# Misc dependencies
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# build-essential: for cython
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# cm-super, dvipng: for latex labels
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# ffmpeg: for matplotlib anim
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build-essential \
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cm-super \
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dvipng \
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ffmpeg \
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&& \
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# Clean up and generate locales
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apt-get clean && rm -rf /var/lib/apt/lists/* && \
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echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
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locale-gen
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# Configure environment
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ENV CONDA_DIR=/opt/conda \
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SHELL=/bin/bash \
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NB_USER="${NB_USER}" \
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NB_UID=${NB_UID} \
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NB_GID=${NB_GID} \
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LC_ALL=en_US.UTF-8 \
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LANG=en_US.UTF-8 \
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LANGUAGE=en_US.UTF-8
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ENV PATH="${CONDA_DIR}/bin:${PATH}" \
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HOME="/home/${NB_USER}"
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# Copy a script that we will use to correct permissions after running certain commands
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COPY fix-permissions.sh /usr/local/bin/fix-permissions
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RUN chmod a+rx /usr/local/bin/fix-permissions
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# Enable prompt color in the skeleton .bashrc before creating the default NB_USER
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RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc && \
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# Add call to conda init script see https://stackoverflow.com/a/58081608/4413446
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echo 'eval "$(command conda shell.bash hook 2> /dev/null)"' >> /etc/skel/.bashrc
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# Create user
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RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
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sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && \
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sed -i.bak -e 's/^%sudo/#%sudo/' /etc/sudoers && \
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useradd \
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--no-log-init \
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--create-home \
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--no-user-group -u "${NB_UID}" \
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--shell /bin/bash \
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"${NB_USER}" \
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&& \
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mkdir -p "${CONDA_DIR}" && \
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chown "${NB_USER}:${NB_GID}" "${CONDA_DIR}" && \
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chmod g+w /etc/passwd && \
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fix-permissions "${HOME}" && \
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fix-permissions "${CONDA_DIR}"
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USER ${NB_UID}
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# Pin python version here, or set it to "default"
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ARG PYTHON_VERSION=3.10
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# Download and install Micromamba, and initialize Conda prefix.
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# <https://github.com/mamba-org/mamba#micromamba>
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# Similar projects using Micromamba:
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# - Micromamba-Docker: <https://github.com/mamba-org/micromamba-docker>
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# - repo2docker: <https://github.com/jupyterhub/repo2docker>
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# Install Python, Mamba, Jupyter Notebook, Lab, and Hub
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# Generate a notebook server config
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# Cleanup temporary files and remove Micromamba
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# Correct permissions
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COPY --chown="${NB_UID}:${NB_GID}" initial-condarc "${CONDA_DIR}/.condarc"
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WORKDIR /tmp
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RUN set -x && \
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# Get micromamba
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arch=$(uname -m) && \
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if [ "${arch}" = "x86_64" ]; then \
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# Should be simpler, see <https://github.com/mamba-org/mamba/issues/1437>
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arch="64"; \
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fi && \
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wget -qO /tmp/micromamba.tar.bz2 \
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"https://micromamba.snakepit.net/api/micromamba/linux-${arch}/latest" && \
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tar -xvjf /tmp/micromamba.tar.bz2 --strip-components=1 bin/micromamba && \
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rm /tmp/micromamba.tar.bz2 && \
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PYTHON_SPECIFIER="python=${PYTHON_VERSION}" && \
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if [[ "${PYTHON_VERSION}" == "default" ]]; then PYTHON_SPECIFIER="python"; fi && \
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#
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# Install packages
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./micromamba install \
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--root-prefix="${CONDA_DIR}" \
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--prefix="${CONDA_DIR}" \
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--yes \
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"${PYTHON_SPECIFIER}" \
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# Jupyter base
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"mamba" \
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"notebook" \
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"jupyterhub" \
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"jupyterlab" \
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&& \
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# Cleanup
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rm micromamba && \
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# Pin major.minor version of python
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mamba list python | \
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grep "^python " | \
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tr -s " " | \
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cut -d " " -f 1,2 \
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>> "${CONDA_DIR}/conda-meta/pinned" \
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&& \
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jupyter notebook --generate-config && \
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mamba clean --all -f -y && \
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npm cache clean --force && \
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jupyter lab clean && \
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rm -rf "/home/${NB_USER}/.cache/yarn" && \
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fix-permissions "${CONDA_DIR}" && \
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fix-permissions "/home/${NB_USER}"
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EXPOSE 8888
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ENTRYPOINT ["tini", "-g", "--"]
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CMD ["start-notebook.sh"]
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COPY start.sh start-notebook.sh start-singleuser.sh /usr/local/bin/
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COPY jupyter_server_config.py /etc/jupyter/
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# Add R mimetype option to specify how the plot returns from R to the browser
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COPY --chown=${NB_UID}:${NB_GID} Rprofile.site /opt/conda/lib/R/etc/
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USER root
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#COPY overrides.json /opt/conda/share/jupyter/lab/settings/
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RUN mkdir "${HOME}/notebooks" && \
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chown "${NB_UID}:${NB_GID}" "${HOME}/notebooks" &&\
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chmod u+rwx "${HOME}/notebooks"
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VOLUME "${HOME}/notebooks"
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# Legacy for Jupyter Notebook Server, see: [#1205](https://github.com/jupyter/docker-stacks/issues/1205)
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#RUN sed -re "s/c.ServerApp/c.NotebookApp/g" \
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# /etc/jupyter/jupyter_server_config.py > /etc/jupyter/jupyter_notebook_config.py && \
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# fix-permissions /etc/jupyter/
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# HEALTHCHECK documentation: https://docs.docker.com/engine/reference/builder/#healthcheck
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# This healtcheck works well for `lab`, `notebook`, `nbclassic`, `server` and `retro` jupyter commands
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# https://github.com/jupyter/docker-stacks/issues/915#issuecomment-1068528799
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HEALTHCHECK --interval=15s --timeout=3s --start-period=5s --retries=3 \
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CMD wget -O- --no-verbose --tries=1 --no-check-certificate \
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http${GEN_CERT:+s}://localhost:8888${JUPYTERHUB_SERVICE_PREFIX:-/}api || exit 1
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USER ${NB_UID}
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WORKDIR "${HOME}"
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# Add R mimetype to specify how the plot returns from R to the browser.
