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Commit a953f55d authored by Emmanuel Bruno's avatar Emmanuel Bruno
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big clean up.

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Dockerfile
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View file @ a953f55d
ARG LAB_BASE=jupyter/scipy-notebook:lab-3.6.1 ARG LAB_BASE=jupyter/minimal-notebook:lab-3.6.1
FROM ${LAB_BASE} FROM ${LAB_BASE}
ARG TARGETPLATFORM
ARG DOCKER_CLI_VERSION="23.0.1"
ARG DOCKER_COMPOSE_VERSION="2.17.0"
ARG DOCKER_BUILDX_VERSION="0.10.4"
ARG DOCKER_CONFIG="/usr/local/lib/docker/cli-plugins"
USER root USER root
# Copy the list artefacts to install
# Ubuntu and PIP packages, ...
COPY list-* /tmp/
# Sets a cache for pip packages
ENV PIP_CACHE_DIR=/var/cache/buildkit/pip ENV PIP_CACHE_DIR=/var/cache/buildkit/pip
# We need to remove the default `docker-clean` to avoid cache cleaning
RUN --mount=type=cache,target=/var/cache/apt \ RUN --mount=type=cache,target=/var/cache/apt \
mkdir -p $PIP_CACHE_DIR && \ mkdir -p $PIP_CACHE_DIR && \
apt-get update --yes && \ rm -f /etc/apt/apt.conf.d/docker-clean && \
apt-get install --yes -qq --no-install-recommends \ apt-get update && \
bash \ apt-get install -qq --yes --no-install-recommends \
curl \ $(cat /tmp/list_packages) && \
less \
vim \
zip && \
rm -rf /var/lib/apt/lists/* rm -rf /var/lib/apt/lists/*
# Installs only the docker client and docker compose
ENV BIN_DIR=/usr/local/bin
RUN if [ "$TARGETPLATFORM" = "linux/amd64" ]; then \
ARCH_LEG=x86_64; \
ARCH=amd64; \
elif [ "$TARGETPLATFORM" = "linux/arm64/v8" ] || [ "$TARGETPLATFORM" = "linux/arm64" ]; then \
ARCH_LEG=aarch64; \
ARCH=arm64; \
else \
ARCH_LEG=amd64; \
ARCH=amd64; \
fi && \
echo -e "\e[93m**** Installs docker ****\e[38;5;241m" && \
echo "https://download.docker.com/linux/static/stable/${ARCH_LEG}/docker-${DOCKER_CLI_VERSION}.tgz" && \
echo "https://github.com/docker/compose/releases/download/v${DOCKER_COMPOSE_VERSION}/docker-compose-linux-${ARCH_LEG}" && \
echo "https://github.com/docker/buildx/releases/download/v${DOCKER_BUILDX_VERSION}/buildx-v${DOCKER_BUILDX_VERSION}.linux-${ARCH}" && \
curl -sL "https://download.docker.com/linux/static/stable/${ARCH_LEG}/docker-${DOCKER_CLI_VERSION}.tgz" | \
tar --directory="${BIN_DIR}" --strip-components=1 -zx docker/docker && \
chmod +x "${BIN_DIR}/docker" && \
mkdir -p "$DOCKER_CONFIG" && \
echo -e "\e[93m**** Installs docker compose ****\e[38;5;241m" && \
curl -sL "https://github.com/docker/compose/releases/download/v${DOCKER_COMPOSE_VERSION}/docker-compose-linux-${ARCH_LEG}" \
-o "$DOCKER_CONFIG/docker-compose" && \
chmod +x "$DOCKER_CONFIG/docker-compose" && \
echo -e "\e[93m**** Installs docker buildx ****\e[38;5;241m" && \
curl -sL "https://github.com/docker/buildx/releases/download/v${DOCKER_BUILDX_VERSION}/buildx-v${DOCKER_BUILDX_VERSION}.linux-${ARCH}" \
-o "$DOCKER_CONFIG/docker-buildx" && \
chmod +x "$DOCKER_CONFIG/docker-buildx"
# Sets Defaults directories # Sets Defaults directories
ENV WORK_DIR $HOME/work ENV WORK_DIR $HOME/work
ENV NOTEBOOKS_DIR $WORK_DIR/notebooks ENV NOTEBOOKS_DIR $WORK_DIR/notebooks
...@@ -26,38 +66,24 @@ ENV DATA_DIR $WORK_DIR/data ...@@ -26,38 +66,24 @@ ENV DATA_DIR $WORK_DIR/data
ENV CODESERVEREXT_DIR /opt/codeserver/extensions ENV CODESERVEREXT_DIR /opt/codeserver/extensions
