docker/jupyter/build/base/Dockerfile

FROM debian:bullseye

ARG NB_USER="jovyan"
ARG NB_UID="1000"
ARG NB_GID="100"


SHELL ["/bin/bash", "-o", "pipefail", "-c"]
USER root


# Install all packages
ENV DEBIAN_FRONTEND noninteractive
RUN apt-get update --yes && \
	apt-get upgrade --yes && \
	apt-get install --yes --no-install-recommends \
	# Basics
	# bzip2: to extract micromamba
	# tini: see https://github.com/krallin/tini#why-tini
	bzip2 \
	ca-certificates \
	fonts-liberation \
	locales \
	wget \
	sudo \
	tini \
	gcc \
	make \
	gnupg \
	curl \
	# Common tools
	# less: needed to run help in R (https://github.com/jupyter/docker-stacks/issues/1588)
	# ffmpeg: for matplotlib anim
	# cm-super, dvipng: for latex labels
	# build-essential: for cython
	build-essential \
	cm-super \
	dvipng \
	git \
	nano \
	tzdata \
	unzip \
	vim \
	openssh-client \
	less \
	ffmpeg \
	# Jupyter dependencies
	# pandoc: convert notebooks to html
	# texlive-*: for nbconvert
	pandoc \
	texlive \
	texlive-xetex \
	texlive-fonts-recommended \
	texlive-plain-generic \
	# Misc dependencies
	# build-essential: for cython
	# cm-super, dvipng: for latex labels
	# ffmpeg: for matplotlib anim
	build-essential \
	cm-super \
	dvipng \
	ffmpeg \
	&& \
	# Clean up and generate locales
	apt-get clean && rm -rf /var/lib/apt/lists/* && \
	echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
	locale-gen

# Configure environment
ENV CONDA_DIR=/opt/conda \
	SHELL=/bin/bash \
	NB_USER="${NB_USER}" \
	NB_UID=${NB_UID} \
	NB_GID=${NB_GID} \
	LC_ALL=en_US.UTF-8 \
	LANG=en_US.UTF-8 \
	LANGUAGE=en_US.UTF-8
ENV PATH="${CONDA_DIR}/bin:${PATH}" \
	HOME="/home/${NB_USER}"

# Copy a script that we will use to correct permissions after running certain commands
COPY fix-permissions.sh /usr/local/bin/fix-permissions
RUN chmod a+rx /usr/local/bin/fix-permissions

# Enable prompt color in the skeleton .bashrc before creating the default NB_USER
RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc && \
	# Add call to conda init script see https://stackoverflow.com/a/58081608/4413446
	echo 'eval "$(command conda shell.bash hook 2> /dev/null)"' >> /etc/skel/.bashrc

# Create user
RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
	sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && \
	sed -i.bak -e 's/^%sudo/#%sudo/' /etc/sudoers && \
	useradd \
		--no-log-init \
		--create-home \
		--no-user-group -u "${NB_UID}" \
		--shell /bin/bash \
		"${NB_USER}" \
	&& \
	mkdir -p "${CONDA_DIR}" && \
	chown "${NB_USER}:${NB_GID}" "${CONDA_DIR}" && \
	chmod g+w /etc/passwd && \
	fix-permissions "${HOME}" && \
	fix-permissions "${CONDA_DIR}"

USER ${NB_UID}


# Pin python version here, or set it to "default"
ARG PYTHON_VERSION=3.10

# Download and install Micromamba, and initialize Conda prefix.
#   <https://github.com/mamba-org/mamba#micromamba>
#   Similar projects using Micromamba:
#     - Micromamba-Docker: <https://github.com/mamba-org/micromamba-docker>
#     - repo2docker: <https://github.com/jupyterhub/repo2docker>
# Install Python, Mamba, Jupyter Notebook, Lab, and Hub
# Generate a notebook server config
# Cleanup temporary files and remove Micromamba
# Correct permissions
COPY --chown="${NB_UID}:${NB_GID}" initial-condarc "${CONDA_DIR}/.condarc"
WORKDIR /tmp
RUN set -x && \
	# Get micromamba
	arch=$(uname -m) && \
	if [ "${arch}" = "x86_64" ]; then \
		# Should be simpler, see <https://github.com/mamba-org/mamba/issues/1437>
		arch="64"; \
	fi && \
	wget -qO /tmp/micromamba.tar.bz2 \
		"https://micromamba.snakepit.net/api/micromamba/linux-${arch}/latest" && \
	tar -xvjf /tmp/micromamba.tar.bz2 --strip-components=1 bin/micromamba && \
	rm /tmp/micromamba.tar.bz2 && \
	PYTHON_SPECIFIER="python=${PYTHON_VERSION}" && \
	if [[ "${PYTHON_VERSION}" == "default" ]]; then PYTHON_SPECIFIER="python"; fi && \
	#
	# Install packages
	./micromamba install \
		--root-prefix="${CONDA_DIR}" \
		--prefix="${CONDA_DIR}" \
		--yes \
		"${PYTHON_SPECIFIER}" \
		# Jupyter base
		"mamba" \
		"notebook" \
		"jupyterhub" \
		"jupyterlab" \
	&& \
	# Cleanup
	rm micromamba && \
	# Pin major.minor version of python
	mamba list python | \
		grep "^python " | \
		tr -s " " | \
		cut -d " " -f 1,2 \
	>> "${CONDA_DIR}/conda-meta/pinned" \
	&& \
	jupyter notebook --generate-config && \
	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}"


EXPOSE 8888

ENTRYPOINT ["tini", "-g", "--"]
CMD ["start-notebook.sh"]

COPY start.sh start-notebook.sh start-singleuser.sh /usr/local/bin/
COPY jupyter_server_config.py /etc/jupyter/

# Add R mimetype option to specify how the plot returns from R to the browser
COPY --chown=${NB_UID}:${NB_GID} Rprofile.site /opt/conda/lib/R/etc/

USER root
#COPY overrides.json /opt/conda/share/jupyter/lab/settings/

RUN mkdir "${HOME}/notebooks" && \
	chown "${NB_UID}:${NB_GID}" "${HOME}/notebooks" &&\
	chmod u+rwx "${HOME}/notebooks"
VOLUME "${HOME}/notebooks"


# Legacy for Jupyter Notebook Server, see: [#1205](https://github.com/jupyter/docker-stacks/issues/1205)
#RUN sed -re "s/c.ServerApp/c.NotebookApp/g" \
#	/etc/jupyter/jupyter_server_config.py > /etc/jupyter/jupyter_notebook_config.py && \
#	fix-permissions /etc/jupyter/

# HEALTHCHECK documentation: https://docs.docker.com/engine/reference/builder/#healthcheck
# This healtcheck works well for `lab`, `notebook`, `nbclassic`, `server` and `retro` jupyter commands
# https://github.com/jupyter/docker-stacks/issues/915#issuecomment-1068528799
HEALTHCHECK --interval=15s --timeout=3s --start-period=5s --retries=3 \
	CMD wget -O- --no-verbose --tries=1 --no-check-certificate \
	http${GEN_CERT:+s}://localhost:8888${JUPYTERHUB_SERVICE_PREFIX:-/}api || exit 1

USER ${NB_UID}
WORKDIR "${HOME}"