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# https://notebook.community/andrie/jupyter-notebook-samples/Changing%20R%20plot%20options%20in%20Jupyter
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options(jupyter.plot_mimetypes = c('text/plain', 'image/png', 'image/jpeg', 'image/svg+xml', 'application/pdf'))
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#!/bin/bash
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# set permissions on a directory
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# after any installation, if a directory needs to be (human) user-writable,
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# run this script on it.
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# It will make everything in the directory owned by the group ${NB_GID}
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# and writable by that group.
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# Deployments that want to set a specific user id can preserve permissions
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# by adding the `--group-add users` line to `docker run`.
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# uses find to avoid touching files that already have the right permissions,
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# which would cause massive image explosion
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# right permissions are:
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# group=${NB_GID}
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# AND permissions include group rwX (directory-execute)
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# AND directories have setuid,setgid bits set
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set -e
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for d in "$@"; do
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find "${d}" \
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! \( \
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-group "${NB_GID}" \
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-a -perm -g+rwX \
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\) \
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-exec chgrp "${NB_GID}" -- {} \+ \
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-exec chmod g+rwX -- {} \+
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# setuid, setgid *on directories only*
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find "${d}" \
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\( \
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-type d \
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-a ! -perm -6000 \
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\) \
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-exec chmod +6000 -- {} \+
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done
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# Conda configuration see https://conda.io/projects/conda/en/latest/configuration.html
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auto_update_conda: false
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show_channel_urls: true
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channels:
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- conda-forge
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import os
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import stat
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import subprocess
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from jupyter_core.paths import jupyter_data_dir
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c = get_config() # noqa: F821
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c.ServerApp.ip = "0.0.0.0"
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c.ServerApp.port = 8888
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c.ServerApp.open_browser = False
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c.ServerApp.root_dir = "/home/joyvan/notebooks"
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# to output both image/svg+xml and application/pdf plot formats in the notebook file
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c.InlineBackend.figure_formats = {"png", "jpeg", "svg", "pdf"}
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# https://github.com/jupyter/notebook/issues/3130
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c.FileContentsManager.delete_to_trash = False
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# Generate a self-signed certificate
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OPENSSL_CONFIG = """\
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[req]
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distinguished_name = req_distinguished_name
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[req_distinguished_name]
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"""
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if "GEN_CERT" in os.environ:
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dir_name = jupyter_data_dir()
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pem_file = os.path.join(dir_name, "notebook.pem")
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os.makedirs(dir_name, exist_ok=True)
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# Generate an openssl.cnf file to set the distinguished name
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cnf_file = os.path.join(os.getenv("CONDA_DIR", "/usr/lib"), "ssl", "openssl.cnf")
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if not os.path.isfile(cnf_file):
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with open(cnf_file, "w") as fh:
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fh.write(OPENSSL_CONFIG)
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# Generate a certificate if one doesn't exist on disk
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subprocess.check_call(
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[
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"openssl",
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"req",
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"-new",
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"-newkey=rsa:2048",
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"-days=365",
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"-nodes",
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"-x509",
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"-subj=/C=XX/ST=XX/L=XX/O=generated/CN=generated",
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f"-keyout={pem_file}",
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f"-out={pem_file}",
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]
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)
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# Restrict access to the file
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os.chmod(pem_file, stat.S_IRUSR | stat.S_IWUSR)
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c.ServerApp.certfile = pem_file
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# Change default umask for all subprocesses of the notebook server if set in
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# the environment
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if "NB_UMASK" in os.environ:
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os.umask(int(os.environ["NB_UMASK"], 8))
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@ -0,0 +1,5 @@
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{
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"@jupyterlab/apputils-extension:themes": {
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"theme": "JupyterLab Dark"
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}
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}
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@ -0,0 +1,21 @@
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#!/bin/bash
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# Copyright (c) Jupyter Development Team.
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# Distributed under the terms of the Modified BSD License.