ENV CODE_WORKINGDIR $HOME/work ENV CODE_WORKINGDIR $HOME/work
ENV CODESERVERDATA_DIR $HOME/work/.codeserver/data ENV CODESERVERDATA_DIR $HOME/work/.codeserver/data
ENV CODE_EXTRA_EXTENSIONSDIR $HOME/work/.codeserver/extensions
ENV PATH=/opt/bin:$PATH ENV PATH=/opt/bin:$PATH
# Enable persistant conda env # Enable persistant conda env
COPY condarc /home/jovyan/.condarc COPY condarc /home/jovyan/.condarc
# Install JupyterLab RUN --mount=type=cache,target=${PIP_CACHE_DIR} \
RUN --mount=type=cache,target=/var/cache/buildkit/pip \
--mount=type=cache,target=/opt/conda/pkgs \ --mount=type=cache,target=/opt/conda/pkgs \
echo -e "\e[93m***** Install Jupyter Lab Extensions ****\e[38;5;241m" && \ echo -e "\e[93m***** Install Jupyter Lab Extensions ****\e[38;5;241m" && \
pip install --quiet --no-cache-dir --upgrade \ pip install --quiet --upgrade \
jupyter-book \ $(cat /tmp/packages) && \
jupyter-server-proxy \
nbgitpuller \
jupyterlab_latex \
jupyterlab-git \
jupyterlab-system-monitor \
jinja-yaml-magic \
jupyterlab_widgets \
# ipympl \
&& \
# pip install jupyterlab_templates && \
# jupyter labextension install jupyterlab_templates && \
# jupyter serverextension enable --py jupyterlab_templates && \
# conda install defaults::nb_conda_kernels && \
mamba install --quiet --yes \ mamba install --quiet --yes \
nb_conda_kernels \ nb_conda_kernels \
&& \ && \
mamba install --quiet --yes -c conda-forge \ mamba install --quiet --yes -c conda-forge \
jupyterlab-drawio \ jupyterlab-drawio \
# jupyterlab_code_formatter \ jupyterlab_code_formatter \
# tectonic texlab chktex \
&& \ && \
echo -e "\e[93m**** Installs Code Server Web ****\e[38;5;241m" && \ echo -e "\e[93m**** Installs Code Server Web ****\e[38;5;241m" && \
curl -fsSL https://code-server.dev/install.sh | sh -s -- --prefix=/opt --method=standalone && \ curl -fsSL https://code-server.dev/install.sh | sh -s -- --prefix=/opt --method=standalone && \
...@@ -66,6 +92,7 @@ RUN --mount=type=cache,target=/var/cache/buildkit/pip \ ...@@ -66,6 +92,7 @@ RUN --mount=type=cache,target=/var/cache/buildkit/pip \
PATH=/opt/bin:$PATH code-server \ PATH=/opt/bin:$PATH code-server \
--user-data-dir $CODESERVERDATA_DIR\ --user-data-dir $CODESERVERDATA_DIR\
--extensions-dir $CODESERVEREXT_DIR \ --extensions-dir $CODESERVEREXT_DIR \
--install-extension ms-python.python \
--install-extension vscjava.vscode-java-pack \ --install-extension vscjava.vscode-java-pack \
--install-extension redhat.vscode-xml \ --install-extension redhat.vscode-xml \
--install-extension vscode-icons-team.vscode-icons \ --install-extension vscode-icons-team.vscode-icons \
...@@ -74,45 +101,43 @@ RUN --mount=type=cache,target=/var/cache/buildkit/pip \ ...@@ -74,45 +101,43 @@ RUN --mount=type=cache,target=/var/cache/buildkit/pip \
--install-extension james-yu.latex-workshop \ --install-extension james-yu.latex-workshop \
--install-extension jebbs.plantuml \ --install-extension jebbs.plantuml \
--install-extension eamodio.gitlens && \ --install-extension eamodio.gitlens && \
groupadd codeserver && \
chgrp -R codeserver $CODESERVEREXT_DIR &&\
chmod 770 -R $CODESERVEREXT_DIR && \
adduser "$NB_USER" codeserver && \
echo -e "\e[93m**** Clean up ****\e[38;5;241m" && \ echo -e "\e[93m**** Clean up ****\e[38;5;241m" && \
