link-r-python/Dockerfile at main · movestore/link-r-python · GitHub

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FROM registry.gitlab.com/couchbits/movestore/movestore-groundcontrol/co-pilot-v3-r:sdk-v3.2.0_geospatial-4.3.2_3649

# install miniconda aka conda-forge
ENV MINICONDA_VERSION=latest
ENV CONDA_DIR=$HOME/miniconda3
RUN wget --quiet -O ~/Miniforge3.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" && \
    chmod +x ~/Miniforge3.sh && \
    bash ~/Miniforge3.sh -b -p $CONDA_DIR && \
    rm ~/Miniforge3.sh
# make non-activate conda commands available
ENV PATH=$CONDA_DIR/bin:$PATH
# make conda activate command available from /bin/bash --login shells
RUN echo ". $CONDA_DIR/etc/profile.d/conda.sh" >> ~/.profile
# make conda activate command available from /bin/bash --interative shells
RUN conda init bash

USER $USER

# the app
ENV PROJECT_DIR=$HOME/co-pilot-r
WORKDIR $PROJECT_DIR

# the python part
WORKDIR $PROJECT_DIR/python
COPY --chown=$UID:$GID python/environment.yml /tmp/
# build the conda environment
# keep in mind that anaconda aka channel `conda` is blocked in production env
# https://gitlab.mpcdf.mpg.de/mpcdf-hpc-cloud/mvpr-moveapps/-/issues/29
# miniconda uses channel `conda-forge` as default - so nothing to do here
ENV ENV_PREFIX=$PROJECT_DIR/python-env
RUN conda env create --prefix $ENV_PREFIX --file /tmp/environment.yml && \
    conda clean --all --yes

# the r part
WORKDIR $PROJECT_DIR/r
# move the co-pilot-r sdk into this sub-directory
USER root:root
RUN mv ../src .
# cleanup: remove unusuded files form co-pilot-r
RUN rm -rf ../renv ../renv.lock ../.Rprofile ../RFunction.R src/io/shiny_bookmark_handler.R
# patch the co-pilot-r file `src/io/rds.R` in order to not dependend on `move1`
COPY r/src/io/rds.R src/io/rds.R
USER $USER
# renv: restore the current snapshot
COPY --chown=$UID:$GID r/renv.lock r/.Rprofile ./
COPY --chown=$UID:$GID r/renv/activate.R r/renv/settings.dcf ./renv/
RUN R -e 'renv::restore()'
# be prepared for the hangar inspection
RUN cp renv.lock ../

# the project
WORKDIR $PROJECT_DIR
# r -> python
COPY --chown=$UID:$GID python/csv_2_pickle.py python/transform_to_pickle.py ./python/
COPY --chown=$UID:$GID r/rds_2_csv.R ./r/
# python -> r
COPY --chown=$UID:$GID python/pickle_2_csv.py python/transform_to_csv.py ./python/
COPY --chown=$UID:$GID r/csv_2_rds.R ./r/

# r -> python
#COPY --chown=$UID:$GID r2python.sh start-process.sh
# python -> r
#COPY --chown=$UID:$GID python2r.sh start-process.sh