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set -e
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# The Jupyter command to launch
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# JupyterLab by default
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||||||
|
DOCKER_STACKS_JUPYTER_CMD="${DOCKER_STACKS_JUPYTER_CMD:=lab}"
|
||||||
|
|
||||||
|
if [[ -n "${JUPYTERHUB_API_TOKEN}" ]]; then
|
||||||
|
echo "WARNING: using start-singleuser.sh instead of start-notebook.sh to start a server associated with JupyterHub."
|
||||||
|
exec /usr/local/bin/start-singleuser.sh "$@"
|
||||||
|
fi
|
||||||
|
|
||||||
|
wrapper=""
|
||||||
|
if [[ "${RESTARTABLE}" == "yes" ]]; then
|
||||||
|
wrapper=""
|
||||||
|
fi
|
||||||
|
|
||||||
|
exec /usr/local/bin/start.sh ${wrapper} jupyter ${DOCKER_STACKS_JUPYTER_CMD} ${NOTEBOOK_ARGS} "$@"
|
||||||
|
|
@ -0,0 +1,13 @@
|
||||||
|
#!/bin/bash
|
||||||
|
# Copyright (c) Jupyter Development Team.
|
||||||
|
# Distributed under the terms of the Modified BSD License.
|
||||||
|
|
||||||
|
set -e
|
||||||
|
|
||||||
|
# set default ip to 0.0.0.0
|
||||||
|
if [[ "${NOTEBOOK_ARGS} $*" != *"--ip="* ]]; then
|
||||||
|
NOTEBOOK_ARGS="--ip=0.0.0.0 ${NOTEBOOK_ARGS}"
|
||||||
|
fi
|
||||||
|
|
||||||
|
# shellcheck disable=SC1091,SC2086
|
||||||
|
. /usr/local/bin/start.sh jupyterhub-singleuser ${NOTEBOOK_ARGS} "$@"
|
||||||
|
|
@ -0,0 +1,262 @@
|
||||||
|
#!/bin/bash
|
||||||
|
# Copyright (c) Jupyter Development Team.
|
||||||
|
# Distributed under the terms of the Modified BSD License.
|
||||||
|
|
||||||
|
set -e
|
||||||
|
|
||||||
|
# The _log function is used for everything this script wants to log. It will
|
||||||
|
# always log errors and warnings, but can be silenced for other messages
|
||||||
|
# by setting JUPYTER_DOCKER_STACKS_QUIET environment variable.
|
||||||
|
_log () {
|
||||||
|
if [[ "$*" == "ERROR:"* ]] || [[ "$*" == "WARNING:"* ]] || [[ "${JUPYTER_DOCKER_STACKS_QUIET}" == "" ]]; then
|
||||||
|
echo "$@"
|
||||||
|
fi
|
||||||
|
}
|
||||||
|
_log "Entered start.sh with args:" "$@"
|
||||||
|
|
||||||
|
# The run-hooks function looks for .sh scripts to source and executable files to
|
||||||
|
# run within a passed directory.
|
||||||
|
run-hooks () {
|
||||||
|
if [[ ! -d "${1}" ]] ; then
|
||||||
|
return
|
||||||
|
fi
|
||||||
|
_log "${0}: running hooks in ${1} as uid / gid: $(id -u) / $(id -g)"
|
||||||
|
for f in "${1}/"*; do
|
||||||
|
case "${f}" in
|
||||||
|
*.sh)
|
||||||
|
_log "${0}: running script ${f}"
|
||||||
|
# shellcheck disable=SC1090
|
||||||
|
source "${f}"
|
||||||
|
;;
|
||||||
|
*)
|
||||||
|
if [[ -x "${f}" ]] ; then
|
||||||
|
_log "${0}: running executable ${f}"
|
||||||
|
"${f}"
|
||||||
|
else
|
||||||
|
_log "${0}: ignoring non-executable ${f}"
|
||||||
|
fi
|
||||||
|
;;
|
||||||
|
esac
|
||||||
|
done
|
||||||
|
_log "${0}: done running hooks in ${1}"
|
||||||
|
}
|
||||||
|
|
||||||
|
# A helper function to unset env vars listed in the value of the env var
|
||||||
|
# JUPYTER_ENV_VARS_TO_UNSET.
|
||||||
|
unset_explicit_env_vars () {
|
||||||
|
if [ -n "${JUPYTER_ENV_VARS_TO_UNSET}" ]; then
|
||||||
|
for env_var_to_unset in $(echo "${JUPYTER_ENV_VARS_TO_UNSET}" | tr ',' ' '); do
|
||||||
|
echo "Unset ${env_var_to_unset} due to JUPYTER_ENV_VARS_TO_UNSET"
|
||||||
|
unset "${env_var_to_unset}"
|
||||||
|
done
|
||||||
|
unset JUPYTER_ENV_VARS_TO_UNSET
|
||||||
|
fi
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
# Default to starting bash if no command was specified
|
||||||
|
if [ $# -eq 0 ]; then
|
||||||
|
cmd=( "bash" )
|
||||||
|
else
|
||||||
|
cmd=( "$@" )
