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update jupyterhub-V1

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TerenceLau 2022-10-08 14:18:24 +00:00
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jupyterhub_V1/README.md Normal file
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# JupyterHub Docker Stacks
## Acknowledgement
[Jupyter Docker Stacks](https://github.com/jupyter/docker-stacks)

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ARG SOURCE=ghcr.io
ARG BASE_CONTAINER=${SOURCE}/jupyter-base:0.0.3
FROM $BASE_CONTAINER
LABEL org.opencontainers.image.authors="Bayes Cluster Maintenance Group"
LABEL org.opencontainers.image.documentation="https://uicstat.com"
SHELL ["/bin/bash", "-o", "pipefail", "-c"]
USER root
# Install all OS dependencies for fully functional notebook server
RUN apt-get update --yes && \
apt-get install --yes --no-install-recommends \
git \
nano-tiny \
tzdata \
unzip \
vim-tiny \
openssh-client \
less \
texlive-xetex \
texlive-fonts-recommended \
texlive-plain-generic \
xclip && \
apt-get clean && rm -rf /var/lib/apt/lists/*

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FROM nvidia/cuda:11.8.0-runtime-ubuntu22.04
LABEL maintainer="Bayes Cluster Maintenance Group <"
ARG NB_USER="bayes"
ARG NB_UID="1000"
ARG NB_GID="100"
SHELL ["/bin/bash", "-o", "pipefail", "-c"]
# Install all OS dependencies for fully functional notebook server
USER root
ENV DEBIAN_FRONTEND noninteractive
RUN apt-get update --yes && \
apt-get upgrade --yes && \
apt-get install --yes --no-install-recommends \
bzip2 \
ca-certificates \
fonts-liberation \
locales \
pandoc \
run-one \
sudo \
tini \
wget \
curl && \
apt-get clean && rm -rf /var/lib/apt/lists/* && \
echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
locale-gen
RUN adduser --disabled-password \
--gecos "Default user" \
--uid ${NB_UID} \
${NB_USER}
# Configure environment
ENV CONDA_DIR=/opt/conda \
SHELL=/bin/bash \
NB_USER="${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/${NB_USER}"
COPY fix-permissions /usr/local/bin/fix-permissions
RUN chmod a+rx /usr/local/bin/fix-permissions
RUN mkdir "/home/${NB_USER}/work" && \
fix-permissions "/home/${NB_USER}"
RUN fix-permissions "/home/${NB_USER}"
# Install miniconda
ENV CONDA_URL="https://mirrors.bfsu.edu.cn/anaconda/miniconda/Miniconda3-latest-Linux-x86_64.sh"
RUN curl -LO ${CONDA_URL}
RUN bash Miniconda3-latest-Linux-x86_64.sh -p ${CONDA_DIR} -b
RUN rm -rf Miniconda3-latest-Linux-x86_64.sh
RUN conda config --system --prepend channels conda-forge
RUN chown ${NB_UID}:${NB_GID} ${CONDA_DIR}
RUN conda init
COPY condarc /home/${NB_USER}/.condarc
RUN conda install -c anaconda jupyter
RUN conda install -c conda-forge jupyterlab
RUN conda install -c conda-forge jupyterhub
RUN conda config --system --prepend envs_dirs '/home/${NB_USER}/.conda/envs'
EXPOSE 8888
ENTRYPOINT ["tini", "--"]
CMD ["jupyter", "lab"]
# Copy local files as late as possible to avoid cache busting
COPY start.sh start-notebook.sh start-singleuser.sh /usr/local/bin/
# Currently need to have both jupyter_notebook_config and jupyter_server_config to support classic and lab
COPY jupyter_server_config.py /etc/jupyter/
# Fix permissions on /etc/jupyter as root
USER root
# Legacy for Jupyter Notebook Server, see: [#1205](https://github.com/jupyter/docker-stacks/issues/1205)
RUN sed -re "s/c.ServerApp/c.NotebookApp/g" \
/etc/jupyter/jupyter_server_config.py > /etc/jupyter/jupyter_notebook_config.py && \
fix-permissions /etc/jupyter/
# HEALTHCHECK documentation: https://docs.docker.com/engine/reference/builder/#healthcheck
# This healtcheck works well for `lab`, `notebook`, `nbclassic`, `server` and `retro` jupyter commands
# https://github.com/jupyter/docker-stacks/issues/915#issuecomment-1068528799
HEALTHCHECK --interval=15s --timeout=3s --start-period=5s --retries=3 \
CMD wget -O- --no-verbose --tries=1 --no-check-certificate \
http${GEN_CERT:+s}://localhost:8888${JUPYTERHUB_SERVICE_PREFIX:-/}api || exit 1
# Switch back to jovyan to avoid accidental container runs as root
USER ${NB_UID}
WORKDIR "${HOME}"

