Merge pull request #790 from nipy/rf-docker

Docker image: Use newer debian stable for the base and newer dcm2niix

Author: yarikoptic

Dockerfile

@@ -1,7 +1,7 @@
 # Generated by Neurodocker and Reproenv.
 
-FROM neurodebian:bullseye
-ENV PATH="/opt/dcm2niix-v1.0.20220720/bin:$PATH"
+FROM neurodebian:bookworm
+ENV PATH="/opt/dcm2niix-v1.0.20240202/bin:$PATH"
 RUN apt-get update -qq \
     && apt-get install -y -q --no-install-recommends \
            ca-certificates \
@@ -16,10 +16,10 @@ RUN apt-get update -qq \
     && git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix \
     && cd /tmp/dcm2niix \
     && git fetch --tags \
-    && git checkout v1.0.20220720 \
+    && git checkout v1.0.20240202 \
     && 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 .. \
+    && cmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20240202 .. \
     && make -j1 \
     && make install \
     && rm -rf /tmp/dcm2niix
@@ -87,19 +87,19 @@ RUN printf '{ \
     { \
       "name": "from_", \
       "kwds": { \
-        "base_image": "neurodebian:bullseye" \
+        "base_image": "neurodebian:bookworm" \
       } \
     }, \
     { \
       "name": "env", \
       "kwds": { \
-        "PATH": "/opt/dcm2niix-v1.0.20220720/bin:$PATH" \
+        "PATH": "/opt/dcm2niix-v1.0.20240202/bin:$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" \
+        "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 v1.0.20240202\\nmkdir /tmp/dcm2niix/build\\ncd /tmp/dcm2niix/build\\ncmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20240202 ..\\nmake -j1\\nmake install\\nrm -rf /tmp/dcm2niix" \
       } \
     }, \
     { \

utils/gen-docker-image.sh

@@ -7,11 +7,20 @@ VER=$(grep -Po '(?<=^__version__ = ).*' $thisd/../heudiconv/info.py | sed 's/"//
 
 image="kaczmarj/neurodocker:0.9.1"
 
-docker run --rm $image generate docker \
-    --base-image neurodebian:bullseye \
+if hash podman; then
+    OCI_BINARY=podman
+elif hash docker; then
+    OCI_BINARY=docker
+else
+    echo "ERROR: no podman or docker found" >&2
+    exit 1
+fi
+
+${OCI_BINARY:-docker} run --rm $image generate docker \
+    --base-image neurodebian:bookworm \
     --pkg-manager apt \
     --dcm2niix \
-        version=v1.0.20220720 \
+        version=v1.0.20240202 \
         method=source \
         cmake_opts="-DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON" \
     --install \