# npm cache clean --force && \ # npm cache clean --force && \
# mamba clean --all -f -y && \ # mamba clean --all -f -y && \
# jupyter lab clean && \ # jupyter lab clean && \
rm -rf "/home/${NB_USER}/.cache/yarn" && \ rm -rf "/home/${NB_USER}/.cache/yarn" && \
fix-permissions "$CODESERVERDATA_DIR" && \
fix-permissions "$CODESERVEREXT_DIR" && \
fix-permissions "$CONDA_DIR" && \ fix-permissions "$CONDA_DIR" && \
fix-permissions /opt/codeserver/extensions && \
fix-permissions "/home/$NB_USER" fix-permissions "/home/$NB_USER"
COPY configs/* /home/jovyan/.jupyter/
COPY code-server/jupyter_codeserver_config.py /tmp/ COPY code-server/jupyter_codeserver_config.py /tmp/
COPY code-server/icons $HOME/.jupyter/icons COPY code-server/icons $HOME/.jupyter/icons
RUN [[ ! -f /home/jovyan/.jupyter/jupyter_config.py ]] && touch /home/jovyan/.jupyter/jupyter_config.py ; \ RUN [[ ! -f /home/jovyan/.jupyter/jupyter_config.py ]] && touch /home/jovyan/.jupyter/jupyter_config.py ; \
cat /tmp/jupyter_codeserver_config.py >> /home/jovyan/.jupyter/jupyter_config.py cat /tmp/jupyter_codeserver_config.py >> /home/jovyan/.jupyter/jupyter_config.py
# INSTALL NB GRADER FIXE NEEDED # Creates dirs and files in $HOME/work (persistent)
#COPY nbgrader_config.py /tmp/nbgrader_config.py # adds links from $HOME (not persistent)
#RUN python3 -m pip install git+https://github.com/jupyter/nbgrader.git@5a81fd5 && \ # usefull for config files like .gitconfig, .ssh, ...
# jupyter nbextension install --symlink --sys-prefix --py nbgrader && \ COPY create_work_subdirs.sh /usr/local/bin/before-notebook.d/create_work_subdirs.sh
# jupyter nbextension enable --sys-prefix --py nbgrader && \
# jupyter serverextension enable --sys-prefix --py nbgrader && \
# python3 -m pip install ngshare_exchange && \
# cat /tmp/nbgrader_config.py >> /etc/jupyter/nbgrader_config.py && \
# echo -e "\e[93m**** Clean up ****\e[38;5;241m" && \
# npm cache clean --force && \
# mamba clean --all -f -y && \
# jupyter lab clean && \
# rm -rf "/home/${NB_USER}/.cache/yarn" && \
# fix-permissions "$CONDA_DIR" && \
# fix-permissions "/home/$NB_USER"
#Adds git and ssh sub directories in works
COPY create_work_subdirs.sh /usr/local/bin/before-notebook.d/
ENV NEEDED_WORK_DIRS .ssh ENV NEEDED_WORK_DIRS .ssh
ENV NEEDED_WORK_FILES .gitconfig ENV NEEDED_WORK_FILES .gitconfig
#Git client default initialisation
COPY gitinitconfig.sh /tmp/gitinitconfig.sh
COPY $PWD/initdockerclient.sh /usr/local/bin/before-notebook.d/initdockerclient.sh
RUN echo -e "\e[93m**** Update Jupyter config ****\e[38;5;241m" && \
mkdir -p $HOME/jupyter_data && \
jupyter lab --generate-config && \
sed -i -e '/c.ServerApp.root_dir =/ s/= .*/= "\/home\/jovyan\/work"/' \
-e "s/# \(c.ServerApp.root_dir\)/\1/" \
$HOME/.jupyter/jupyter_lab_config.py
RUN ln -s /usr/share/plantuml/plantuml.jar /usr/local/bin/
USER $NB_USER USER $NB_USER
WORKDIR "${HOME}/work" WORKDIR "${HOME}/work"
README.md
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View file @ a953f55d
# JupyterLab UTLN Default Image # JupyterLab Base Image
A base image for the UTLN Jupyter Hub. A base image for the Jupyter Lab ased on jupyter/minimal-notebook :
* Based on jupyter/scipy-notebook:584f43f06586 * ZSH
* LateX editor * TexLive
* Code Server Web IDE * Code Server Web IDE
* Jupyter Book
## Quickstart
```bash
docker run --rm --name JupyterDocker-${PWD##*/} \
--volume data-${PWD##*/}:/home/jovyan/work/${PWD##*/} \
--publish 8888:8888 \
--env NB_UID=$UID \