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channels:
- defaults
show_channel_urls: true
default_channels:
- https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
- https://mirrors.bfsu.edu.cn/anaconda/pkgs/r
- https://mirrors.bfsu.edu.cn/anaconda/pkgs/msys2
custom_channels:
conda-forge: https://mirrors.bfsu.edu.cn/anaconda/cloud
msys2: https://mirrors.bfsu.edu.cn/anaconda/cloud
bioconda: https://mirrors.bfsu.edu.cn/anaconda/cloud
menpo: https://mirrors.bfsu.edu.cn/anaconda/cloud
pytorch: https://mirrors.bfsu.edu.cn/anaconda/cloud
pytorch-lts: https://mirrors.bfsu.edu.cn/anaconda/cloud
simpleitk: https://mirrors.bfsu.edu.cn/anaconda/cloud

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jupyterhub_V1/singleuser-nvidia/fix-permissions Normal file
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#!/bin/bash
# set permissions on a directory
# after any installation, if a directory needs to be (human) user-writable,
# run this script on it.
# It will make everything in the directory owned by the group ${NB_GID}
# and writable by that group.
# Deployments that want to set a specific user id can preserve permissions
# by adding the `--group-add users` line to `docker run`.
# uses find to avoid touching files that already have the right permissions,
# which would cause massive image explosion
# right permissions are:
# group=${NB_GID}
# AND permissions include group rwX (directory-execute)
# AND directories have setuid,setgid bits set
set -e
for d in "$@"; do
find "${d}" \
! \( \
-group "${NB_GID}" \
-a -perm -g+rwX \
\) \
-exec chgrp "${NB_GID}" -- {} \+ \
-exec chmod g+rwX -- {} \+
# setuid, setgid *on directories only*
find "${d}" \
\( \
-type d \
-a ! -perm -6000 \
\) \
-exec chmod +6000 -- {} \+
done

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jupyterhub_V1/singleuser-nvidia/jupyter_server_config.py Normal file
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# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.
# mypy: ignore-errors
import os
import stat
import subprocess
from jupyter_core.paths import jupyter_data_dir
c = get_config() # noqa: F821
c.ServerApp.ip = "0.0.0.0"
c.ServerApp.port = 8888
c.ServerApp.open_browser = False
# to output both image/svg+xml and application/pdf plot formats in the notebook file
c.InlineBackend.figure_formats = {"png", "jpeg", "svg", "pdf"}
# https://github.com/jupyter/notebook/issues/3130
c.FileContentsManager.delete_to_trash = False
# Generate a self-signed certificate
OPENSSL_CONFIG = """\
[req]
distinguished_name = req_distinguished_name
[req_distinguished_name]
"""
if "GEN_CERT" in os.environ:
dir_name = jupyter_data_dir()
pem_file = os.path.join(dir_name, "notebook.pem")
os.makedirs(dir_name, exist_ok=True)
# Generate an openssl.cnf file to set the distinguished name
cnf_file = os.path.join(os.getenv("CONDA_DIR", "/usr/lib"), "ssl", "openssl.cnf")
if not os.path.isfile(cnf_file):
with open(cnf_file, "w") as fh:
fh.write(OPENSSL_CONFIG)
# 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",
f"-keyout={pem_file}",
f"-out={pem_file}",
]
)
# Restrict access to the file
os.chmod(pem_file, stat.S_IRUSR | stat.S_IWUSR)
c.ServerApp.certfile = pem_file
# Change default umask for all subprocesses of the notebook server if set in
# the environment
if "NB_UMASK" in os.environ:
os.umask(int(os.environ["NB_UMASK"], 8))