|
||||||
|
fi
|
||||||
|
|
||||||
|
# NOTE: This hook will run as the user the container was started with!
|
||||||
|
run-hooks /usr/local/bin/start-notebook.d
|
||||||
|
|
||||||
|
# If the container started as the root user, then we have permission to refit
|
||||||
|
# the jovyan user, and ensure file permissions, grant sudo rights, and such
|
||||||
|
# things before we run the command passed to start.sh as the desired user
|
||||||
|
# (NB_USER).
|
||||||
|
#
|
||||||
|
if [ "$(id -u)" == 0 ] ; then
|
||||||
|
# Environment variables:
|
||||||
|
# - NB_USER: the desired username and associated home folder
|
||||||
|
# - NB_UID: the desired user id
|
||||||
|
# - NB_GID: a group id we want our user to belong to
|
||||||
|
# - NB_GROUP: a group name we want for the group
|
||||||
|
# - GRANT_SUDO: a boolean ("1" or "yes") to grant the user sudo rights
|
||||||
|
# - CHOWN_HOME: a boolean ("1" or "yes") to chown the user's home folder
|
||||||
|
# - CHOWN_EXTRA: a comma separated list of paths to chown
|
||||||
|
# - CHOWN_HOME_OPTS / CHOWN_EXTRA_OPTS: arguments to the chown commands
|
||||||
|
|
||||||
|
# Refit the jovyan user to the desired the user (NB_USER)
|
||||||
|
if id jovyan &> /dev/null ; then
|
||||||
|
if ! usermod --home "/home/${NB_USER}" --login "${NB_USER}" jovyan 2>&1 | grep "no changes" > /dev/null; then
|
||||||
|
_log "Updated the jovyan user:"
|
||||||
|
_log "- username: jovyan -> ${NB_USER}"
|
||||||
|
_log "- home dir: /home/jovyan -> /home/${NB_USER}"
|
||||||
|
fi
|
||||||
|
elif ! id -u "${NB_USER}" &> /dev/null; then
|
||||||
|
_log "ERROR: Neither the jovyan user or '${NB_USER}' exists. This could be the result of stopping and starting, the container with a different NB_USER environment variable."
|
||||||
|
exit 1
|
||||||
|
fi
|
||||||
|
# Ensure the desired user (NB_USER) gets its desired user id (NB_UID) and is
|
||||||
|
# a member of the desired group (NB_GROUP, NB_GID)
|
||||||
|
if [ "${NB_UID}" != "$(id -u "${NB_USER}")" ] || [ "${NB_GID}" != "$(id -g "${NB_USER}")" ]; then
|
||||||
|
_log "Update ${NB_USER}'s UID:GID to ${NB_UID}:${NB_GID}"
|
||||||
|
# Ensure the desired group's existence
|
||||||
|
if [ "${NB_GID}" != "$(id -g "${NB_USER}")" ]; then
|
||||||
|
groupadd --force --gid "${NB_GID}" --non-unique "${NB_GROUP:-${NB_USER}}"
|
||||||
|
fi
|
||||||
|
# Recreate the desired user as we want it
|
||||||
|
userdel "${NB_USER}"
|
||||||
|
useradd --home "/home/${NB_USER}" --uid "${NB_UID}" --gid "${NB_GID}" --groups 100 --no-log-init "${NB_USER}"
|
||||||
|
fi
|
||||||
|
|
||||||
|
# Move or symlink the jovyan home directory to the desired users home
|
||||||
|
# directory if it doesn't already exist, and update the current working
|
||||||
|
# directory to the new location if needed.
|
||||||
|
if [[ "${NB_USER}" != "jovyan" ]]; then
|
||||||
|
if [[ ! -e "/home/${NB_USER}" ]]; then
|
||||||
|
_log "Attempting to copy /home/jovyan to /home/${NB_USER}..."
|
||||||
|
mkdir "/home/${NB_USER}"
|
||||||
|
if cp -a /home/jovyan/. "/home/${NB_USER}/"; then
|
||||||
|
_log "Success!"
|
||||||
|
else
|
||||||
|
_log "Failed to copy data from /home/jovyan to /home/${NB_USER}!"
|
||||||
|
_log "Attempting to symlink /home/jovyan to /home/${NB_USER}..."
|
||||||
|
if ln -s /home/jovyan "/home/${NB_USER}"; then
|
||||||
|
_log "Success creating symlink!"
|
||||||
|
else
|
||||||
|
_log "ERROR: Failed copy data from /home/jovyan to /home/${NB_USER} or to create symlink!"
