From dd7c6c75ef636791738b41823e8b56c348e98707 Mon Sep 17 00:00:00 2001 From: Christoph Schranz Date: Thu, 20 Feb 2020 11:03:48 +0100 Subject: [PATCH] build Dockerfile on latest version of docker-stack --- .build/.gitkeep | 0 .gitignore | 3 + Dockerfile | 432 ++++++++++++++++++++++++++++++++++ generate_Dockerfile.sh | 77 ++++++ run_Dockerfile.sh | 28 +++ src/Dockerfile.header | 3 + src/Dockerfile.pytorch | 15 ++ src/Dockerfile.usefulpackages | 40 ++++ 8 files changed, 598 insertions(+) create mode 100644 .build/.gitkeep create mode 100644 Dockerfile create mode 100644 generate_Dockerfile.sh create mode 100644 run_Dockerfile.sh create mode 100644 src/Dockerfile.header create mode 100644 src/Dockerfile.pytorch create mode 100644 src/Dockerfile.usefulpackages diff --git a/.build/.gitkeep b/.build/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/.gitignore b/.gitignore index 0a92bab..e601071 100644 --- a/.gitignore +++ b/.gitignore @@ -112,3 +112,6 @@ venv.bak/ # Added config to hide hashe of changed password src/jupyter_notebook_config.json +.build/ +!.build/.gitkeep +.idea \ No newline at end of file diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..730f8f6 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,432 @@ +# Use NVIDIA CUDA as base image and run the same installation as in the other packages. +FROM nvidia/cuda:10.1-base-ubuntu18.04 +LABEL maintainer="Jupyter Project " + +############################################################################ +#################### Dependency: jupyter/base-image ######################## +############################################################################ + +# Copyright (c) Jupyter Development Team. +# Distributed under the terms of the Modified BSD License. + +# Ubuntu 18.04 (bionic) +# https://hub.docker.com/_/ubuntu/?tab=tags&name=bionic +ARG ROOT_CONTAINER=ubuntu:bionic-20200112@sha256:bc025862c3e8ec4a8754ea4756e33da6c41cba38330d7e324abd25c8e0b93300 + +LABEL maintainer="Jupyter Project " +ARG NB_USER="jovyan" +ARG NB_UID="1000" +ARG NB_GID="100" + +USER root + +# Install all OS dependencies for notebook server that starts but lacks all +# features (e.g., download as all possible file formats) +ENV DEBIAN_FRONTEND noninteractive +RUN apt-get update \ + && apt-get install -yq --no-install-recommends \ + wget \ + bzip2 \ + ca-certificates \ + sudo \ + locales \ + fonts-liberation \ + run-one \ + && apt-get clean && rm -rf /var/lib/apt/lists/* + +RUN 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 /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 + +# Create NB_USER wtih name jovyan user with UID=1000 and in the 'users' group +# and make sure these dirs are writable by the `users` group. +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 -m -s /bin/bash -N -u $NB_UID $NB_USER && \ + mkdir -p $CONDA_DIR && \ + chown $NB_USER:$NB_GID $CONDA_DIR && \ + chmod g+w /etc/passwd && \ + fix-permissions $HOME && \ + fix-permissions "$(dirname $CONDA_DIR)" + +USER $NB_UID +WORKDIR $HOME +ARG PYTHON_VERSION=default + +# Setup work directory for backward-compatibility +RUN mkdir /home/$NB_USER/work && \ + fix-permissions /home/$NB_USER + +# Install conda as jovyan and check the md5 sum provided on the download site +ENV MINICONDA_VERSION=4.7.12.1 \ + MINICONDA_MD5=81c773ff87af5cfac79ab862942ab6b3 \ + CONDA_VERSION=4.7.12 + +RUN cd /tmp && \ + wget --quiet https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \ + echo "${MINICONDA_MD5} *Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" | md5sum -c - && \ + /bin/bash Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh -f -b -p $CONDA_DIR && \ + rm Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \ + echo "conda ${CONDA_VERSION}" >> $CONDA_DIR/conda-meta/pinned && \ + conda config --system --prepend channels conda-forge && \ + conda config --system --set auto_update_conda false && \ + conda config --system --set show_channel_urls true && \ + if [ ! $PYTHON_VERSION = 'default' ]; then conda install --yes python=$PYTHON_VERSION; fi && \ + conda list python | grep '^python ' | tr -s ' ' | cut -d '.' -f 1,2 | sed 's/$/.