481 lines
17 KiB
Docker
Executable File
481 lines
17 KiB
Docker
Executable File
# This Dockerfile is generated by 'generate-Dockerfile.sh' from elements within 'src/'
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# **Please do not change this file directly!**
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# To adapt this Dockerfile, adapt 'generate-Dockerfile.sh' or 'src/Dockerfile.usefulpackages'.
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# More information can be found in the README under configuration.
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# Use NVIDIA CUDA as base image and run the same installation as in the other packages.
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# The version of cudatoolkit must match those of the base image, see Dockerfile.pytorch
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FROM nvidia/cuda:10.1-cudnn7-runtime-ubuntu18.04
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LABEL authors="Christoph Schranz <christoph.schranz@salzburgresearch.at>, Mathematical Michael <consistentbayes@gmail.com>"
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# This is a concatenated Dockerfile, the maintainers of subsequent sections may vary.
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RUN chmod 1777 /tmp && chmod 1777 /var/tmp
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############################################################################
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#################### Dependency: jupyter/base-image ########################
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############################################################################
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# Copyright (c) Jupyter Development Team.
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# Distributed under the terms of the Modified BSD License.
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# Ubuntu 20.04 (focal)
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# https://hub.docker.com/_/ubuntu/?tab=tags&name=focal
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# OS/ARCH: linux/amd64
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ARG ROOT_CONTAINER=ubuntu:focal-20201106@sha256:4e4bc990609ed865e07afc8427c30ffdddca5153fd4e82c20d8f0783a291e241
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LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
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ARG NB_USER="jovyan"
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ARG NB_UID="1000"
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ARG NB_GID="100"
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# Fix DL4006
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SHELL ["/bin/bash", "-o", "pipefail", "-c"]
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USER root
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# ---- Miniforge installer ----
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# Default values can be overridden at build time
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# (ARGS are in lower case to distinguish them from ENV)
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# Check https://github.com/conda-forge/miniforge/releases
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# Conda version
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ARG conda_version="4.9.2"
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# Miniforge installer patch version
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ARG miniforge_patch_number="0"
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# Miniforge installer architecture
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ARG miniforge_arch="x86_64"
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# Python implementation to use
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# can be either Miniforge3 to use Python or Miniforge-pypy3 to use PyPy
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ARG miniforge_python="Miniforge3"
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# Miniforge archive to install
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ARG miniforge_version="${conda_version}-${miniforge_patch_number}"
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# Miniforge installer
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ARG miniforge_installer="${miniforge_python}-${miniforge_version}-Linux-${miniforge_arch}.sh"
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# Miniforge checksum
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ARG miniforge_checksum="6321775eb2c02d7f51d3a9004ce0be839099f126f4099c781531428536669560"
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# Install all OS dependencies for notebook server that starts but lacks all
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# features (e.g., download as all possible file formats)
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ENV DEBIAN_FRONTEND noninteractive
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RUN apt-get update \
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&& apt-get install -yq --no-install-recommends \
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wget \
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ca-certificates \
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sudo \
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locales \
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fonts-liberation \
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run-one \
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&& apt-get clean && rm -rf /var/lib/apt/lists/*
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RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
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locale-gen
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# Configure environment
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ENV CONDA_DIR=/opt/conda \
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SHELL=/bin/bash \
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NB_USER=$NB_USER \
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NB_UID=$NB_UID \
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NB_GID=$NB_GID \
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LC_ALL=en_US.UTF-8 \
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LANG=en_US.UTF-8 \
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LANGUAGE=en_US.UTF-8
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ENV PATH=$CONDA_DIR/bin:$PATH \
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HOME=/home/$NB_USER \
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CONDA_VERSION="${conda_version}" \
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MINIFORGE_VERSION="${miniforge_version}"
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# Copy a script that we will use to correct permissions after running certain commands
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COPY fix-permissions /usr/local/bin/fix-permissions
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RUN chmod a+rx /usr/local/bin/fix-permissions
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# Enable prompt color in the skeleton .bashrc before creating the default NB_USER
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# hadolint ignore=SC2016
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RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc && \
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# Add call to conda init script see https://stackoverflow.com/a/58081608/4413446
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echo 'eval "$(command conda shell.bash hook 2> /dev/null)"' >> /etc/skel/.bashrc
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# Create NB_USER with name jovyan user with UID=1000 and in the 'users' group
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# and make sure these dirs are writable by the `users` group.
