From a953f55dea9a1e372688a5f593c0eb533cd0d54c Mon Sep 17 00:00:00 2001
From: Emmanuel Bruno <emmanuelbruno@users.noreply.github.com>
Date: Sat, 25 Mar 2023 17:36:16 +0100
Subject: [PATCH] big clean up.
---
Dockerfile | 187 +++++++++++++++++++++++------------------
README.md | 45 ++++++++--
condeserver-extensions | 9 ++
create_work_subdirs.sh | 26 +++---
gitinitconfig.sh | 2 +
initdockerclient.sh | 12 +++
list_packages | 15 ++++
list_pip | 16 ++++
8 files changed, 212 insertions(+), 100 deletions(-)
create mode 100644 condeserver-extensions
create mode 100755 gitinitconfig.sh
create mode 100755 initdockerclient.sh
create mode 100644 list_packages
create mode 100644 list_pip
diff --git a/Dockerfile b/Dockerfile
index 56b34bc..909487d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,22 +1,62 @@
-ARG LAB_BASE=jupyter/scipy-notebook:lab-3.6.1
+ARG LAB_BASE=jupyter/minimal-notebook:lab-3.6.1
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
+# 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
+# We need to remove the default `docker-clean` to avoid cache cleaning
RUN --mount=type=cache,target=/var/cache/apt \
- mkdir -p $PIP_CACHE_DIR &&\
- apt-get update --yes && \
- apt-get install --yes -qq --no-install-recommends \
- bash \
- curl \
- less \
- vim \
- zip && \
+ mkdir -p $PIP_CACHE_DIR && \
+ rm -f /etc/apt/apt.conf.d/docker-clean && \
+ apt-get update && \
+ apt-get install -qq --yes --no-install-recommends \
+ $(cat /tmp/list_packages) && \
rm -rf /var/lib/apt/lists/*
+# Installs only the docker client and docker compose
+ENV BIN_DIR=/usr/local/bin
+RUN if [ "$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
ENV WORK_DIR $HOME/work
ENV NOTEBOOKS_DIR $WORK_DIR/notebooks
@@ -26,93 +66,78 @@ ENV DATA_DIR $WORK_DIR/data
ENV CODESERVEREXT_DIR /opt/codeserver/extensions
ENV CODE_WORKINGDIR $HOME/work
ENV CODESERVERDATA_DIR $HOME/work/.codeserver/data
+ENV CODE_EXTRA_EXTENSIONSDIR $HOME/work/.codeserver/extensions
ENV PATH=/opt/bin:$PATH
# Enable persistant conda env
COPY condarc /home/jovyan/.condarc
-# Install JupyterLab
-RUN --mount=type=cache,target=/var/cache/buildkit/pip \
+RUN --mount=type=cache,target=${PIP_CACHE_DIR} \
--mount=type=cache,target=/opt/conda/pkgs \
- echo -e "\e[93m***** Install Jupyter Lab Extensions ****\e[38;5;241m" && \
- pip install --quiet --no-cache-dir --upgrade \
- jupyter-book \
- 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 \
- nb_conda_kernels \
- && \
- mamba install --quiet --yes -c conda-forge \
- jupyterlab-drawio \
- # jupyterlab_code_formatter \
- # tectonic texlab chktex \
- && \
- 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 && \
- mkdir -p $CODESERVERDATA_DIR &&\
- mkdir -p $CODESERVEREXT_DIR && \
- PATH=/opt/bin:$PATH code-server \
- --user-data-dir $CODESERVERDATA_DIR\
- --extensions-dir $CODESERVEREXT_DIR \
- --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 && \
- 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" && \
-# 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"
-
-COPY configs/* /home/jovyan/.jupyter/
+ echo -e "\e[93m***** Install Jupyter Lab Extensions ****\e[38;5;241m" && \
+ pip install --quiet --upgrade \
+ $(cat /tmp/packages) && \
+ mamba install --quiet --yes \
+ nb_conda_kernels \
+ && \
+ mamba install --quiet --yes -c conda-forge \
+ jupyterlab-drawio \
+ jupyterlab_code_formatter \
+ && \
+ 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 && \
+ mkdir -p $CODESERVERDATA_DIR &&\
+ mkdir -p $CODESERVEREXT_DIR && \
+ PATH=/opt/bin:$PATH code-server \
+ --user-data-dir $CODESERVERDATA_DIR\
+ --extensions-dir $CODESERVEREXT_DIR \
+ --install-extension ms-python.python \
+ --install-extension vscjava.vscode-java-pack \
+ --install-extension redhat.vscode-xml \
+ --install-extension vscode-icons-team.vscode-icons \
+ --install-extension SonarSource.sonarlint-vscode \
+ --install-extension GabrielBB.vscode-lombok \
+ --install-extension james-yu.latex-workshop \
+ --install-extension jebbs.plantuml \
+ --install-extension eamodio.gitlens && \
+ echo -e "\e[93m**** Clean up ****\e[38;5;241m" && \
+# npm cache clean --force && \