*/' >> $CONDA_DIR/conda-meta/pinned && \ + conda install --quiet --yes conda && \ + conda install --quiet --yes pip && \ + conda update --all --quiet --yes && \ + conda clean --all -f -y && \ + rm -rf /home/$NB_USER/.cache/yarn && \ + fix-permissions $CONDA_DIR && \ + fix-permissions /home/$NB_USER + +# Install Tini +RUN conda install --quiet --yes 'tini=0.18.0' && \ + conda list tini | grep tini | tr -s ' ' | cut -d ' ' -f 1,2 >> $CONDA_DIR/conda-meta/pinned && \ + conda clean --all -f -y && \ + fix-permissions $CONDA_DIR && \ + fix-permissions /home/$NB_USER + +# Install Jupyter Notebook, Lab, and Hub +# Generate a notebook server config +# Cleanup temporary files +# Correct permissions +# Do all this in a single RUN command to avoid duplicating all of the +# files across image layers when the permissions change +RUN conda install --quiet --yes \ + 'notebook=6.0.3' \ + 'jupyterhub=1.1.0' \ + 'jupyterlab=1.2.5' && \ + conda clean --all -f -y && \ + npm cache clean --force && \ + jupyter notebook --generate-config && \ + rm -rf $CONDA_DIR/share/jupyter/lab/staging && \ + rm -rf /home/$NB_USER/.cache/yarn && \ + fix-permissions $CONDA_DIR && \ + fix-permissions /home/$NB_USER + +EXPOSE 8888 + +# Configure container startup +ENTRYPOINT ["tini", "-g", "--"] +CMD ["start-notebook.sh"] + +# Copy local files as late as possible to avoid cache busting +COPY start.sh /usr/local/bin/ +COPY start-notebook.sh /usr/local/bin/ +COPY start-singleuser.sh /usr/local/bin/ +COPY jupyter_notebook_config.py /etc/jupyter/ + +# Fix permissions on /etc/jupyter as root +USER root +RUN fix-permissions /etc/jupyter/ + +# Switch back to jovyan to avoid accidental container runs as root +USER $NB_UID + +############################################################################ +################# Dependency: jupyter/minimal-notebook ##################### +############################################################################ + +# Copyright (c) Jupyter Development Team. +# Distributed under the terms of the Modified BSD License. + +LABEL maintainer="Jupyter Project " + +USER root + +# Install all OS dependencies for fully functional notebook server +RUN apt-get update && apt-get install -yq --no-install-recommends \ + build-essential \ + emacs \ + git \ + inkscape \ + jed \ + libsm6 \ + libxext-dev \ + libxrender1 \ + lmodern \ + netcat \ + python-dev \ + # ---- nbconvert dependencies ---- + texlive-xetex \ + texlive-fonts-recommended \ + texlive-generic-recommended \ + # Optional dependency + texlive-fonts-extra \ + # ---- + tzdata \ + unzip \ + nano \ + && apt-get clean && rm -rf /var/lib/apt/lists/* + +# Switch back to jovyan to avoid accidental container runs as root +USER $NB_UID + +############################################################################ +################# Dependency: jupyter/scipy-notebook ####################### +############################################################################ + +# Copyright (c) Jupyter Development Team. +# Distributed under the terms of the Modified BSD License. + +LABEL maintainer="Jupyter Project " + +USER root + +# ffmpeg for matplotlib anim +RUN apt-get update && \ + apt-get install -y --no-install-recommends ffmpeg && \ + rm -rf /var/lib/apt/lists/* + +USER $NB_UID + +# Install Python 3 packages +RUN conda install --quiet --yes \ + 'beautifulsoup4=4.8.*' \ + 'conda-forge::blas=*=openblas' \ + 'bokeh=1.4.*' \ + 'cloudpickle=1.2.