make lighter alpine multi-stage build docker image, ~60% smaller

Dockerfile

@@ -1,159 +1,34 @@
-# Generated by Neurodocker and Reproenv.
+FROM python:3.10-alpine AS builder
 
-FROM neurodebian:bullseye
-ENV PATH="/opt/dcm2niix-v1.0.20220720/bin:$PATH"
-RUN apt-get update -qq \
-    && apt-get install -y -q --no-install-recommends \
-           ca-certificates \
-           cmake \
-           g++ \
-           gcc \
-           git \
-           make \
-           pigz \
-           zlib1g-dev \
-    && rm -rf /var/lib/apt/lists/* \
-    && git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix \
-    && cd /tmp/dcm2niix \
-    && git fetch --tags \
-    && git checkout v1.0.20220720 \
-    && mkdir /tmp/dcm2niix/build \
-    && cd /tmp/dcm2niix/build \
-    && cmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20220720 .. \
-    && make -j1 \
-    && make install \
-    && rm -rf /tmp/dcm2niix
-RUN apt-get update -qq \
-           && apt-get install -y -q --no-install-recommends \
-                  gcc \
-                  git \
-                  git-annex-standalone \
-                  libc-dev \
-                  liblzma-dev \
-                  netbase \
-                  pigz \
-           && rm -rf /var/lib/apt/lists/*
-COPY [".", \
-      "/src/heudiconv"]
-ENV CONDA_DIR="/opt/miniconda-py39_4.12.0" \
-    PATH="/opt/miniconda-py39_4.12.0/bin:$PATH"
-RUN apt-get update -qq \
-    && apt-get install -y -q --no-install-recommends \
-           bzip2 \
-           ca-certificates \
-           curl \
-    && rm -rf /var/lib/apt/lists/* \
-    # Install dependencies.
-    && export PATH="/opt/miniconda-py39_4.12.0/bin:$PATH" \
-    && echo "Downloading Miniconda installer ..." \
-    && conda_installer="/tmp/miniconda.sh" \
-    && curl -fsSL -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh \
-    && bash "$conda_installer" -b -p /opt/miniconda-py39_4.12.0 \
-    && rm -f "$conda_installer" \
-    # Prefer packages in conda-forge
-    && conda config --system --prepend channels conda-forge \
-    # Packages in lower-priority channels not considered if a package with the same
-    # name exists in a higher priority channel. Can dramatically speed up installations.
-    # Conda recommends this as a default
-    # https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html
-    && conda config --set channel_priority strict \
-    && conda config --system --set auto_update_conda false \
-    && conda config --system --set show_channel_urls true \
-    # Enable `conda activate`
-    && conda init bash \
-    && conda install -y  --name base \
-           "python=3.9" \
-           "traits>=4.6.0" \
-           "scipy" \
-           "numpy" \
-           "nomkl" \
-           "pandas" \
-           "gdcm" \
-    && bash -c "source activate base \
-    &&   python -m pip install --no-cache-dir --editable \
-             "/src/heudiconv[all]"" \
-    # Clean up
-    && sync && conda clean --all --yes && sync \
-    && rm -rf ~/.cache/pip/*
-ENTRYPOINT ["heudiconv"]
+RUN apk add bash \
+  gcc \
+  g++ \
+  libc-dev \
+  make \
+  cmake \
+  util-linux-dev \
+  curl \
+  git
+RUN pip install --no-cache-dir pylibjpeg-libjpeg traits==6.3.2
+
+ARG DCM2NIIX_VERSION=v1.0.20240202
+RUN git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix \
+  && cd /tmp/dcm2niix \
+  && git fetch --tags \
+  && git checkout $DCM2NIIX_VERSION \
+  && mkdir /tmp/dcm2niix/build \
+  && cd /tmp/dcm2niix/build \
+  && cmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON -DCMAKE_INSTALL_PREFIX:PATH=/usr/ .. \
+  && make -j1 \
+  && make install \
+  && rm -rf /tmp/dcm2niix
+
+FROM python:3.10-alpine
+COPY --from=builder /usr/local/lib/python3.10/site-packages /usr/local/lib/python3.10/site-packages
+COPY --from=builder /usr/bin/dcm2niix /usr/bin/dcm2niix
 