|
||||||
|
exit 1
|
||||||
|
fi
|
||||||
|
fi
|
||||||
|
fi
|
||||||
|
# Ensure the current working directory is updated to the new path
|
||||||
|
if [[ "${PWD}/" == "/home/jovyan/"* ]]; then
|
||||||
|
new_wd="/home/${NB_USER}/${PWD:13}"
|
||||||
|
_log "Changing working directory to ${new_wd}"
|
||||||
|
cd "${new_wd}"
|
||||||
|
fi
|
||||||
|
fi
|
||||||
|
|
||||||
|
# Optionally ensure the desired user get filesystem ownership of it's home
|
||||||
|
# folder and/or additional folders
|
||||||
|
if [[ "${CHOWN_HOME}" == "1" || "${CHOWN_HOME}" == "yes" ]]; then
|
||||||
|
_log "Ensuring /home/${NB_USER} is owned by ${NB_UID}:${NB_GID} ${CHOWN_HOME_OPTS:+(chown options: ${CHOWN_HOME_OPTS})}"
|
||||||
|
# shellcheck disable=SC2086
|
||||||
|
chown ${CHOWN_HOME_OPTS} "${NB_UID}:${NB_GID}" "/home/${NB_USER}"
|
||||||
|
fi
|
||||||
|
if [ -n "${CHOWN_EXTRA}" ]; then
|
||||||
|
for extra_dir in $(echo "${CHOWN_EXTRA}" | tr ',' ' '); do
|
||||||
|
_log "Ensuring ${extra_dir} is owned by ${NB_UID}:${NB_GID} ${CHOWN_EXTRA_OPTS:+(chown options: ${CHOWN_EXTRA_OPTS})}"
|
||||||
|
# shellcheck disable=SC2086
|
||||||
|
chown ${CHOWN_EXTRA_OPTS} "${NB_UID}:${NB_GID}" "${extra_dir}"
|
||||||
|
done
|
||||||
|
fi
|
||||||
|
|
||||||
|
# Update potentially outdated environment variables since image build
|
||||||
|
export XDG_CACHE_HOME="/home/${NB_USER}/.cache"
|
||||||
|
|
||||||
|
# Prepend ${CONDA_DIR}/bin to sudo secure_path
|
||||||
|
sed -r "s#Defaults\s+secure_path\s*=\s*\"?([^\"]+)\"?#Defaults secure_path=\"${CONDA_DIR}/bin:\1\"#" /etc/sudoers | grep secure_path > /etc/sudoers.d/path
|
||||||
|
|
||||||
|
# Optionally grant passwordless sudo rights for the desired user
|
||||||
|
if [[ "$GRANT_SUDO" == "1" || "$GRANT_SUDO" == "yes" ]]; then
|
||||||
|
_log "Granting ${NB_USER} passwordless sudo rights!"
|
||||||
|
echo "${NB_USER} ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers.d/added-by-start-script
|
||||||
|
fi
|
||||||
|
|
||||||
|
# NOTE: This hook is run as the root user!
|
||||||
|
run-hooks /usr/local/bin/before-notebook.d
|
||||||
|
|
||||||
|
unset_explicit_env_vars
|
||||||
|
_log "Running as ${NB_USER}:" "${cmd[@]}"
|
||||||
|
exec sudo --preserve-env --set-home --user "${NB_USER}" \
|
||||||
|
PATH="${PATH}" \
|
||||||
|
PYTHONPATH="${PYTHONPATH:-}" \
|
||||||
|
"${cmd[@]}"
|
||||||
|
# Notes on how we ensure that the environment that this container is started
|
||||||
|
# with is preserved (except vars listed in JUPYTER_ENV_VARS_TO_UNSET) when
|
||||||
|
# we transition from running as root to running as NB_USER.
|
||||||
|
#
|
||||||
|
# - We use `sudo` to execute the command as NB_USER. What then
|
||||||
|
# happens to the environment will be determined by configuration in
|
||||||
|
# /etc/sudoers and /etc/sudoers.d/* as well as flags we pass to the sudo
|
||||||
|
# command. The behavior can be inspected with `sudo -V` run as root.
|
||||||
|
#
|
||||||
|
# ref: `man sudo` https://linux.die.net/man/8/sudo
|
||||||
|
# ref: `man sudoers` https://www.sudo.ws/man/1.8.15/sudoers.man.html
|
||||||
|
#
|
||||||
|
# - We use the `--preserve-env` flag to pass through most environment
|
||||||
|
# variables, but understand that exceptions are caused by the sudoers
|
||||||
|
# configuration: `env_delete` and `env_check`.
|
||||||
|
#
|
||||||
|
# - We use the `--set-home` flag to set the HOME variable appropriately.
|
||||||
|
#
|
||||||
|
# - To reduce the default list of variables deleted by sudo, we could have
|
||||||
|
# used `env_delete` from /etc/sudoers. It has higher priority than the
|
||||||
|
# `--preserve-env` flag and the `env_keep` configuration.
|
||||||
|
#
|
||||||
|
# - We preserve PATH and PYTHONPATH explicitly. Note however that sudo
|
||||||
|
# resolves `${cmd[@]}` using the "secure_path" variable we modified
|
||||||
|
# above in /etc/sudoers.d/path. Thus PATH is irrelevant to how the above
|
||||||
|
# sudo command resolves the path of `${cmd[@]}`. The PATH will be relevant
|
||||||
|
# for resolving paths of any subprocesses spawned by `${cmd[@]}`.
|
||||||
|
|
||||||
|
# The container didn't start as the root user, so we will have to act as the
|
||||||
|
# user we started as.
|
||||||
|
else
|
||||||
|
# Warn about misconfiguration of: granting sudo rights
|
||||||
|
if [[ "${GRANT_SUDO}" == "1" || "${GRANT_SUDO}" == "yes" ]]; then
|
||||||
|
_log "WARNING: container must be started as root to grant sudo permissions!"
|
||||||
|
fi
|
||||||
|
|
||||||
|
JOVYAN_UID="$(id -u jovyan 2>/dev/null)" # The default UID for the jovyan user
|
||||||
|
JOVYAN_GID="$(id -g jovyan 2>/dev/null)" # The default GID for the jovyan user
|
||||||
|
|
||||||
|
# Attempt to ensure the user uid we currently run as has a named entry in
|
||||||
|
# the /etc/passwd file, as it avoids software crashing on hard assumptions
|
||||||
|
# on such entry. Writing to the /etc/passwd was allowed for the root group
|
||||||
|
# from the Dockerfile during build.
|
||||||
|
#
|
||||||
|
# ref: https://github.com/jupyter/docker-stacks/issues/552
|
||||||
|
if ! whoami &> /dev/null; then
|
||||||
|
_log "There is no entry in /etc/passwd for our UID=$(id -u). Attempting to fix..."