*' \ + 'cython=0.29.*' \ + 'dask=2.9.*' \ + 'dill=0.3.*' \ + 'h5py=2.10.*' \ + 'hdf5=1.10.*' \ + 'ipywidgets=7.5.*' \ + 'matplotlib-base=3.1.*' \ + 'numba=0.48.*' \ + 'numexpr=2.7.*' \ + 'pandas=0.25.*' \ + 'patsy=0.5.*' \ + 'protobuf=3.11.*' \ + 'scikit-image=0.16.*' \ + 'scikit-learn=0.22.*' \ + 'scipy=1.4.*' \ + 'seaborn=0.9.*' \ + 'sqlalchemy=1.3.*' \ + 'statsmodels=0.11.*' \ + 'sympy=1.5.*' \ + 'vincent=0.4.*' \ + 'xlrd' \ + && \ + conda clean --all -f -y && \ + # Activate ipywidgets extension in the environment that runs the notebook server + jupyter nbextension enable --py widgetsnbextension --sys-prefix && \ + # Also activate ipywidgets extension for JupyterLab + # Check this URL for most recent compatibilities + # https://github.com/jupyter-widgets/ipywidgets/tree/master/packages/jupyterlab-manager + jupyter labextension install @jupyter-widgets/jupyterlab-manager@^1.0.1 --no-build && \ + jupyter labextension install jupyterlab_bokeh@1.0.0 --no-build && \ + jupyter lab build && \ + npm cache clean --force && \ + rm -rf $CONDA_DIR/share/jupyter/lab/staging && \ + rm -rf /home/$NB_USER/.cache/yarn && \ + rm -rf /home/$NB_USER/.node-gyp && \ + fix-permissions $CONDA_DIR && \ + fix-permissions /home/$NB_USER + +# Install facets which does not have a pip or conda package at the moment +RUN cd /tmp && \ + git clone https://github.com/PAIR-code/facets.git && \ + cd facets && \ + jupyter nbextension install facets-dist/ --sys-prefix && \ + cd && \ + rm -rf /tmp/facets && \ + fix-permissions $CONDA_DIR && \ + fix-permissions /home/$NB_USER + +# Import matplotlib the first time to build the font cache. +ENV XDG_CACHE_HOME /home/$NB_USER/.cache/ +RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" && \ + fix-permissions /home/$NB_USER + +USER $NB_UID + +############################################################################ +################ Dependency: jupyter/datascience-notebook ################## +############################################################################ + +# Copyright (c) Jupyter Development Team. +# Distributed under the terms of the Modified BSD License. + +LABEL maintainer="Jupyter Project " + +# Set when building on Travis so that certain long-running build steps can +# be skipped to shorten build time. +ARG TEST_ONLY_BUILD + +USER root + +# R pre-requisites +RUN apt-get update && \ + apt-get install -y --no-install-recommends \ + fonts-dejavu \ + gfortran \ + gcc && \ + rm -rf /var/lib/apt/lists/* + +# Julia dependencies +# install Julia packages in /opt/julia instead of $HOME +ENV JULIA_DEPOT_PATH=/opt/julia +ENV JULIA_PKGDIR=/opt/julia +ENV JULIA_VERSION=1.3.1 + +RUN mkdir /opt/julia-${JULIA_VERSION} && \ + cd /tmp && \ + wget -q https://julialang-s3.julialang.org/bin/linux/x64/`echo ${JULIA_VERSION} | cut -d. -f 1,2`/julia-${JULIA_VERSION}-linux-x86_64.tar.gz && \ + echo "faa707c8343780a6fe5eaf13490355e8190acf8e2c189b9e7ecbddb0fa2643ad *julia-${JULIA_VERSION}-linux-x86_64.tar.gz" | sha256sum -c - && \ + tar xzf julia-${JULIA_VERSION}-linux-x86_64.tar.gz -C /opt/julia-${JULIA_VERSION} --strip-components=1 && \ + rm /tmp/julia-${JULIA_VERSION}-linux-x86_64.tar.gz +RUN ln -fs /opt/julia-*/bin/julia /usr/local/bin/julia + +# Show Julia where conda libraries are \ +RUN mkdir /etc/julia && \ + echo "push!