Merge pull request #596 from nipy/bf-docker

BF docker build: use python3.9 (not 3.7 which gets upgraded to 3.9) and newer dcm2niix

Author: yarikoptic

Dockerfile

@@ -1,7 +1,7 @@
 # Generated by Neurodocker and Reproenv.
 
 FROM neurodebian:bullseye
-ENV PATH="/opt/dcm2niix-v1.0.20211006/bin:$PATH"
+ENV PATH="/opt/dcm2niix-v1.0.20220720/bin:$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 v1.0.20211006 \
+    && git checkout v1.0.20220720 \
     && mkdir /tmp/dcm2niix/build \
     && cd /tmp/dcm2niix/build \
-    && cmake  -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20211006 .. \
+    && cmake  -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20220720 .. \
     && make -j1 \
     && make install \
     && rm -rf /tmp/dcm2niix
@@ -63,7 +63,7 @@ RUN apt-get update -qq \
     # Enable `conda activate`
     && conda init bash \
     && conda install -y  --name base \
-           "python=3.7" \
+           "python=3.9" \
            "traits>=4.6.0" \
            "scipy" \
            "numpy" \
@@ -93,13 +93,13 @@ RUN printf '{ \
     { \
       "name": "env", \
       "kwds": { \
-        "PATH": "/opt/dcm2niix-v1.0.20211006/bin:$PATH" \
+        "PATH": "/opt/dcm2niix-v1.0.20220720/bin:$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 v1.0.20211006\\nmkdir /tmp/dcm2niix/build\\ncd /tmp/dcm2niix/build\\ncmake  -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20211006 ..\\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 v1.0.20220720\\nmkdir /tmp/dcm2niix/build\\ncd /tmp/dcm2niix/build\\ncmake  -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20220720 ..\\nmake -j1\\nmake install\\nrm -rf /tmp/dcm2niix" \
       } \
     }, \
     { \
@@ -143,7 +143,7 @@ RUN printf '{ \
     { \
       "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-latest/bin:$PATH\\"\\necho \\"Downloading Miniconda installer ...\\"\\nconda_installer=\\"/tmp/miniconda.sh\\"\\ncurl -fsSL -o \\"$conda_installer\\" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh\\nbash \\"$conda_installer\\" -b -p /opt/miniconda-latest\\nrm -f \\"$conda_installer\\"\\nconda update -yq -nbase conda\\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=3.7\\" \\\\\\n    \\"traits>=4.6.0\\" \\\\\\n    \\"scipy\\" \\\\\\n    \\"numpy\\" \\\\\\n    \\"nomkl\\" \\\\\\n    \\"pandas\\"\\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/*" \
+        "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-latest/bin:$PATH\\"\\necho \\"Downloading Miniconda installer ...\\"\\nconda_installer=\\"/tmp/miniconda.sh\\"\\ncurl -fsSL -o \\"$conda_installer\\" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh\\nbash \\"$conda_installer\\" -b -p /opt/miniconda-latest\\nrm -f \\"$conda_installer\\"\\nconda update -yq -nbase conda\\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\\"\\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/*" \
       } \
     }, \
     { \

utils/gen-docker-image.sh

@@ -8,11 +8,11 @@ VER=$(grep -Po '(?<=^__version__ = ).*' $thisd/../heudiconv/info.py | sed 's/"//
 image="kaczmarj/neurodocker:0.9.1"
 
 docker run --rm $image generate docker -b neurodebian:bullseye -p apt \
-    --dcm2niix version=v1.0.20211006 method=source \
+    --dcm2niix version=v1.0.20220720 method=source \
     --install git gcc pigz liblzma-dev libc-dev git-annex-standalone netbase \
     --copy . /src/heudiconv \
-    --miniconda version=latest conda_install="python=3.7 traits>=4.6.0 scipy numpy nomkl pandas" \
+    --miniconda version=latest conda_install="python=3.9 traits>=4.6.0 scipy numpy nomkl pandas" \
       pip_install="/src/heudiconv[all]" \
       pip_opts="--editable" \
     --entrypoint "heudiconv" \
-> ../Dockerfile
+> $thisd/../Dockerfile