|
||||||
|
if [[ -w /etc/passwd ]]; then
|
||||||
|
_log "Renaming old jovyan user to nayvoj ($(id -u jovyan):$(id -g jovyan))"
|
||||||
|
|
||||||
|
# We cannot use "sed --in-place" since sed tries to create a temp file in
|
||||||
|
# /etc/ and we may not have write access. Apply sed on our own temp file:
|
||||||
|
sed --expression="s/^jovyan:/nayvoj:/" /etc/passwd > /tmp/passwd
|
||||||
|
echo "${NB_USER}:x:$(id -u):$(id -g):,,,:/home/jovyan:/bin/bash" >> /tmp/passwd
|
||||||
|
cat /tmp/passwd > /etc/passwd
|
||||||
|
rm /tmp/passwd
|
||||||
|
|
||||||
|
_log "Added new ${NB_USER} user ($(id -u):$(id -g)). Fixed UID!"
|
||||||
|
|
||||||
|
if [[ "${NB_USER}" != "jovyan" ]]; then
|
||||||
|
_log "WARNING: user is ${NB_USER} but home is /home/jovyan. You must run as root to rename the home directory!"
|
||||||
|
fi
|
||||||
|
else
|
||||||
|
_log "WARNING: unable to fix missing /etc/passwd entry because we don't have write permission. Try setting gid=0 with \"--user=$(id -u):0\"."
|
||||||
|
fi
|
||||||
|
fi
|
||||||
|
|
||||||
|
# Warn about misconfiguration of: desired username, user id, or group id.
|
||||||
|
# A misconfiguration occurs when the user modifies the default values of
|
||||||
|
# NB_USER, NB_UID, or NB_GID, but we cannot update those values because we
|
||||||
|
# are not root.
|
||||||
|
if [[ "${NB_USER}" != "jovyan" && "${NB_USER}" != "$(id -un)" ]]; then
|
||||||
|
_log "WARNING: container must be started as root to change the desired user's name with NB_USER=\"${NB_USER}\"!"
|
||||||
|
fi
|
||||||
|
if [[ "${NB_UID}" != "${JOVYAN_UID}" && "${NB_UID}" != "$(id -u)" ]]; then
|
||||||
|
_log "WARNING: container must be started as root to change the desired user's id with NB_UID=\"${NB_UID}\"!"
|
||||||
|
fi
|
||||||
|
if [[ "${NB_GID}" != "${JOVYAN_GID}" && "${NB_GID}" != "$(id -g)" ]]; then
|
||||||
|
_log "WARNING: container must be started as root to change the desired user's group id with NB_GID=\"${NB_GID}\"!"
|
||||||
|
fi
|
||||||
|
|
||||||
|
# Warn if the user isn't able to write files to ${HOME}
|
||||||
|
if [[ ! -w /home/jovyan ]]; then
|
||||||
|
_log "WARNING: no write access to /home/jovyan. Try starting the container with group 'users' (100), e.g. using \"--group-add=users\"."
|
||||||
|
fi
|
||||||
|
|
||||||
|
# NOTE: This hook is run as the user we started the container as!
|
||||||
|
run-hooks /usr/local/bin/before-notebook.d
|
||||||
|
unset_explicit_env_vars
|
||||||
|
_log "Executing the command:" "${cmd[@]}"
|
||||||
|
exec "${cmd[@]}"
|
||||||
|
fi
|
||||||
|
|
@ -0,0 +1,61 @@
|
||||||
|
#!/usr/bin/fish
|
||||||
|
|
||||||
|
set img_idx 0
|
||||||
|
set is_quiet true
|
||||||
|
set root_dir "."
