Switch to micromamba

Dockerfile

@@ -1,17 +1,26 @@
-FROM docker.io/fnndsc/pl-fetal-surface-extract:base-1
+FROM docker.io/fnndsc/pl-fetal-surface-extract:base-2
 
 LABEL org.opencontainers.image.authors="Jennings Zhang <[email protected]>" \
       org.opencontainers.image.title="pl-fetal-surface-extract" \
       org.opencontainers.image.description="Fetal brain MRI surface extraction using CIVET marching-cubes"
 
-WORKDIR /usr/local/src/pl-fetal-surface-extract
+RUN \
+    --mount=type=cache,sharing=private,target=/home/mambauser/.mamba/pkgs,uid=57439,gid=57439 \
+    --mount=type=cache,sharing=private,target=/opt/conda/pkgs,uid=57439,gid=57439 \
+    micromamba install -y -n base -c conda-forge python=3.11.5 numpy=1.26.0
 
-RUN conda install -c conda-forge -y numpy=1.22.3
+ARG SRCDIR=/home/mambauser/pl-fetal-surface-extract
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+WORKDIR ${SRCDIR}
 
-COPY requirements.txt .
-RUN pip install -r requirements.txt
+COPY --chown=57439:57439 requirements.txt .
+RUN --mount=type=cache,sharing=private,target=/home/mambauser/.cache/pip,uid=57439,gid=57439 \
+    pip install -r requirements.txt
 
-COPY . .
-RUN pip install .
+COPY --chown=mambauser:mambauser . .
+ARG extras_require=none
+RUN pip install ".[${extras_require}]" \
+    && cd / && rm -rf ${SRCDIR}
+WORKDIR /
 
-CMD ["extract_cp", "--help"]
+CMD ["extract_cp"]

base/Dockerfile

@@ -32,10 +32,20 @@ RUN cp -r /opt/CIVET/dist/perl /microminc/perl
 RUN mkdir -vp /microminc/share  \
     && cp -rv "$MNI_DATAPATH/surface-extraction" "/microminc/share"
 
-FROM fnndsc/conda:python3.11.2
+FROM ghcr.io/mamba-org/micromamba:1.5.1-bookworm-slim
+
+USER root
+RUN --mount=target=/var/lib/apt/lists,type=cache,sharing=locked \
+    --mount=target=/var/cache/apt,type=cache,sharing=locked \
+    rm -f /etc/apt/apt.conf.d/docker-clean \
+    && apt-get update \
+    && apt-get -y --no-install-recommends install perl
+
 COPY --from=builder /microminc /opt/microminc
 ENV PATH=/opt/microminc/bin:$PATH \
     LD_LIBRARY_PATH=/opt/microminc/lib:$LD_LIBRARY_PATH \
     MINC_FORCE_V2=1 MINC_COMPRESS=4 VOLUME_CACHE_THRESHOLD=-1 \
     MNI_DATAPATH=/opt/microminc/share \
     PERL5LIB=/opt/microminc/perl
+
+USER mambauser

base/build.sh

@@ -3,4 +3,4 @@
 exec docker buildx build --push \
     --platform linux/amd64,linux/arm64,linux/ppc64le \
     --build-arg http_proxy=$http_proxy \
-    -t docker.io/fnndsc/pl-fetal-surface-extract:base-1 .
+    -t docker.io/fnndsc/pl-fetal-surface-extract:base-2 .

requirements.txt

@@ -2,4 +2,4 @@ chris_plugin==0.3.1
 pycivet==0.1.2
 loguru==0.6.0
 pybicpl==0.5.1
-numpy~=1.22
+numpy~=1.26.0