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RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
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sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && \
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sed -i.bak -e 's/^%sudo/#%sudo/' /etc/sudoers && \
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useradd -m -s /bin/bash -N -u $NB_UID $NB_USER && \
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mkdir -p $CONDA_DIR && \
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chown $NB_USER:$NB_GID $CONDA_DIR && \
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chmod g+w /etc/passwd && \
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fix-permissions $HOME && \
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fix-permissions $CONDA_DIR
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USER $NB_UID
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ARG PYTHON_VERSION=default
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# Setup work directory for backward-compatibility
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RUN mkdir "/home/$NB_USER/work" && \
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fix-permissions "/home/$NB_USER"
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# Install conda as jovyan and check the sha256 sum provided on the download site
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WORKDIR /tmp
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# Prerequisites installation: conda, pip, tini
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RUN wget --quiet "https://github.com/conda-forge/miniforge/releases/download/${miniforge_version}/${miniforge_installer}" && \
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echo "${miniforge_checksum} *${miniforge_installer}" | sha256sum --check && \
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/bin/bash "${miniforge_installer}" -f -b -p $CONDA_DIR && \
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rm "${miniforge_installer}" && \
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# Conda configuration see https://conda.io/projects/conda/en/latest/configuration.html
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echo "conda ${CONDA_VERSION}" >> $CONDA_DIR/conda-meta/pinned && \
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conda config --system --set auto_update_conda false && \
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conda config --system --set show_channel_urls true && \
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if [ ! $PYTHON_VERSION = 'default' ]; then conda install --yes python=$PYTHON_VERSION; fi && \
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conda list python | grep '^python ' | tr -s ' ' | cut -d '.' -f 1,2 | sed 's/$/.*/' >> $CONDA_DIR/conda-meta/pinned && \
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conda install --quiet --yes \
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"conda=${CONDA_VERSION}" \
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'pip' \
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'tini=0.18.0' && \
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conda update --all --quiet --yes && \
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conda list tini | grep tini | tr -s ' ' | cut -d ' ' -f 1,2 >> $CONDA_DIR/conda-meta/pinned && \
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conda clean --all -f -y && \
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rm -rf /home/$NB_USER/.cache/yarn && \
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fix-permissions $CONDA_DIR && \
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fix-permissions /home/$NB_USER
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# Install Jupyter Notebook, Lab, and Hub
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# Generate a notebook server config
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# Cleanup temporary files
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# Correct permissions
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# Do all this in a single RUN command to avoid duplicating all of the
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# files across image layers when the permissions change
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RUN conda install --quiet --yes \
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'notebook=6.1.6' \
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'jupyterhub=1.3.0' \
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'jupyterlab=2.2.9' && \
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conda clean --all -f -y && \
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npm cache clean --force && \
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jupyter notebook --generate-config && \
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rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
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rm -rf /home/$NB_USER/.cache/yarn && \
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fix-permissions $CONDA_DIR && \
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fix-permissions /home/$NB_USER
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EXPOSE 8888
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# Configure container startup
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ENTRYPOINT ["tini", "-g", "--"]
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CMD ["start-notebook.sh"]
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# Copy local files as late as possible to avoid cache busting
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COPY start.sh start-notebook.sh start-singleuser.sh /usr/local/bin/
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# Currently need to have both jupyter_notebook_config and jupyter_server_config to support classic and lab
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COPY jupyter_notebook_config.py /etc/jupyter/
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# Fix permissions on /etc/jupyter as root
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USER root
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# Prepare upgrade to JupyterLab V3.0 #1205
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RUN sed -re "s/c.NotebookApp/c.ServerApp/g" \
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/etc/jupyter/jupyter_notebook_config.py > /etc/jupyter/jupyter_server_config.py
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RUN fix-permissions /etc/jupyter/
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# Switch back to jovyan to avoid accidental container runs as root
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USER $NB_UID
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WORKDIR $HOME
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############################################################################
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################# Dependency: jupyter/minimal-notebook #####################
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############################################################################
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# Copyright (c) Jupyter Development Team.