|
||||||
|
|
||||||
|
function build_image
|
||||||
|
# First argument: (optional) remove parent image? (true or false)
|
||||||
|
# Second argument: file name to build
|
||||||
|
|
||||||
|
# Parse arguments
|
||||||
|
if test (count $argv) -eq 2
|
||||||
|
set remove_previous $argv[1]
|
||||||
|
set build_file $argv[2]
|
||||||
|
else if test (count $argv) -eq 1
|
||||||
|
set remove_previous true
|
||||||
|
set build_file $argv[1]
|
||||||
|
end
|
||||||
|
|
||||||
|
printf "Building $build_file...\n"
|
||||||
|
|
||||||
|
docker build $root_dir \
|
||||||
|
--quiet=$is_quiet \
|
||||||
|
--build-arg BASE_CONTAINER=betalupi/jupyter-inter-$img_idx \
|
||||||
|
-f $build_file.Dockerfile \
|
||||||
|
-t betalupi/jupyter-inter-(math $img_idx + 1)
|
||||||
|
|
||||||
|
|
||||||
|
if $remove_previous
|
||||||
|
printf "Done, cleaning up.\n\n"
|
||||||
|
sleep 1
|
||||||
|
docker image rm betalupi/jupyter-inter-$img_idx
|
||||||
|
else
|
||||||
|
printf "Done. \n\n"
|
||||||
|
end
|
||||||
|
|
||||||
|
set img_idx (math $img_idx + 1)
|
||||||
|
end
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
# Base image MUST be built first
|
||||||
|
printf "Building base image...\n"
|
||||||
|
docker $root_dir/build \
|
||||||
|
--quiet=$is_quiet \
|
||||||
|
-t betalupi/jupyter-inter-0
|
||||||
|
printf "Done. \n\n"
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
build_image false octave
|
||||||
|
build_image false r
|
||||||
|
build_image false sage
|
||||||
|
|
||||||
|
build_image false plugins
|
||||||
|
build_image pymodules
|
||||||
|
|
||||||
|
# Rename final image
|
||||||
|
docker image tag betalupi/jupyter-inter-(math $img_idx) betalupi/jupyter
|
||||||
|
docker image rm betalupi/jupyter-inter-(math $img_idx)
|
||||||
|
|
@ -0,0 +1,24 @@
|
||||||
|
ARG BASE_CONTAINER=betalupi/jupyter-base
|
||||||
|
FROM $BASE_CONTAINER
|
||||||
|
LABEL maintainer="Mark <mark@betalupi.com>"
|
||||||
|
|
||||||
|
USER root
|
||||||
|
RUN apt-get update --yes && apt-get install --yes --no-install-recommends \
|
||||||
|
octave \
|
||||||
|
gnuplot \
|
||||||
|
&& \
|
||||||
|
apt-get clean && rm -rf /var/lib/apt/lists/*
|
||||||
|
|
||||||
|
USER ${NB_UID}
|
||||||
|
RUN mamba install --quiet --yes \
|
||||||
|
"octave_kernel" \
|
||||||
|
&& \
|
||||||
|
# Cleanup
|
||||||
|
mamba clean --all -f -y && \
|
||||||
|
npm cache clean --force && \
|
||||||
|
jupyter lab clean && \
|
||||||
|
rm -rf "/home/${NB_USER}/.cache/yarn" && \
|
||||||
|
fix-permissions "${CONDA_DIR}" && \
|
||||||
|
fix-permissions "/home/${NB_USER}"
|
||||||
|
|
||||||
|
USER ${NB_UID}
|
||||||
|
|
@ -0,0 +1,16 @@
|
||||||
|
ARG BASE_CONTAINER=betalupi/jupyter-base
|
||||||
|
FROM $BASE_CONTAINER
|
||||||
|
LABEL maintainer="Mark <mark@betalupi.com>"
|
||||||
|
|
||||||
|
USER ${NB_UID}
|
||||||
|
|
||||||
|
RUN mamba install --yes \
|
||||||
|
"jupyterlab-git" \
|
||||||
|
&& \
|
||||||
|
# Cleanup
|
||||||
|
mamba clean --all -f -y && \
|
||||||
|
npm cache clean --force && \
|
||||||
|
jupyter lab clean && \
|
||||||
|
rm -rf "/home/${NB_USER}/.cache/yarn" && \
|
||||||
|
fix-permissions "${CONDA_DIR}" && \
|
||||||
|
fix-permissions "/home/${NB_USER}"
|
||||||
|
|
@ -0,0 +1,82 @@
|
||||||
|
ARG BASE_CONTAINER=betalupi/jupyter-base
|
||||||
|
FROM $BASE_CONTAINER
|
||||||
|
LABEL maintainer="Mark <mark@betalupi.com>"
|
||||||
|
|
||||||
|
USER ${NB_UID}
|
||||||
|
|
||||||
|
RUN mamba install --yes \
|
||||||
|
# Python packages
|
||||||
|
# Scraping
|
||||||
|
"beautifulsoup4" \
|
||||||
|
"requests" \
|
||||||
|
"schedule" \
|
||||||
|
# Misc
|
||||||
|
"altair" \
|
||||||
|
"bokeh" \
|
||||||
|
"bottleneck" \
|
||||||
|
"cloudpickle" \
|
||||||
|
"conda-forge::blas=*=openblas" \
|
||||||
|
"cython" \
|
||||||
|
"dask" \
|
||||||
|
"dill" \
|
||||||
|
"h5py" \
|
||||||
|
"ipympl" \
|
||||||
|
"ipywidgets" \
|
||||||
|
"matplotlib-base" \
|
||||||
|
"numba" \
|
||||||
|
"numpy" \
|
||||||
|
"numexpr" \
|
||||||
|
"pandas" \
|
||||||
|
"patsy" \
|
||||||
|
"protobuf" \
|
||||||
|
"pytables" \
|
||||||
|
"scikit-image" \
|
||||||
|
"scikit-learn" \
|
||||||
|
"scipy" \
|
||||||
|
"seaborn" \
|
||||||
|
"sqlalchemy" \
|
||||||
|
"statsmodels" \
|
||||||
|
"sympy" \
|
||||||
|
"widgetsnbextension" \
|
||||||
|
"xlrd" \
|
||||||
|
"tensorflow" \
|
||||||
|
&& \
|
||||||
|
# Cleanup
|
||||||
|
mamba clean --all -f -y && \
|
||||||
|
npm cache clean --force && \
|
||||||
|
jupyter lab clean && \
|
||||||
|
rm -rf "/home/${NB_USER}/.cache/yarn" && \
|
||||||
|
fix-permissions "${CONDA_DIR}" && \
|
||||||
|
fix-permissions "/home/${NB_USER}"
