demo Docker container with working PyMB

Dockerfile

FROM ubuntu:17.04

MAINTAINER Kyle Foreman <[email protected]>

# update/install packages
RUN apt-get update --fix-missing && \
    apt-get install --yes \
        wget \
        curl \
        bzip2 \
        ca-certificates \
        libglib2.0-0 \
        libxext6 \
        libsm6 \
        libxrender1 \
        git \
        tar \
        build-essential && \
    apt-get purge && \
    apt-get clean

# install Anaconda (Python 2.7)
ENV APP_DIR /srv/app
RUN mkdir -p ${APP_DIR} && \
    echo 'export PATH=/opt/conda/bin:${PATH}' > /etc/profile.d/conda.sh && \
    wget --quiet https://repo.continuum.io/archive/Anaconda2-5.0.1-Linux-x86_64.sh -O ~/anaconda.sh && \
    /bin/bash ~/anaconda.sh -b -p ${APP_DIR}/conda && \
    rm ~/anaconda.sh
ENV PATH ${APP_DIR}/conda/bin:${PATH}
RUN conda config --add channels conda-forge

## TODO: move some of these into a conda environment.yaml?
# install R
RUN conda install -c conda-forge --yes r-base=3.4.1 rpy2=2.8.5
# install xarray
RUN conda install -c conda-forge --yes xarray=0.10.0
# install scikit-sparse (sksparse)
RUN conda install -c conda-forge --yes scikit-sparse=0.4.2
# install TMB
# Note: originally tried using CRAN, but not sure where it installed e.g. Eigen etc so I had trouble compiling models...
# also, this lets us install with the fancy metis orderings
# RUN Rscript -e 'install.packages("TMB", repos="http://cran.us.r-project.org")'
ENV TMB_SHA fbdd6c2a39bdb37d467b282e9a34922179fda505
ENV TMB_DIR ${APP_DIR}/conda/lib/R/library/TMB
RUN Rscript -e 'install.packages("Matrix", repos="http://cran.us.r-project.org")' && \
    wget --quiet https://github.com/kaskr/adcomp/archive/${TMB_SHA}.tar.gz -O ~/tmb.tgz && \
    mkdir ${TMB_DIR} && \
    tar -xzvf ~/tmb.tgz --strip 1 -C ${TMB_DIR} && \
    cd ${TMB_DIR} && \
    make install-metis-full && \
    rm ~/tmb.tgz
# install PyMB
# specify latest commit manually since I haven't setup e.g. versioneer...
ENV PYMB_SHA 2503586a5f54318c7dc328477902b0163fda45ef
ENV PYMB_DIR ${APP_DIR}/conda/lib/python2.7/site-packages/PyMB/
RUN wget --quiet https://github.com/kforeman/pymb/archive/${PYMB_SHA}.tar.gz -O ~/pymb.tgz && \
    mkdir ${PYMB_DIR} && \
    tar -xzvf ~/pymb.tgz --strip 1 -C ${PYMB_DIR} && \
    rm ~/pymb.tgz

# monkey patch PyMB so you can use default PyMB.model.compile() args
# I'm so, so sorry, Drew
# I welcome PRs on PyMB to make this more automagic!
RUN sed -i 's/\/usr\/share\/R\/include/\/srv\/app\/conda\/lib\/R\/include/g' ${PYMB_DIR}/model.py && \
    sed -i 's/\/usr\/local\/lib\/R\/site-library\/TMB\/include/\/srv\/app\/conda\/lib\/R\/library\/TMB\/include/g' ${PYMB_DIR}/model.py && \
    sed -i 's/\/usr\/lib\/R\/lib/\/srv\/app\/conda\/lib\/R\/lib/g' ${PYMB_DIR}/model.py

# run a test PyMB script to make sure it actually is able to compile and run models
## Note: should remove this from the final image
## _and I bet there's some actual testing you can do with Docker that I'm not aware of_
RUN wget --quiet https://gist.githubusercontent.com/kforeman/39a9595bf2b40df82e81aa531ea855a2/raw/951e1ed37b29e45397ee75686a5baae6e01ae30e/pymb-test-script.py -O ~/pymb-test-script.py && \
    python ~/pymb-test-script.py