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 JUPYTERHUB_PYTHON_VERSION=3.8

RUN curl -sL https://deb.nodesource.com/setup_10.x | bash - && \
    apt-get update && \
    apt-get install -y \
        nodejs \
        node-gyp \
        libssl1.0-dev \
        openjdk-11-jre-headless && \
    apt-get clean

RUN python${JUPYTERHUB_PYTHON_VERSION} -m pip --no-cache-dir install \
        jupyterlab \
        jupyterhub \
        ipympl \
	&& \
    python${JUPYTERHUB_PYTHON_VERSION} -m jupyter labextension install \
        @jupyter-widgets/jupyterlab-manager && \
    python${JUPYTERHUB_PYTHON_VERSION} -m jupyter serverextension enable --sys-prefix --py jupyterlab && \
    python${JUPYTERHUB_PYTHON_VERSION} -m jupyter labextension install \
        jupyter-webrtc \
        ipyvolume \
        jupyter-threejs \
        jupyterlab-execute-time \
    && \
    python${JUPYTERHUB_PYTHON_VERSION} -m jupyter labextension install @ryantam626/jupyterlab_code_formatter && \
    python${JUPYTERHUB_PYTHON_VERSION} -m pip --no-cache-dir install jupyterlab_code_formatter && \
    python${JUPYTERHUB_PYTHON_VERSION} -m jupyter serverextension enable --sys-prefix --py jupyterlab_code_formatter && \
    python${JUPYTERHUB_PYTHON_VERSION} -m pip --no-cache-dir install black isort && \
    python${JUPYTERHUB_PYTHON_VERSION} -m pip --no-cache-dir install jupyterlab-git && \
    python${JUPYTERHUB_PYTHON_VERSION} -m jupyter lab build

RUN mkdir -p ~/.venv && \
    python${JUPYTERHUB_PYTHON_VERSION} -m venv ~/.venv/robofish && \
    . ~/.venv/robofish/bin/activate && \
    python${JUPYTERHUB_PYTHON_VERSION} -m pip --no-cache-dir install --upgrade pip==20.2.2 && \
    pip --no-cache-dir install --upgrade setuptools==49.1.0 && \
    pip install tensorflow==1.15.3 && \
    pip --no-cache-dir install \
        wheel \
        black \
        isort \
        scipy \
        matplotlib \
        pandas \
        tables \
        xlrd \
        hsluv \
        ipympl \
        ipywebrtc \
        ipyvolume \
        seaborn \
        JPype1 \
        PySide2 \
        ipykernel \
        tqdm \
        sklearn \
        'mxnet-cu101>=1.6.0,<1.7.0' \
        && \
    ipython kernel install --user --name=robofish

COPY jupyter_notebook_config.py /root/.jupyter/
ENV JUPYTERLAB_SETTINGS_DIR=/data/home/.config/jupyter/lab/user-settings
ENV JUPYTERLAB_WORKSPACES_DIR=/data/home/.config/jupyter/lab/workspaces

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

WORKDIR "/data"
CMD [ "jupyterhub-singleuser" ]