Dockerfile

# use debian as base image
# FROM debian:stretch
FROM ubuntu:21.04

EXPOSE 8888

# Label image
LABEL \
    "Description"="Connecting Hyp3 and MintPy. Amalgamation of the two existing dockerfiles" \
    "Github Source"="https://github.com/benjym/insar/" \
    "Dockerfile Author"="Benjy Marks" \
    "Email"="benjy.marks@sydney.edu.au"

# Install useful programs
RUN apt-get update && \
    DEBIAN_FRONTEND=noninteractive apt-get install -y \
    git \
    python3 \
    python3-pip \
    wget \
    vim \
    zip \
    libgdal-dev \
    nano \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

# Change default shell from dash to bash permanently
RUN ln -sf bash /bin/sh

# Prepare build time environment for conda and mintpy
ARG MINTPY_HOME=/home/python/MintPy
ARG PYTHON3DIR=/home/python/miniconda3
ARG PYAPS_HOME=/home/python/PyAPS
ARG WORK_DIR=/home/work/
ARG MINICONDA_VERSION=Miniconda3-py38_4.9.2-Linux-x86_64.sh
# ARG MINICONDA_VERSION=Miniconda3-4.5.4-Linux-x86_64.sh

# Prepare container environment
ENV MINTPY_HOME=${MINTPY_HOME}
ENV PYTHON3DIR=${PYTHON3DIR}
ENV PYAPS_HOME=${PYAPS_HOME}
ENV PATH=${MINTPY_HOME}/mintpy:${MINTPY_HOME}/sh:${PYTHON3DIR}/bin:${PATH}
ENV PYTHONPATH=${PYTHONPATH}:${MINTPY_HOME}:${PYAPS_HOME}
ENV PROJ_LIB=${PYTHON3DIR}/share/proj

# Set workdir
WORKDIR /home/python

# Pull and config mintpy and related tutorials
RUN git clone https://github.com/insarlab/MintPy.git
RUN git clone https://github.com/insarlab/MintPy-tutorial.git

# Pull and config PyAPS
RUN git clone https://github.com/yunjunz/pyaps3.git PyAPS

# Install miniconda
RUN wget https://repo.continuum.io/miniconda/${MINICONDA_VERSION} && \
    chmod +x ./${MINICONDA_VERSION}  && \
    ./${MINICONDA_VERSION} -b -p ${PYTHON3DIR} && \
    rm ./${MINICONDA_VERSION}

# Install dependencies
RUN ${PYTHON3DIR}/bin/conda install mamba -n base -c conda-forge
RUN ${PYTHON3DIR}/bin/mamba install --yes --file ${MINTPY_HOME}/docs/requirements.txt -c conda-forge
# RUN ${PYTHON3DIR}/bin/conda config --add channels conda-forge && \
    # ${PYTHON3DIR}/bin/conda install --yes --file ${MINTPY_HOME}/docs/requirements.txt

# Install hyp3 dependencies
# RUN ${PYTHON3DIR}/bin/conda install gdal
RUN ${PYTHON3DIR}/bin/mamba install gdal -c conda-forge
RUN ${PYTHON3DIR}/bin/python -m pip install hyp3_sdk hyp3lib ipython jupyterlab geodepy

# Install pykml
RUN ${PYTHON3DIR}/bin/pip install git+https://github.com/yunjunz/pykml.git

# Install DASK - not tested yet
#RUN mkdir -p /home/.config/dask && \
#    cp ${MINTPY_HOME}/mintpy/defaults/dask_mintpy.yaml /home/.config/dask/dask_mintpy.yaml

# Set working directory ENV - map a host data volume to this using "docker build . -t benjym/insar:latest && docker run benjym/insar:latest -v /host/path/to/data:/home/work/"
RUN mkdir -p ${WORK_DIR}
ENV WORK_DIR=${WORK_DIR}
WORKDIR ${WORK_DIR}

# Set some bash aliases so I don't freak out
RUN echo 'alias ..="cd .."' >> ~/.bashrc
RUN echo 'alias ll="ls -lha"' >> ~/.bashrc

# Not necessary scripts
# COPY ["./", "/home/work/"]
# COPY ["./asf.ini", "/root/asf.ini"] # for downloading directly from ASF via wget (I think?), currently not needed
# COPY ["./ecmwfapirc", "/root/.ecmwfapirc"] # needed for mintpy

# Actually necessary scripts
#COPY ["./netrc", "/root/.netrc"] # needed for hyp3_sdk
#COPY ["./model.cfg", "/home/python/PyAPS/pyaps3/model.cfg"] # needed for mintpy

# copy across credentials on run
RUN echo 'cp /home/work/logins/netrc     /root/.netrc' >> ~/.bashrc
RUN echo 'cp /home/work/logins/model.cfg /home/python/PyAPS/pyaps3/model.cfg' >> ~/.bashrc
# these ones are non-essential
RUN echo 'cp /home/work/asf.ini          /root/asf.ini' >> ~/.bashrc
RUN echo 'cp /home/work/ecmwfapirc       /root/.ecmwfapirc' >> ~/.bashrc


# Run entrypoint script - not required
# CMD ["sh", "/home/work/app.sh"]