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# This file is the input to requirements.txt,
# which is a frozen version of this. To update
# requirements.txt, use the "Run workflow" button at
# https://github.com/jupyterhub/zero-to-jupyterhub-k8s/actions/workflows/watch-dependencies.yaml
# that will also update the jupyterhub version if needed.
# README.md file.
# JupyterHub itself, update this version pinning by running the workflow
# mentioned above.
jupyterhub==3.0.0
# UI
jupyterlab
nbclassic
retrolab
# plugins
nbgitpuller

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#
# This file is autogenerated by pip-compile with python 3.9
# To update, run:
#
# Use the "Run workflow" button at https://github.com/jupyterhub/zero-to-jupyterhub-k8s/actions/workflows/watch-dependencies.yaml
#
alembic==1.8.1
# via jupyterhub
anyio==3.6.1
# via jupyter-server
argon2-cffi==21.3.0
# via
# jupyter-server
# nbclassic
# notebook
argon2-cffi-bindings==21.2.0
# via argon2-cffi
asttokens==2.0.8
# via stack-data
async-generator==1.10
# via jupyterhub
attrs==22.1.0
# via jsonschema
babel==2.10.3
# via jupyterlab-server
backcall==0.2.0
# via ipython
beautifulsoup4==4.11.1
# via nbconvert
bleach==5.0.1
# via nbconvert
certifi==2022.9.24
# via requests
certipy==0.1.3
# via jupyterhub
cffi==1.15.1
# via
# argon2-cffi-bindings
# cryptography
charset-normalizer==2.1.1
# via requests
cryptography==38.0.1
# via pyopenssl
debugpy==1.6.3
# via ipykernel
decorator==5.1.1
# via ipython
defusedxml==0.7.1
# via nbconvert
entrypoints==0.4
# via jupyter-client
executing==1.1.0
# via stack-data
fastjsonschema==2.16.2
# via nbformat
greenlet==1.1.3
# via sqlalchemy
idna==3.4
# via
# anyio
# requests
importlib-metadata==5.0.0
# via
# jupyterhub
# jupyterlab-server
# nbconvert
ipykernel==6.16.0
# via
# nbclassic
# notebook
ipython==8.5.0
# via
# ipykernel
# jupyterlab
ipython-genutils==0.2.0
# via
# nbclassic
# notebook
jedi==0.18.1
# via ipython
jinja2==3.1.2
# via
# jupyter-server
# jupyterhub
# jupyterlab
# jupyterlab-server
# nbclassic
# nbconvert
# notebook
json5==0.9.10
# via jupyterlab-server
jsonschema==4.16.0
# via
# jupyter-telemetry
# jupyterlab-server
# nbformat
jupyter-client==7.3.5
# via
# ipykernel
# jupyter-server
# nbclassic
# nbclient
# notebook
jupyter-core==4.11.1
# via
# jupyter-client
# jupyter-server
# jupyterlab
# nbclassic
# nbconvert
# nbformat
# notebook
jupyter-server==1.19.1
# via
# jupyterlab
# jupyterlab-server
# nbclassic
# nbgitpuller
# notebook-shim
# retrolab
jupyter-telemetry==0.1.0
# via jupyterhub
jupyterhub==3.0.0
# via -r requirements.in
jupyterlab==3.4.7
# via
# -r requirements.in
# retrolab
jupyterlab-pygments==0.2.2
# via nbconvert
jupyterlab-server==2.15.2
# via
# jupyterlab
# retrolab
lxml==4.9.1
# via nbconvert
mako==1.2.3
# via alembic
markupsafe==2.1.1
# via
# jinja2
# mako
# nbconvert
matplotlib-inline==0.1.6
# via
# ipykernel
# ipython
mistune==2.0.4
# via nbconvert
nbclassic==0.4.4
# via
# -r requirements.in
# jupyterlab
# retrolab
nbclient==0.6.8
# via nbconvert
nbconvert==7.0.0