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# Distributed under the terms of the Modified BSD License.
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LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
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USER root
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# Install all OS dependencies for fully functional notebook server
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RUN apt-get update && apt-get install -yq --no-install-recommends \
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build-essential \
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vim-tiny \
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git \
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inkscape \
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libsm6 \
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libxext-dev \
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libxrender1 \
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lmodern \
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netcat \
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# ---- nbconvert dependencies ----
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texlive-xetex \
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texlive-fonts-recommended \
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texlive-plain-generic \
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# ----
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tzdata \
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unzip \
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nano-tiny \
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&& apt-get clean && rm -rf /var/lib/apt/lists/*
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# Create alternative for nano -> nano-tiny
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RUN update-alternatives --install /usr/bin/nano nano /bin/nano-tiny 10
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# Switch back to jovyan to avoid accidental container runs as root
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USER $NB_UID
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############################################################################
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################# Dependency: jupyter/scipy-notebook #######################
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############################################################################
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# Copyright (c) Jupyter Development Team.
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# Distributed under the terms of the Modified BSD License.
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LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
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USER root
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# ffmpeg for matplotlib anim & dvipng+cm-super for latex labels
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RUN apt-get update && \
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apt-get install -y --no-install-recommends ffmpeg dvipng cm-super && \
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apt-get clean && rm -rf /var/lib/apt/lists/*
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USER $NB_UID
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# Install Python 3 packages
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RUN conda install --quiet --yes \
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'beautifulsoup4=4.9.*' \
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'conda-forge::blas=*=openblas' \
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'bokeh=2.2.*' \
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'bottleneck=1.3.*' \
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'cloudpickle=1.6.*' \
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'cython=0.29.*' \
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'dask=2020.12.*' \
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'dill=0.3.*' \
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'h5py=3.1.*' \
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'ipywidgets=7.6.*' \
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'ipympl=0.5.*'\
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'matplotlib-base=3.3.*' \
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'numba=0.52.*' \
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'numexpr=2.7.*' \
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'pandas=1.1.*' \
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'patsy=0.5.*' \
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'protobuf=3.14.*' \
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'pytables=3.6.*' \
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'scikit-image=0.18.*' \
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'scikit-learn=0.24.*' \
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'scipy=1.5.*' \
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'seaborn=0.11.*' \
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'sqlalchemy=1.3.*' \
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'statsmodels=0.12.*' \
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'sympy=1.7.*' \
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'vincent=0.4.*' \
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'widgetsnbextension=3.5.*'\
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'xlrd=1.2.*' \
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&& \
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conda clean --all -f -y && \
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# Activate ipywidgets extension in the environment that runs the notebook server
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jupyter nbextension enable --py widgetsnbextension --sys-prefix && \
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# Also activate ipywidgets extension for JupyterLab
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# Check this URL for most recent compatibilities
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# https://github.com/jupyter-widgets/ipywidgets/tree/master/packages/jupyterlab-manager
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jupyter labextension install @jupyter-widgets/jupyterlab-manager@^2.0.0 --no-build && \
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jupyter labextension install @bokeh/jupyter_bokeh@^2.0.0 --no-build && \
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jupyter labextension install jupyter-matplotlib@^0.7.2 --no-build && \
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jupyter lab build -y && \
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jupyter lab clean -y && \
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npm cache clean --force && \
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rm -rf "/home/${NB_USER}/.cache/yarn" && \
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rm -rf "/home/${NB_USER}/.node-gyp" && \
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fix-permissions "${CONDA_DIR}" && \
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fix-permissions "/home/${NB_USER}"
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# Install facets which does not have a pip or conda package at the moment
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WORKDIR /tmp
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RUN git clone https://github.com/PAIR-code/facets.git && \
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jupyter nbextension install facets/facets-dist/ --sys-prefix && \
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rm -rf /tmp/facets && \
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fix-permissions "${CONDA_DIR}" && \
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fix-permissions "/home/${NB_USER}"
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# Import matplotlib the first time to build the font cache.
