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fix: docker build warnings #495

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Merged
mgxd merged 1 commit into from
Oct 13, 2025
Merged

fix: docker build warnings #495

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17 changes: 8 additions & 9 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -32,12 +32,12 @@ COPY . /src
RUN uvx --from build pyproject-build --installer uv -w /src

# Older Python to support legacy MCRIBS
FROM python:3.6.15-slim as pyenv
FROM python:3.6.15-slim AS pyenv
RUN pip install --no-cache-dir numpy nibabel scipy pandas numexpr contextlib2 \
&& cp /usr/lib/x86_64-linux-gnu/libffi.so.7* /usr/local/lib

# Intermediate step with utilities for downloading packages
FROM ${BASE_IMAGE} as downloader
FROM ${BASE_IMAGE} AS downloader
RUN apt-get update && \
apt-get install -y --no-install-recommends \
binutils \
Expand All @@ -48,7 +48,7 @@ RUN apt-get update && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# AFNI
FROM downloader as afni
FROM downloader AS afni
# The download link can point to newer releases
# As a safeguard, take advantage of Docker caching, and
# Bump the date to current to update AFNI
Expand All @@ -71,7 +71,7 @@ RUN mkdir -p /opt/afni-latest \
-name "3dvolreg" \) -delete

# Micromamba
FROM downloader as micromamba
FROM downloader AS micromamba

# Install a C compiler to build extensions when needed.
# traits<6.4 wheels are not available for Python 3.11+, but build easily.
Expand All @@ -95,7 +95,7 @@ RUN npm install -g svgo@^3.2.0 [email protected] && \
rm -r ~/.npm

# Main container
FROM ${BASE_IMAGE} as nibabies
FROM ${BASE_IMAGE} AS nibabies
ENV DEBIAN_FRONTEND="noninteractive" \
LANG="en_US.UTF-8" \
LC_ALL="en_US.UTF-8"
Expand Down Expand Up @@ -179,7 +179,6 @@ ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
MINC_BIN_DIR="$FREESURFER_HOME/mni/bin" \
MINC_LIB_DIR="$FREESURFER_HOME/mni/lib" \
MNI_DATAPATH="$FREESURFER_HOME/mni/data" \
FSL_DIR=${FSLDIR} \
FREESURFER="/opt/freesurfer"
ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
Expand All @@ -191,7 +190,7 @@ COPY --from=pyenv /usr/local/lib/ /usr/local/lib/
ENV PATH="/opt/MCRIBS/bin:/opt/MCRIBS/MIRTK/MIRTK-install/bin:/opt/MCRIBS/MIRTK/MIRTK-install/lib/tools:${PATH}" \
LD_LIBRARY_PATH="/opt/MCRIBS/lib:/opt/MCRIBS/ITK/ITK-install/lib:/opt/MCRIBS/VTK/VTK-install/lib:/opt/MCRIBS/MIRTK/MIRTK-install/lib:/usr/local/lib:${LD_LIBRARY_PATH}" \
MCRIBS_HOME="/opt/MCRIBS" \
PYTHONPATH="/opt/MCRIBS/lib/python:$PYTHONPATH"
PYTHONPATH="/opt/MCRIBS/lib/python"

# Create a shared $HOME directory
RUN useradd -m -s /bin/bash -G users nibabies && chmod -R 777 /home/nibabies
Expand All @@ -205,8 +204,8 @@ ENV MAMBA_ROOT_PREFIX="/opt/conda"
RUN micromamba shell init -s bash && \
echo "micromamba activate nibabies" >> $HOME/.bashrc
ENV PATH="/opt/conda/envs/nibabies/bin:$PATH" \
CPATH="/opt/conda/envs/nibabies/include:$CPATH" \
LD_LIBRARY_PATH="/opt/conda/envs/nibabies/lib:$LD_LIBRARY_PATH" \
CPATH="/opt/conda/envs/nibabies/include" \
LD_LIBRARY_PATH="/opt/conda/envs/nibabies/lib" \
CONDA_PYTHON="/opt/conda/envs/nibabies/bin/python"

# FSL environment
Expand Down