(Libdl.DL_LOAD_PATH, \"$CONDA_DIR/lib\")" >> /etc/julia/juliarc.jl && \ + # Create JULIA_PKGDIR \ + mkdir $JULIA_PKGDIR && \ + chown $NB_USER $JULIA_PKGDIR && \ + fix-permissions $JULIA_PKGDIR + +USER $NB_UID + +# R packages including IRKernel which gets installed globally. +RUN conda install --quiet --yes \ + 'r-base=3.6.2' \ + 'r-caret=6.0*' \ + 'r-crayon=1.3*' \ + 'r-devtools=2.2*' \ + 'r-forecast=8.10*' \ + 'r-hexbin=1.28*' \ + 'r-htmltools=0.4*' \ + 'r-htmlwidgets=1.5*' \ + 'r-irkernel=1.1*' \ + 'r-nycflights13=1.0*' \ + 'r-plyr=1.8*' \ + 'r-randomforest=4.6*' \ + 'r-rcurl=1.98*' \ + 'r-reshape2=1.4*' \ + 'r-rmarkdown=2.1*' \ + 'r-rsqlite=2.1*' \ + 'r-shiny=1.3*' \ + 'r-tidyverse=1.3*' \ + 'rpy2=3.1*' \ + && \ + conda clean --all -f -y && \ + fix-permissions $CONDA_DIR && \ + fix-permissions /home/$NB_USER + +# Add Julia packages. Only add HDF5 if this is not a test-only build since +# it takes roughly half the entire build time of all of the images on Travis +# to add this one package and often causes Travis to timeout. +# +# Install IJulia as jovyan and then move the kernelspec out +# to the system share location. Avoids problems with runtime UID change not +# taking effect properly on the .local folder in the jovyan home dir. +RUN julia -e 'import Pkg; Pkg.update()' && \ + (test $TEST_ONLY_BUILD || julia -e 'import Pkg; Pkg.add("HDF5")') && \ + julia -e "using Pkg; pkg\"add IJulia\"; pkg\"precompile\"" && \ + # move kernelspec out of home \ + mv $HOME/.local/share/jupyter/kernels/julia* $CONDA_DIR/share/jupyter/kernels/ && \ + chmod -R go+rx $CONDA_DIR/share/jupyter && \ + rm -rf $HOME/.local && \ + fix-permissions $JULIA_PKGDIR $CONDA_DIR/share/jupyter + +############################################################################ +################ Dependency: jupyter/tensorflow-notebook ################### +############################################################################ + +# Copyright (c) Jupyter Development Team. +# Distributed under the terms of the Modified BSD License. + +LABEL maintainer="Jupyter Project " + +# Install Tensorflow +RUN pip install --quiet \ + 'tensorflow==2.1.0' && \ + fix-permissions $CONDA_DIR && \ + fix-permissions /home/$NB_USER + +############################################################################ +########################## Dependency: pytorch ############################# +############################################################################ + +# Install PyTorch dependencies +RUN conda install --quiet --yes \ + pyyaml mkl mkl-include setuptools cmake cffi typing && \ + conda clean --all -f -y && \ + fix-permissions $CONDA_DIR && \ + fix-permissions /home/$NB_USER + +# Install PyTorch +RUN conda install -y -c pytorch \ + cudatoolkit=10.1 \ + 'pytorch=1.3.1' \ + torchvision && \ + conda clean --all -f -y && \ + fix-permissions $CONDA_DIR && \ + fix-permissions /home/$NB_USER + +############################################################################ +############################ Useful packages ############################### +############################################################################ + +# Update conda +RUN conda update -n base conda -y + +USER root + +# Install rpy2 to share data between Python and R +RUN conda install rpy2=2.9.4 plotly=4.4.1 +RUN conda install -c conda-forge ipyleaflet + +# Install important packages and Graphviz +RUN set -ex \ + && buildDeps=' \ + graphviz==0.11 \ +' \ + && apt-get update \ + && apt-get -y install htop apt-utils graphviz libgraphviz-dev \ + && pip install --no-cache-dir $buildDeps + +# Install various extensions +RUN jupyter labextension install @jupyterlab/github +RUN jupyter labextension install jupyterlab-drawio +RUN jupyter labextension install jupyter-leaflet +RUN jupyter labextension install @jupyterlab/plotly-extension +RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager +RUN pip install --no-cache-dir jupyter-tabnine==1.0.2 && \ + jupyter nbextension install --py jupyter_tabnine && \ + jupyter nbextension enable --py jupyter_tabnine && \ + jupyter serverextension enable --py jupyter_tabnine +RUN fix-permissions $CONDA_DIR +RUN conda install -c conda-forge jupyter_contrib_nbextensions && \ + conda install -c conda-forge jupyter_nbextensions_configurator && \ + jupyter nbextension enable codefolding/main +RUN jupyter labextension install @ijmbarr/jupyterlab_spellchecker + +# Copying config and fix permissions +COPY jupyter_notebook_config.json /etc/jupyter/ +RUN fix-permissions /home/$NB_USER + +# Switch back to jovyan to avoid accidental container runs as root +USER $NB_UID diff --git a/generate_Dockerfile.sh b/generate_Dockerfile.sh new file mode 100644 index 0000000..7887da1 --- /dev/null +++ b/generate_Dockerfile.sh @@ -0,0 +1,77 @@ +#!