brunoe/jupyter-base:develop start-notebook.sh --notebook-dir=work/${PWD##*/}
```
## Host files and UIDs
```bash
docker run --rm --name JupyterDocker-${PWD##*/} \
--user root
--volume $PWD:/home/jovyan/work/${PWD##*/} \
--volume /var/run/docker.sock:/var/run/docker.sock \
--publish 8888:8888 \
--env NB_UID=$UID \
brunoe/jupyter-base:develop start-notebook.sh --notebook-dir=work/${PWD##*/}
```
## With Docker support
```bash
docker run --rm --name JupyterDocker-${PWD##*/} \
--user root \
--privileged=true \
--volume $PWD:/home/jovyan/work/${PWD##*/} \
--volume /var/run/docker.sock:/var/run/docker.sock \
--publish 8888:8888 \
--env NB_UID=$UID \
brunoe/jupyter-base:develop start-notebook.sh --notebook-dir=work/${PWD##*/}
```
condeserver-extensions 0 → 100644
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− 0
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--install-extension vscjava.vscode-java-pack
--install-extension redhat.vscode-xml
--install-extension vscode-icons-team.vscode-icons
--install-extension SonarSource.sonarlint-vscode
--install-extension GabrielBB.vscode-lombok
--install-extension james-yu.latex-workshop
--install-extension jebbs.plantuml
--install-extension eamodio.gitlens
--install-extension ms-python.python
\ No newline at end of file
create_work_subdirs.sh
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View file @ a953f55d
#!/bin/bash #!/bin/bash
for subdir in $NEEDED_WORK_DIRS; do for subdir in $NEEDED_WORK_DIRS; do
dir=/home/jovyan/work/$subdir dir="/home/jovyan/work/$subdir"
ln -s $dir /home/jovyan/$subdir ln -s "$dir" "/home/jovyan/$subdir"
if [ ! -f $dir ]; then if [ ! -f "$dir" ]; then
echo Creating $dir echo Creating "$dir"
mkdir -p $dir mkdir -p "$dir"
fix-permissions $dir
# chmod 700 $dir
fi fi
fix-permissions "$dir"
done done
for subfile in $NEEDED_WORK_FILES; do for subfile in $NEEDED_WORK_FILES; do
file=/home/jovyan/work/$subfile file="/home/jovyan/work/$subfile"
ln -s $file /home/jovyan/$subfile ln -s "$file" "/home/jovyan/$subfile"
if [ ! -f $file ]; then if [ ! -f "$file" ]; then
echo Creating $file echo Creating "$file"
touch $file touch "$file"
fix-permissions $file
# chmod 700 $dir
fi fi
fix-permissions "$file"
done done
gitinitconfig.sh 0 → 100755
+ 2
− 0
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!#/bin/bash
git config --global init.defaultBranch master
\ No newline at end of file
initdockerclient.sh 0 → 100755
+ 12
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#/bin/bash
## Direct sock mount
if [[ -S /var/run/docker.sock ]]; then
chown jovyan: /var/run/docker.sock
## Remote docker daemon (like DIND)
elif [[ -f ${DOCKER_TLS_CERTDIR:-/certs}/client ]]; then
mkdir -p /home/jovyan/.docker
cp -v ${DOCKER_TLS_CERTDIR:-/certs}/client/{ca,cert,key}.pem /home/jovyan/.docker
chown -R $NB_USER: /home/jovyan/.docker
fi
list_packages 0 → 100644
+ 15
− 0
View file @ a953f55d
bash
curl
graphviz
grep
host
imagemagick
jq
latexmk
less
make
plantuml
texlive-full
vim
zip
zsh
list_pip 0 → 100644
+ 16
− 0
View file @ a953f55d
jinja-yaml-magic
jupyter-book
jupyterlab-myst
jupyter-server-proxy
jupyterlab_latex
jupyterlab_widgets
jupyterlab-code-formatter
black
isort
jupyterlab-git
jupyterlab-system-monitor
nbgitpuller
iplantuml
sphinx-inline-tabs
sphinxcontrib-plantuml
sphinxcontrib-svg2pdfconverter
\ No newline at end of file
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