Use a multistage build to reduce image size

docker/Dockerfile

@@ -1,15 +1,38 @@
-FROM ghcr.io/hivtools/naomi-base:minimal
+FROM naomi-base:main AS stage1
 
 COPY . /src
-COPY docker/Rprofile.site /usr/local/lib/R/etc/Rprofile.site
 COPY docker/bin /usr/local/bin/
+COPY docker/Rprofile.site /usr/local/lib/R/etc/Rprofile.site
+
+## Remove the large test data not needed for runtime
+RUN install_packages remotes \
+    && install_remote mrc-ide/naomi \
+    && rm -r /usr/local/lib/R/site-library/naomi/extdata
 
-RUN cd /src \
-    && ./scripts/build_test_data \
+WORKDIR /src
+RUN ./scripts/build_test_data \
     && find /src/inst/output -type f ! -name "malawi_model_output.qs" -delete \
     && R CMD INSTALL /src \
     && rm -r /src
 
+FROM rocker/r-ver:4 AS stage2
+
+## Install just the runtime-dependencies
+RUN apt-get update && apt-get -y install --no-install-recommends \
+        libudunits2-0 \
+        libhiredis1.1.0 \
+        libjq1 \
+        libsodium23 \
+        libssl3 \
+        gdal-bin \
+        && apt-get clean \
+        && rm -rf /var/lib/apt/lists/* \
+        && rm -rf /tmp/*
+
+COPY --from=stage1 /usr/local/lib/R/site-library /usr/local/lib/R/site-library
+COPY --from=stage1 /usr/local/bin /usr/local/bin
+COPY --from=stage1 /usr/bin/pandoc /usr/bin/pandoc
+
 EXPOSE 8888
 ENV HINTR_QUEUE_ID=hintr
 

docker/Rprofile.site

@@ -1 +1 @@
-options(knitr.chunk.dev = 'svglite')
+options(repos = c(CRAN = 'https://packagemanager.rstudio.com/all/__linux__/noble/latest'), download.file.method = 'libcurl')