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ENV XDG_CACHE_HOME="/home/${NB_USER}/.cache/"
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RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" && \
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fix-permissions "/home/${NB_USER}"
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USER $NB_UID
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WORKDIR $HOME
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############################################################################
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################ Dependency: jupyter/datascience-notebook ##################
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############################################################################
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# Copyright (c) Jupyter Development Team.
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# Distributed under the terms of the Modified BSD License.
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LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
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# Set when building on Travis so that certain long-running build steps can
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# be skipped to shorten build time.
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ARG TEST_ONLY_BUILD
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# Fix DL4006
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SHELL ["/bin/bash", "-o", "pipefail", "-c"]
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USER root
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# Julia installation
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# Default values can be overridden at build time
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# (ARGS are in lower case to distinguish them from ENV)
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# Check https://julialang.org/downloads/
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ARG julia_version="1.5.3"
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# SHA256 checksum
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ARG julia_checksum="f190c938dd6fed97021953240523c9db448ec0a6760b574afd4e9924ab5615f1"
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# R pre-requisites
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RUN apt-get update && \
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apt-get install -y --no-install-recommends \
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fonts-dejavu \
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gfortran \
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gcc && \
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apt-get clean && rm -rf /var/lib/apt/lists/*
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# Julia dependencies
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# install Julia packages in /opt/julia instead of $HOME
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ENV JULIA_DEPOT_PATH=/opt/julia \
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JULIA_PKGDIR=/opt/julia \
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JULIA_VERSION="${julia_version}"
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WORKDIR /tmp
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# hadolint ignore=SC2046
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RUN mkdir "/opt/julia-${JULIA_VERSION}" && \
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wget -q https://julialang-s3.julialang.org/bin/linux/x64/$(echo "${JULIA_VERSION}" | cut -d. -f 1,2)"/julia-${JULIA_VERSION}-linux-x86_64.tar.gz" && \
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echo "${julia_checksum} *julia-${JULIA_VERSION}-linux-x86_64.tar.gz" | sha256sum -c - && \
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tar xzf "julia-${JULIA_VERSION}-linux-x86_64.tar.gz" -C "/opt/julia-${JULIA_VERSION}" --strip-components=1 && \
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rm "/tmp/julia-${JULIA_VERSION}-linux-x86_64.tar.gz"
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RUN ln -fs /opt/julia-*/bin/julia /usr/local/bin/julia
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# Show Julia where conda libraries are \
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RUN mkdir /etc/julia && \
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echo "push!(Libdl.DL_LOAD_PATH, \"$CONDA_DIR/lib\")" >> /etc/julia/juliarc.jl && \
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# Create JULIA_PKGDIR \
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mkdir "${JULIA_PKGDIR}" && \
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chown "${NB_USER}" "${JULIA_PKGDIR}" && \
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fix-permissions "${JULIA_PKGDIR}"
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USER $NB_UID
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# R packages including IRKernel which gets installed globally.
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RUN conda install --quiet --yes \
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'r-base=4.0.3' \
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'r-caret=6.0*' \
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'r-crayon=1.3*' \
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'r-devtools=2.3*' \
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'r-forecast=8.13*' \
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'r-hexbin=1.28*' \
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'r-htmltools=0.5*' \
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'r-htmlwidgets=1.5*' \
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'r-irkernel=1.1*' \
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'r-nycflights13=1.0*' \
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'r-randomforest=4.6*' \
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'r-rcurl=1.98*' \
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'r-rmarkdown=2.6*' \
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'r-rsqlite=2.2*' \
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'r-shiny=1.5*' \
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'r-tidyverse=1.3*' \
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'rpy2=3.3*' && \
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conda clean --all -f -y && \
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fix-permissions "${CONDA_DIR}" && \
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fix-permissions "/home/${NB_USER}"
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# Add Julia packages. Only add HDF5 if this is not a test-only build since
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# it takes roughly half the entire build time of all of the images on Travis
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# to add this one package and often causes Travis to timeout.