|
||||||
|
|
||||||
|
# Import matplotlib the first time to build the font cache.
|
||||||
|
ENV XDG_CACHE_HOME="/home/${NB_USER}/.cache/"
|
||||||
|
RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" && \
|
||||||
|
fix-permissions "/home/${NB_USER}"
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
#FROM pymodules as selenium
|
||||||
|
#USER ${NB_UID}
|
||||||
|
#
|
||||||
|
#RUN mamba install --yes \
|
||||||
|
# "selenium" \
|
||||||
|
# && \
|
||||||
|
# # Cleanup
|
||||||
|
# mamba clean --all -f -y && \
|
||||||
|
# npm cache clean --force && \
|
||||||
|
# jupyter lab clean && \
|
||||||
|
# rm -rf "/home/${NB_USER}/.cache/yarn" && \
|
||||||
|
# fix-permissions "${CONDA_DIR}" && \
|
||||||
|
# fix-permissions "/home/${NB_USER}"
|
||||||
|
#
|
||||||
|
## Install google chrome
|
||||||
|
#RUN wget -q -O - https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add -
|
||||||
|
#RUN sh -c 'echo "deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main" >> /etc/apt/#sources.list.d/google-chrome.list'
|
||||||
|
#RUN apt-get -y update
|
||||||
|
#RUN apt-get install -y google-chrome-stable
|
||||||
|
#
|
||||||
|
## Install chromedriver
|
||||||
|
#RUN apt-get install -yqq unzip
|
||||||
|
#RUN wget -O /tmp/chromedriver.zip http://chromedriver.storage.googleapis.com/`curl -sS #chromedriver.storage.googleapis.com/LATEST_RELEASE`/chromedriver_linux64.zip
|
||||||
|
#RUN unzip /tmp/chromedriver.zip chromedriver -d /usr/local/bin/
|
||||||
|
|
@ -0,0 +1,57 @@
|
||||||
|
ARG BASE_CONTAINER=betalupi/jupyter-base
|
||||||
|
FROM $BASE_CONTAINER
|
||||||
|
LABEL maintainer="Mark <mark@betalupi.com>"
|
||||||
|
|
||||||
|
# R pre-requisites
|
||||||
|
USER root
|
||||||
|
RUN apt-get update --yes && apt-get install --yes --no-install-recommends \
|
||||||
|
fonts-dejavu \
|
||||||
|
unixodbc \
|
||||||
|
unixodbc-dev \
|
||||||
|
r-cran-rodbc \
|
||||||
|
gfortran \
|
||||||
|
gcc && \
|
||||||
|
apt-get clean && rm -rf /var/lib/apt/lists/*
|
||||||
|
|
||||||
|
USER ${NB_UID}
|
||||||
|
RUN mamba install --quiet --yes \
|
||||||
|
"r-base" \
|
||||||
|
"r-caret" \
|
||||||
|
"r-crayon" \
|
||||||
|
"r-devtools" \
|
||||||
|
"r-e1071" \
|
||||||
|
"r-forecast" \
|
||||||
|
"r-hexbin" \
|
||||||
|
"r-htmltools" \
|
||||||
|
"r-htmlwidgets" \
|
||||||
|
"r-irkernel" \
|
||||||
|
"r-nycflights13" \
|
||||||
|
"r-randomforest" \
|
||||||
|
"r-rcurl" \
|
||||||
|
"r-rmarkdown" \
|
||||||
|
"r-rodbc" \
|
||||||
|
"r-rsqlite" \
|
||||||
|
"r-shiny" \
|
||||||
|
"r-tidyverse" \
|
||||||
|
"unixodbc" && \
|
||||||
|
# Cleanup
|
||||||
|
mamba clean --all -f -y && \
|
||||||
|
npm cache clean --force && \
|
||||||
|
jupyter lab clean && \
|
||||||
|
rm -rf "/home/${NB_USER}/.cache/yarn" && \
|
||||||
|
fix-permissions "${CONDA_DIR}" && \
|
||||||
|
fix-permissions "/home/${NB_USER}"
|
||||||
|
|
||||||
|
# `rpy2` and `r-tidymodels` are not easy to install under arm
|
||||||
|
RUN set -x && \
|
||||||
|
arch=$(uname -m) && \
|
||||||
|
if [ "${arch}" == "x86_64" ]; then \
|
||||||
|
mamba install --quiet --yes \
|
||||||
|
"rpy2" \
|
||||||
|
"r-tidymodels" && \
|
||||||
|
mamba clean --all -f -y && \
|
||||||
|
fix-permissions "${CONDA_DIR}" && \
|
||||||
|
fix-permissions "/home/${NB_USER}"; \
|
||||||
|
fi;
|
||||||
|
|
||||||
|
USER ${NB_UID}
|
||||||
|
|
@ -0,0 +1,14 @@
|
||||||
|
version: "3"
|
||||||
|
|
||||||
|
services:
|
||||||
|
jupyter:
|
||||||
|
image: git.betalupi.com/mark/jupyter
|
||||||
|
container_name: jupyter
|
||||||
|
restart: unless-stopped
|
||||||
|
|
||||||
|
volumes:
|
||||||
|
- "./notebooks:/home/joyvan/notebooks"
|
||||||
|
|
||||||
|
# host:container
|
||||||
|
ports:
|
||||||
|
- "8888:8888"
|
||||||
Loading…
Reference in New Issue