/usr/bin/env bash +cd $(cd -P -- "$(dirname -- "$0")" && pwd -P) + +# Set the path of the generated Dockerfile +export DOCKERFILE=".build/Dockerfile" +export STACKS_DIR=".build/docker-stacks" + + +# Clone if docker-stacks doesn't exist, and pull. +ls $STACKS_DIR/README.md > /dev/null 2>&1 || (echo "Docker-stacks was not found, cloning repository" \ + && git clone https://github.com/jupyter/docker-stacks.git $STACKS_DIR) +git pull -f $STACKS_DIR + +# Write the contents into the DOCKERFILE and start with the header +cat src/Dockerfile.header > $DOCKERFILE +cp src/jupyter_notebook_config.json .build/ + +echo " +############################################################################ +#################### Dependency: jupyter/base-image ######################## +############################################################################ +" >> $DOCKERFILE +cat $STACKS_DIR/base-notebook/Dockerfile | grep -v BASE_CONTAINER >> $DOCKERFILE +cp $STACKS_DIR/base-notebook/fix-permissions .build/ +cp $STACKS_DIR/base-notebook/jupyter_notebook_config.py .build/ +cp $STACKS_DIR/base-notebook/start.sh .build/ +cp $STACKS_DIR/base-notebook/start-notebook.sh .build/ +cp $STACKS_DIR/base-notebook/start-singleuser.sh .build/ + +echo " +############################################################################ +################# Dependency: jupyter/minimal-notebook ##################### +############################################################################ +" >> $DOCKERFILE +cat $STACKS_DIR/minimal-notebook/Dockerfile | grep -v BASE_CONTAINER >> $DOCKERFILE + +echo " +############################################################################ +################# Dependency: jupyter/scipy-notebook ####################### +############################################################################ +" >> $DOCKERFILE +cat $STACKS_DIR/scipy-notebook/Dockerfile | grep -v BASE_CONTAINER >> $DOCKERFILE + +echo " +############################################################################ +################ Dependency: jupyter/datascience-notebook ################## +############################################################################ +" >> $DOCKERFILE +cat $STACKS_DIR/datascience-notebook/Dockerfile | grep -v BASE_CONTAINER >> $DOCKERFILE + +echo " +############################################################################ +################ Dependency: jupyter/tensorflow-notebook ################### +############################################################################ +" >> $DOCKERFILE +cat $STACKS_DIR/tensorflow-notebook/Dockerfile | grep -v BASE_CONTAINER >> $DOCKERFILE + +# Note that the following step also installs the cudatoolkit, which is +# essential to access the GPU. +echo " +############################################################################ +########################## Dependency: pytorch ############################# +############################################################################ +" >> $DOCKERFILE +cat src/Dockerfile.pytorch >> $DOCKERFILE + + +echo " +############################################################################ +############################ Useful packages ############################### +############################################################################ +" >> $DOCKERFILE +cat src/Dockerfile.usefulpackages >> $DOCKERFILE + +cp $DOCKERFILE Dockerfile +echo "GPU Dockerfile was generated sucessfully in file $(pwd)/${DOCKERFILE} and copied to ./Dockerfile" +echo "Run 'bash run_Dockerfile.sh -p [PORT]' to start the GPU-based Juyterlab instance." diff --git a/run_Dockerfile.sh b/run_Dockerfile.sh new file mode 100644 index 0000000..eeb1f9d --- /dev/null +++ b/run_Dockerfile.sh @@ -0,0 +1,28 @@ +#!