Dockerfile-base

FROM debian:latest
MAINTAINER Tristan Salles

# install things
RUN apt-get update -qq && \
    DEBIAN_FRONTEND=noninteractive apt-get install -yq --no-install-recommends \
        bash-completion \
        build-essential \
        git \
        python3-minimal \
        python3-dev \
        python3-pip \
        libxml2-dev \
        xorg-dev \
        ssh \
        curl \
        libfreetype6-dev \
        libpng-dev \
        libxft-dev \
        xvfb \
        freeglut3 \
        freeglut3-dev \
        libgl1-mesa-dri \
        libgl1-mesa-glx \
        python3-tk \
        mesa-utils \
        libavcodec-dev \
        libavformat-dev \
        libavutil-dev \
        libswscale-dev \
        rsync \
        vim \
        less \
        xauth \
        swig \
        gdb-minimal \
        python3-dbg \
        cmake \
        python3-setuptools \
        wget \
        gfortran  && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/*

ENV LANG=C.UTF-8
# Install setuptools and wheel first, needed by plotly
RUN pip3 install -U setuptools  && \
    pip3 install -U wheel       && \
    pip3 install --no-cache-dir packaging \
        appdirs \
        numpy \
        jupyter \
        plotly \
        matplotlib \
        pillow \
        pyvirtualdisplay \
        ipython \
        ipyparallel \
        pint \
        sphinx \
        sphinx_rtd_theme \
        sphinxcontrib-napoleon \
        mock \
        scipy \
        tabulate \
        scons

RUN update-alternatives --install /usr/bin/python python /usr/bin/python3.5 1

# Hack for scons.. should be able to remove in future.
ENV SCONS_LIB_DIR /usr/local/lib/python3.5/dist-packages/scons-3.0.1

# Hack for scons.. should be able to remove in future.
ENV SCONS_LIB_DIR /usr/local/lib/python3.5/dist-packages/scons-3.0.1

# install extras in a new layer
RUN pip3 install --no-cache-dir h5py \
      tribad \
      numpy>=1.15.0 \
      h5py>=2.8.0 \
      six>=1.11.0 \
      setuptools>=38.4.0 \
      pandas>=0.24 \
      scipy>=1.2 \
      scikit-image>=0.15 \
      gFlex>=1.1.0 \
      matplotlib>=3.0

# Install Tini.. this is required because CMD (below) doesn't play nice with notebooks for some reason: https://github.com/ipython/ipython/issues/7062, https://github.com/jupyter/notebook/issues/334
RUN curl -L https://github.com/krallin/tini/releases/download/v0.10.0/tini > tini && \
    echo "1361527f39190a7338a0b434bd8c88ff7233ce7b9a4876f3315c22fce7eca1b0 *tini" | sha256sum -c - && \
    mv tini /usr/local/bin/tini && \
    chmod +x /usr/local/bin/tini

# expose notebook port
EXPOSE 8888

# expose lavavu port
EXPOSE 9999

# LavaVu stuff
# script for xvfb-run.  all docker commands will effectively run under this via the entrypoint
RUN printf "#\041/bin/sh \n rm -f /tmp/.X99-lock && xvfb-run -s '-screen 0 1600x1200x16' \$@" >> /usr/local/bin/xvfbrun.sh && \
chmod +x /usr/local/bin/xvfbrun.sh

RUN git clone https://github.com/j08lue/pycpt.git && \
    cd pycpt && \
    git checkout b45f720d09da79bcd567c5cbba9a554b0a7cc1d9 && \
    python3 setup.py install && \
    cd .. && \
    rm -rf pycpt

RUN apt-get update -qq && \
    DEBIAN_FRONTEND=noninteractive apt-get install -yq --no-install-recommends \
        gmsh \
        python3-gdal \
        gdal-bin \
        libgeos++ \
        libgeos-dev \
        libgdal-dev \
        libproj-dev \
        libproj-dev

RUN python3 -m pip install --no-cache-dir setuptools wheel && \
    python3 -m pip install --no-cache-dir \
    pathlib \
    pandas \
    descartes \
    meshio \
    shapely \
    geopy \
    rasterio \
    pygeotools \
    pygmsh \
    meshplex \
    ruamel.yaml \
    stripy

# add default user jovyan and change permissions on NB_WORK
#ENV NB_USER jovyan
#RUN useradd -m -s /bin/bash -N jovyan
#USER $NB_USER
#ENV NB_WORK /workspace

# install extras in a new layer
RUN python3 -m pip install --no-cache-dir \
        ipython \
        jupyter \
        lavavu \
        scikit-fuzzy

RUN python3 -m pip install --no-cache-dir -U git+https://github.com/matplotlib/basemap.git

# Install Tini.. this is required because CMD (below) doesn't play nice with notebooks for some reason: https://github.com/ipython/ipython/issues/7062, https://github.com/jupyter/notebook/issues/334
RUN curl -L https://github.com/krallin/tini/releases/download/v0.10.0/tini > tini && \
    echo "1361527f39190a7338a0b434bd8c88ff7233ce7b9a4876f3315c22fce7eca1b0 *tini" | sha256sum -c - && \
    mv tini /usr/local/bin/tini && \
    chmod +x /usr/local/bin/tini

# create a volume
RUN mkdir /live && \
    mkdir /live/lib

VOLUME /live/share
WORKDIR /live

# LavaVu stuff
# script for xvfb-run.  all docker commands will effectively run under this via the entrypoint
RUN printf "#\041/bin/sh \n rm -f /tmp/.X99-lock && xvfb-run -s '-screen 0 1600x1200x16' \$@" >> /usr/local/bin/xvfbrun.sh && \
chmod +x /usr/local/bin/xvfbrun.sh

# Add Tini
EXPOSE 8888
ENV TINI_VERSION v0.18.0
ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /usr/local/bin/tini
RUN chmod +x /usr/local/bin/tini
ENTRYPOINT ["/usr/local/bin/tini", "--"]

# expose LavaVu port
EXPOSE 9999

# note we use xvfb which to mimic the X display for lavavu
ENTRYPOINT ["/usr/local/bin/xvfbrun.sh"]


# launch notebook
ADD run-jupyter.sh /usr/local/bin/run-jupyter.sh
RUN chmod +x /usr/local/bin/run-jupyter.sh
CMD /usr/local/bin/run-jupyter.sh