Added jupyter docker files
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201
jupyter/build/base/Dockerfile
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201
jupyter/build/base/Dockerfile
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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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