/usr/bin/env bash +cd $(cd -P -- "$(dirname -- "$0")" && pwd -P) + +# Fetching port +PORT=0 +HELP=0 +while [[ "$#" -gt 0 ]]; do case $1 in + -p|--port) PORT="$2"; shift;; + -h|--help) HELP=1;; + *) echo "Unknown parameter passed: $1"; exit 1;; +esac; shift; done + +# Print help +if [[ $HELP != 0 ]]; then + echo "Usage: $0 -p [port] # port must be an integer with 4 or more digits." + exit 21 +fi + +# Check if port is valid +if [[ $PORT != [0-9][0-9][0-9][0-9]* ]]; then + echo "The port is not set or invalid." + echo "Usage: $0 -p [port] # port must be an integer with 4 or more digits." + exit 22 +fi + +# Build and run the Dockerfile +docker build -t gpu-jupyter . +docker run -d -p "$PORT":8888 gpu-jupyter diff --git a/src/Dockerfile.header b/src/Dockerfile.header new file mode 100644 index 0000000..1e5d21d --- /dev/null +++ b/src/Dockerfile.header @@ -0,0 +1,3 @@ +# Use NVIDIA CUDA as base image and run the same installation as in the other packages. +FROM nvidia/cuda:10.1-base-ubuntu18.04 +LABEL maintainer="Jupyter Project " diff --git a/src/Dockerfile.pytorch b/src/Dockerfile.pytorch new file mode 100644 index 0000000..439b1b1 --- /dev/null +++ b/src/Dockerfile.pytorch @@ -0,0 +1,15 @@ +# Install PyTorch dependencies +RUN conda install --quiet --yes \ + pyyaml mkl mkl-include setuptools cmake cffi typing && \ + conda clean --all -f -y && \ + fix-permissions $CONDA_DIR && \ + fix-permissions /home/$NB_USER + +# Install PyTorch +RUN conda install -y -c pytorch \ + cudatoolkit=10.1 \ + 'pytorch=1.3.1' \ + torchvision && \ + conda clean --all -f -y && \ + fix-permissions $CONDA_DIR && \ + fix-permissions /home/$NB_USER diff --git a/src/Dockerfile.usefulpackages b/src/Dockerfile.usefulpackages new file mode 100644 index 0000000..f0863a0 --- /dev/null +++ b/src/Dockerfile.usefulpackages @@ -0,0 +1,40 @@ +# Update conda +RUN conda update -n base conda -y + +USER root + +# Install rpy2 to share data between Python and R +RUN conda install rpy2=2.9.4 plotly=4.4.1 +RUN conda install -c conda-forge ipyleaflet + +# Install important packages and Graphviz +RUN set -ex \ + && buildDeps=' \ + graphviz==0.11 \ +' \ + && apt-get update \ + && apt-get -y install htop apt-utils graphviz libgraphviz-dev \ + && pip install --no-cache-dir $buildDeps + +# Install various extensions +RUN jupyter labextension install @jupyterlab/github +RUN jupyter labextension install jupyterlab-drawio +RUN jupyter labextension install jupyter-leaflet +RUN jupyter labextension install @jupyterlab/plotly-extension +RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager +RUN pip install --no-cache-dir jupyter-tabnine==1.0.2 && \ + jupyter nbextension install --py jupyter_tabnine && \ + jupyter nbextension enable --py jupyter_tabnine && \ + jupyter serverextension enable --py jupyter_tabnine +RUN fix-permissions $CONDA_DIR +RUN conda install -c conda-forge jupyter_contrib_nbextensions && \ + conda install -c conda-forge jupyter_nbextensions_configurator && \ + jupyter nbextension enable codefolding/main +RUN jupyter labextension install @ijmbarr/jupyterlab_spellchecker + +# Copying config and fix permissions +COPY jupyter_notebook_config.json /etc/jupyter/ +RUN fix-permissions /home/$NB_USER + +# Switch back to jovyan to avoid accidental container runs as root +USER $NB_UID