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#
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# Install IJulia as jovyan and then move the kernelspec out
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# to the system share location. Avoids problems with runtime UID change not
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# taking effect properly on the .local folder in the jovyan home dir.
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RUN julia -e 'import Pkg; Pkg.update()' && \
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(test $TEST_ONLY_BUILD || julia -e 'import Pkg; Pkg.add("HDF5")') && \
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julia -e "using Pkg; pkg\"add IJulia\"; pkg\"precompile\"" && \
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# move kernelspec out of home \
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mv "${HOME}/.local/share/jupyter/kernels/julia"* "${CONDA_DIR}/share/jupyter/kernels/" && \
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chmod -R go+rx "${CONDA_DIR}/share/jupyter" && \
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rm -rf "${HOME}/.local" && \
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fix-permissions "${JULIA_PKGDIR}" "${CONDA_DIR}/share/jupyter"
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WORKDIR $HOME
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############################################################################
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########################## Dependency: gpulibs #############################
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############################################################################
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LABEL maintainer="Christoph Schranz <christoph.schranz@salzburgresearch.at>"
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# Install Tensorflow, check compatibility here: https://www.tensorflow.org/install/gpu
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# installation via conda leads to errors in version 4.8.2
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RUN pip install --upgrade pip && \
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pip install --no-cache-dir "tensorflow==2.3.2" && \
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pip install --no-cache-dir keras
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# Install PyTorch with dependencies
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RUN conda install --quiet --yes \
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pyyaml mkl mkl-include setuptools cmake cffi typing
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# Check compatibility here: https://pytorch.org/get-started/locally/
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RUN conda install --quiet --yes \
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pytorch \
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torchvision \
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cudatoolkit=10.1 -c pytorch
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# pip install torch_nightly -f https://download.pytorch.org/whl/nightly/cu90/torch_nightly.html && \
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RUN pip install --no-cache-dir torchviz
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# Clean installation
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RUN conda clean --all -f -y && \
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fix-permissions $CONDA_DIR && \
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fix-permissions /home/$NB_USER
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############################################################################
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############################ Useful packages ###############################
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############################################################################
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LABEL authors="Christoph Schranz <christoph.schranz@salzburgresearch.at>, Mathematical Michael <consistentbayes@gmail.com>"
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USER root
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RUN pip install --no-cache-dir ipyleaflet plotly==4.8.* "ipywidgets>=7.5"
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# Install important packages and Graphviz
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RUN set -ex \
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|
&& buildDeps=' \
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|
graphviz==0.11 \
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|
' \
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|
&& apt-get update \
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&& apt-get -y install htop apt-utils graphviz libgraphviz-dev openssh-client \
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&& pip install --no-cache-dir $buildDeps
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|
# Install various extensions
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|
RUN fix-permissions $CONDA_DIR
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|
RUN jupyter labextension install @jupyterlab/github
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|
RUN jupyter labextension install jupyterlab-drawio
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|
RUN jupyter labextension install jupyter-leaflet
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|
RUN jupyter labextension install jupyterlab-plotly@4.8.1
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|
RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager
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|
RUN pip install --no-cache-dir jupyter-tabnine==1.1.0 --user && \
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jupyter nbextension install --py jupyter_tabnine --user && \
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jupyter nbextension enable --py jupyter_tabnine --user && \
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|
jupyter serverextension enable --py jupyter_tabnine --user
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|
RUN pip install --no-cache-dir jupyter_contrib_nbextensions \
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|
jupyter_nbextensions_configurator rise
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|
# jupyter nbextension enable codefolding/main
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|
RUN jupyter labextension install @ijmbarr/jupyterlab_spellchecker
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|
|
|
RUN fix-permissions /home/$NB_USER
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|
|
|
# Switch back to jovyan to avoid accidental container runs as root
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|
USER $NB_UID
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|
|
|
# Copy jupyter_notebook_config.json
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|
COPY jupyter_notebook_config.json /etc/jupyter/
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