+# mamba clean --all -f -y && \
+# jupyter lab clean && \
+ rm -rf "/home/${NB_USER}/.cache/yarn" && \
+ fix-permissions "$CODESERVERDATA_DIR" && \
+ fix-permissions "$CODESERVEREXT_DIR" && \
+ fix-permissions "$CONDA_DIR" && \
+ fix-permissions /opt/codeserver/extensions && \
+ fix-permissions "/home/$NB_USER"
+
COPY code-server/jupyter_codeserver_config.py /tmp/
COPY code-server/icons $HOME/.jupyter/icons
RUN [[ ! -f /home/jovyan/.jupyter/jupyter_config.py ]] && touch /home/jovyan/.jupyter/jupyter_config.py ; \
cat /tmp/jupyter_codeserver_config.py >> /home/jovyan/.jupyter/jupyter_config.py
-# INSTALL NB GRADER FIXE NEEDED
-#COPY nbgrader_config.py /tmp/nbgrader_config.py
-#RUN python3 -m pip install git+https://github.com/jupyter/nbgrader.git@5a81fd5 && \
-# jupyter nbextension install --symlink --sys-prefix --py nbgrader && \
-# jupyter nbextension enable --sys-prefix --py nbgrader && \
-# jupyter serverextension enable --sys-prefix --py nbgrader && \
-# python3 -m pip install ngshare_exchange && \
- # cat /tmp/nbgrader_config.py >> /etc/jupyter/nbgrader_config.py && \
-# echo -e "\e[93m**** Clean up ****\e[38;5;241m" && \
- # npm cache clean --force && \
-# mamba clean --all -f -y && \
-# jupyter lab clean && \
-# rm -rf "/home/${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/
+# Creates dirs and files in $HOME/work (persistent)
+# adds links from $HOME (not persistent)
+# usefull for config files like .gitconfig, .ssh, ...
+COPY create_work_subdirs.sh /usr/local/bin/before-notebook.d/create_work_subdirs.sh
ENV NEEDED_WORK_DIRS .ssh
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 $NB_USER
WORKDIR "${HOME}/work"
diff --git a/README.md b/README.md
index 8792d5d..3b9388f 100644
--- a/README.md
+++ b/README.md
@@ -1,8 +1,43 @@
-# 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 :
+
+* ZSH
+* TexLive
+* Code Server Web IDE
+* Jupyter Book
- * Based on jupyter/scipy-notebook:584f43f06586
- * LateX editor
- * Code Server Web IDE
+## 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##*/}
+```
diff --git a/condeserver-extensions b/condeserver-extensions
new file mode 100644
index 0000000..c121263
--- /dev/null
+++ b/condeserver-extensions
@@ -0,0 +1,9 @@
+--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
diff --git a/create_work_subdirs.sh b/create_work_subdirs.sh
index e3e792f..67922fb 100755
--- a/create_work_subdirs.sh
+++ b/create_work_subdirs.sh
@@ -1,22 +1,20 @@
#!/bin/bash
for subdir in $NEEDED_WORK_DIRS; do
- dir=/home/jovyan/work/$subdir
- ln -s $dir /home/jovyan/$subdir
- if [ ! -f $dir ]; then
- echo Creating $dir
- mkdir -p $dir
- fix-permissions $dir
- # chmod 700 $dir
+ dir="/home/jovyan/work/$subdir"
+ ln -s "$dir" "/home/jovyan/$subdir"
+ if [ ! -f "$dir" ]; then
+ echo Creating "$dir"
+ mkdir -p "$dir"
fi
+ fix-permissions "$dir"
done
for subfile in $NEEDED_WORK_FILES; do
- file=/home/jovyan/work/$subfile
- ln -s $file /home/jovyan/$subfile
- if [ ! -f $file ]; then
- echo Creating $file
- touch $file
- fix-permissions $file
- # chmod 700 $dir
+ file="/home/jovyan/work/$subfile"
+ ln -s "$file" "/home/jovyan/$subfile"
+ if [ ! -f "$file" ]; then
+ echo Creating "$file"
+ touch "$file"
fi
+ fix-permissions "$file"
done
diff --git a/gitinitconfig.sh b/gitinitconfig.sh
new file mode 100755
index 0000000..0ea4201
--- /dev/null
+++ b/gitinitconfig.sh
@@ -0,0 +1,2 @@
+!#/bin/bash
+git config --global init.defaultBranch master
\ No newline at end of file
diff --git a/initdockerclient.sh b/initdockerclient.sh
new file mode 100755
index 0000000..41b42ac
--- /dev/null
+++ b/initdockerclient.sh
@@ -0,0 +1,12 @@
+#/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
diff --git a/list_packages b/list_packages
new file mode 100644
index 0000000..a60aad0
--- /dev/null
+++ b/list_packages
@@ -0,0 +1,15 @@
+bash
+curl
+graphviz
+grep
+host
+imagemagick
+jq
+latexmk
+less
+make
+plantuml
+texlive-full
+vim
+zip
+zsh
diff --git a/list_pip b/list_pip
new file mode 100644
index 0000000..8d421e0
--- /dev/null
+++ b/list_pip
@@ -0,0 +1,16 @@
+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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