-# Save specification to JSON.
-RUN printf '{ \
-  "pkg_manager": "apt", \
-  "existing_users": [ \
-    "root" \
-  ], \
-  "instructions": [ \
-    { \
-      "name": "from_", \
-      "kwds": { \
-        "base_image": "neurodebian:bullseye" \
-      } \
-    }, \
-    { \
-      "name": "env", \
-      "kwds": { \
-        "PATH": "/opt/dcm2niix-v1.0.20220720/bin:$PATH" \
-      } \
-    }, \
-    { \
-      "name": "run", \
-      "kwds": { \
-        "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n    ca-certificates \\\\\\n    cmake \\\\\\n    g++ \\\\\\n    gcc \\\\\\n    git \\\\\\n    make \\\\\\n    pigz \\\\\\n    zlib1g-dev\\nrm -rf /var/lib/apt/lists/*\\ngit clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix\\ncd /tmp/dcm2niix\\ngit fetch --tags\\ngit checkout v1.0.20220720\\nmkdir /tmp/dcm2niix/build\\ncd /tmp/dcm2niix/build\\ncmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20220720 ..\\nmake -j1\\nmake install\\nrm -rf /tmp/dcm2niix" \
-      } \
-    }, \
-    { \
-      "name": "install", \
-      "kwds": { \
-        "pkgs": [ \
-          "git", \
-          "gcc", \
-          "pigz", \
-          "liblzma-dev", \
-          "libc-dev", \
-          "git-annex-standalone", \
-          "netbase" \
-        ], \
-        "opts": null \
-      } \
-    }, \
-    { \
-      "name": "run", \
-      "kwds": { \
-        "command": "apt-get update -qq \\\\\\n    && apt-get install -y -q --no-install-recommends \\\\\\n           gcc \\\\\\n           git \\\\\\n           git-annex-standalone \\\\\\n           libc-dev \\\\\\n           liblzma-dev \\\\\\n           netbase \\\\\\n           pigz \\\\\\n    && rm -rf /var/lib/apt/lists/*" \
-      } \
-    }, \
-    { \
-      "name": "copy", \
-      "kwds": { \
-        "source": [ \
-          ".", \
-          "/src/heudiconv" \
-        ], \
-        "destination": "/src/heudiconv" \
-      } \
-    }, \
-    { \
-      "name": "env", \
-      "kwds": { \
-        "CONDA_DIR": "/opt/miniconda-py39_4.12.0", \
-        "PATH": "/opt/miniconda-py39_4.12.0/bin:$PATH" \
-      } \
-    }, \
-    { \
-      "name": "run", \
-      "kwds": { \
-        "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n    bzip2 \\\\\\n    ca-certificates \\\\\\n    curl\\nrm -rf /var/lib/apt/lists/*\\n# Install dependencies.\\nexport PATH=\\"/opt/miniconda-py39_4.12.0/bin:$PATH\\"\\necho \\"Downloading Miniconda installer ...\\"\\nconda_installer=\\"/tmp/miniconda.sh\\"\\ncurl -fsSL -o \\"$conda_installer\\" https://repo.continuum.io/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh\\nbash \\"$conda_installer\\" -b -p /opt/miniconda-py39_4.12.0\\nrm -f \\"$conda_installer\\"\\n# Prefer packages in conda-forge\\nconda config --system --prepend channels conda-forge\\n# Packages in lower-priority channels not considered if a package with the same\\n# name exists in a higher priority channel. Can dramatically speed up installations.\\n# Conda recommends this as a default\\n# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html\\nconda config --set channel_priority strict\\nconda config --system --set auto_update_conda false\\nconda config --system --set show_channel_urls true\\n# Enable `conda activate`\\nconda init bash\\nconda install -y  --name base \\\\\\n    \\"python=3.9\\" \\\\\\n    \\"traits>=4.6.0\\" \\\\\\n    \\"scipy\\" \\\\\\n    \\"numpy\\" \\\\\\n    \\"nomkl\\" \\\\\\n    \\"pandas\\" \\\\\\n    \\"gdcm\\"\\nbash -c \\"source activate base\\n  python -m pip install --no-cache-dir --editable \\\\\\n      \\"/src/heudiconv[all]\\"\\"\\n# Clean up\\nsync && conda clean --all --yes && sync\\nrm -rf ~/.cache/pip/*" \
-      } \
-    }, \
-    { \
-      "name": "entrypoint", \
-      "kwds": { \
-        "args": [ \
-          "heudiconv" \
-        ] \
-      } \
-    } \
-  ] \
-}' > /.reproenv.json
-# End saving to specification to JSON.
+RUN apk update && apk add --no-cache git git-annex pigz gcompat
+
+RUN pip install --no-cache-dir heudiconv
+
+ENTRYPOINT ["heudiconv"]