# via
# jupyter-server
# nbclassic
# notebook
nbformat==5.6.1
# via
# jupyter-server
# nbclassic
# nbclient
# nbconvert
# notebook
nbgitpuller==1.1.0
# via -r requirements.in
nest-asyncio==1.5.6
# via
# ipykernel
# jupyter-client
# nbclassic
# nbclient
# notebook
notebook==6.4.12
# via
# jupyterlab
# nbgitpuller
notebook-shim==0.1.0
# via nbclassic
oauthlib==3.2.1
# via jupyterhub
packaging==21.3
# via
# ipykernel
# jupyter-server
# jupyterhub
# jupyterlab
# jupyterlab-server
# nbconvert
pamela==1.0.0
# via jupyterhub
pandocfilters==1.5.0
# via nbconvert
parso==0.8.3
# via jedi
pexpect==4.8.0
# via ipython
pickleshare==0.7.5
# via ipython
prometheus-client==0.14.1
# via
# jupyter-server
# jupyterhub
# nbclassic
# notebook
prompt-toolkit==3.0.31
# via ipython
psutil==5.9.2
# via ipykernel
ptyprocess==0.7.0
# via
# pexpect
# terminado
pure-eval==0.2.2
# via stack-data
pycparser==2.21
# via cffi
pygments==2.13.0
# via
# ipython
# nbconvert
pyopenssl==22.1.0
# via certipy
pyparsing==3.0.9
# via packaging
pyrsistent==0.18.1
# via jsonschema
python-dateutil==2.8.2
# via
# jupyter-client
# jupyterhub
python-json-logger==2.0.4
# via jupyter-telemetry
pytz==2022.4
# via babel
pyzmq==24.0.1
# via
# ipykernel
# jupyter-client
# jupyter-server
# nbclassic
# notebook
requests==2.28.1
# via
# jupyterhub
# jupyterlab-server
retrolab==0.3.21
# via -r requirements.in
ruamel-yaml==0.17.21
# via jupyter-telemetry
ruamel-yaml-clib==0.2.6
# via ruamel-yaml
send2trash==1.8.0
# via
# jupyter-server
# nbclassic
# notebook
six==1.16.0
# via
# asttokens
# bleach
# python-dateutil
sniffio==1.3.0
# via anyio
soupsieve==2.3.2.post1
# via beautifulsoup4
sqlalchemy==1.4.41
# via
# alembic
# jupyterhub
stack-data==0.5.1
# via ipython
terminado==0.16.0
# via
# jupyter-server
# nbclassic
# notebook
tinycss2==1.1.1
# via nbconvert
tomli==2.0.1
# via jupyterlab
tornado==6.2
# via
# ipykernel
# jupyter-client
# jupyter-server
# jupyterhub
# jupyterlab
# nbclassic
# nbgitpuller
# notebook
# retrolab
# terminado
traitlets==5.4.0
# via
# ipykernel
# ipython
# jupyter-client
# jupyter-core
# jupyter-server
# jupyter-telemetry
# jupyterhub
# matplotlib-inline
# nbclassic
# nbclient
# nbconvert
# nbformat
# notebook
urllib3==1.26.12
# via requests
wcwidth==0.2.5
# via prompt-toolkit
webencodings==0.5.1
# via
# bleach
# tinycss2
websocket-client==1.4.1
# via jupyter-server
zipp==3.8.1
# via importlib-metadata

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#!/bin/bash
# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.
set -e
# The Jupyter command to launch
# JupyterLab by default
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="run-one-constantly"
fi
# shellcheck disable=SC1091,SC2086
exec /usr/local/bin/start.sh ${wrapper} jupyter ${DOCKER_STACKS_JUPYTER_CMD} ${NOTEBOOK_ARGS} "$@"

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#!/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 ${NOTEBOOK_ARGS} "$@"

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#!/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