Dockerfile

# SPDX-License-Identifier: Apache-2.0
FROM git.imp.fu-berlin.de:5000/bioroboticslab/robofish/docker/ubuntu

LABEL maintainer="Moritz Maxeiner <moritz.maxeiner@fu-berlin.de>"
LABEL authors="Moritz Maxeiner <moritz.maxeiner@fu-berlin.de>"

RUN apt-get update && \
    apt-get install -y \
        curl && \
    apt-get clean

ENV NO_UPDATE_NOTIFIER=true
RUN curl -sL https://deb.nodesource.com/setup_12.x | bash - && \
    apt-get update && \
    apt-get install -y \
        nodejs \
        node-gyp \
        libssl1.0-dev \
        openjdk-11-jre-headless && \
    apt-get clean && \
    npm config set cache /var/cache/npm --global && \
    npm config set update-notifier false --global

RUN sed -i -e 's|root:/root|root:/home|g' /etc/passwd

ENV HOME=/home
ENV XDG_DATA_HOME=/usr/local/share
ENV IPYTHONDIR=/usr/local/etc/ipython
ENV JUPYTER_CONFIG_DIR=/usr/local/etc/jupyter
COPY jupyter_notebook_config.py ${JUPYTER_CONFIG_DIR}/
ENV JUPYTERLAB_SETTINGS_DIR=$HOME/.config/jupyter/lab/user-settings
ENV JUPYTERLAB_WORKSPACES_DIR=$HOME/.config/jupyter/lab/workspaces

RUN python${PYTHON_VERSION} -m pip install \
        jupyterlab==2.2.9 \
        jupyterhub==1.2.2 \
        ipympl==0.5.8 \
        black \
        isort \
	&& \
    python${PYTHON_VERSION} -m jupyter labextension install \
        @jupyter-widgets/jupyterlab-manager \
    && \
    python${PYTHON_VERSION} -m jupyter serverextension enable --sys-prefix --py jupyterlab

RUN python${PYTHON_VERSION} -m jupyter labextension install \
        jupyter-webrtc \
        ipyvolume \
        jupyter-threejs \
        jupyterlab-execute-time

RUN python${PYTHON_VERSION} -m pip install jupyterlab_code_formatter==1.3.8 && \
    python${PYTHON_VERSION} -m jupyter labextension install @ryantam626/jupyterlab_code_formatter && \
    python${PYTHON_VERSION} -m jupyter serverextension enable --sys-prefix --py jupyterlab_code_formatter

RUN python${PYTHON_VERSION} -m pip install jupyterlab-git && \
    python${PYTHON_VERSION} -m jupyter lab build

RUN python${PYTHON_VERSION} -m pip install jupyterlab_iframe && \
    python${PYTHON_VERSION} -m jupyter labextension install jupyterlab_iframe && \
    python${PYTHON_VERSION} -m jupyter serverextension enable --py jupyterlab_iframe

RUN mkdir -p /usr/local/venv && \
    python${PYTHON_VERSION} -m venv /usr/local/venv/default && \
    . /usr/local/venv/default/bin/activate && \
    python${PYTHON_VERSION} -m pip install --upgrade \
        pip==${PYTHON_PIP_VERSION} \
        setuptools==${PYTHON_SETUPTOOLS_VERSION} && \
    pip install tensorflow==1.15.3 && \
    pip install \
        wheel \
        black \
        isort \
        pandas \
        scipy \
        pingouin \
        statsmodels \
        matplotlib \
        seaborn \
        brokenaxes \
        tables \
        xlrd \
        hsluv \
        ipympl \
        ipywebrtc \
        ipyvolume \
        JPype1 \
        PySide2 \
        ipykernel \
        tqdm \
        sklearn \
        ffmpeg-python \
        neo \
        'mxnet-cu101>=1.6.0,<1.7.0' \
        && \
    ipython kernel install --name=default --display-name "Python 3.8 (Default)"

RUN mkdir -p /usr/local/venv && \
    python${PYTHON_VERSION} -m venv /usr/local/venv/tf2 && \
    . /usr/local/venv/tf2/bin/activate && \
    python${PYTHON_VERSION} -m pip install --upgrade \
        pip==${PYTHON_PIP_VERSION} \
        setuptools==${PYTHON_SETUPTOOLS_VERSION} && \
    pip install tensorflow-gpu==2.3.1 && \
    pip install \
        wheel \
        black \
        isort \
        pandas \
        scipy \
        pingouin \
        statsmodels \
        matplotlib \
        seaborn \
        brokenaxes \
        tables \
        xlrd \
        hsluv \
        ipympl \
        ipywebrtc \
        ipyvolume \
        JPype1 \
        PySide2 \
        ipykernel \
        tqdm \
        sklearn \
        ffmpeg-python \
        neo \
        'mxnet-cu101>=1.6.0,<1.7.0' \
        && \
    ipython kernel install --name=tf2 --display-name "Python 3.8 (TensorFlow 2)"

RUN apt-get update && \
    apt-get install -y \
        texlive-full \
    && \
    apt-get clean && \
    python${PYTHON_VERSION} -m pip install jupyterlab_latex && \
    jupyter labextension install @jupyterlab/latex

RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 && \
    add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu/ bionic-cran40/' && \
    apt-get update && \
    apt-get install -y  r-base r-base-html && \
    apt-get clean

RUN R -e "install.packages('IRkernel')" && \
    R -e "IRkernel::installspec(user = FALSE)" && \
    jupyter labextension install @techrah/text-shortcuts

RUN R -e "install.packages('IRkernel')" && \
    R -e "install.packages('readr')" && \
    R -e "install.packages('car')" && \
    R -e "install.packages('lme4')" && \
    R -e "install.packages('nlme')" && \
    R -e "install.packages('lmerTest')" && \
    R -e "install.packages('ggplot2')" && \
    R -e "install.packages('emmeans')"

RUN chmod -x /etc/update-motd.d/*

WORKDIR "${HOME}"
CMD [ "jupyterhub-singleuser" ]