dcm2niix explicitly noted as a (PyPI) dependency and removed from being installed via apt-get etc

.github/workflows/test.yml

@@ -34,7 +34,7 @@ jobs:
           # The ultimate one-liner setup for NeuroDebian repository
           bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
           sudo apt-get update -qq
-          sudo apt-get install git-annex-standalone dcm2niix
+          sudo apt-get install git-annex-standalone
 
       - name: Install dependencies
         run: |

Dockerfile

@@ -1,28 +1,6 @@
 # Generated by Neurodocker and Reproenv.
 
 FROM neurodebian:bullseye
-ENV PATH="/opt/dcm2niix-v1.0.20220720/bin:$PATH"
-RUN apt-get update -qq \
-    && apt-get install -y -q --no-install-recommends \
-           ca-certificates \
-           cmake \
-           g++ \
-           gcc \
-           git \
-           make \
-           pigz \
-           zlib1g-dev \
-    && rm -rf /var/lib/apt/lists/* \
-    && git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix \
-    && cd /tmp/dcm2niix \
-    && git fetch --tags \
-    && git checkout v1.0.20220720 \
-    && mkdir /tmp/dcm2niix/build \
-    && cd /tmp/dcm2niix/build \
-    && cmake  -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20220720 .. \
-    && make -j1 \
-    && make install \
-    && rm -rf /tmp/dcm2niix
 RUN apt-get update -qq \
            && apt-get install -y -q --no-install-recommends \
                   gcc \
@@ -89,18 +67,6 @@ RUN printf '{ \
         "base_image": "neurodebian:bullseye" \
       } \
     }, \
-    { \
-      "name": "env", \
-      "kwds": { \
-        "PATH": "/opt/dcm2niix-v1.0.20220720/bin:$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  -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20220720 ..\\nmake -j1\\nmake install\\nrm -rf /tmp/dcm2niix" \
-      } \
-    }, \
     { \
       "name": "install", \
       "kwds": { \

docs/installation.rst

@@ -13,9 +13,6 @@ If installing through ``PyPI``, eg::
 
     pip install heudiconv[all]
 
-Manual installation of `dcm2niix <https://github.com/rordenlab/dcm2niix#install>`_
-is required.
-
 On Debian-based systems we recommend using `NeuroDebian <http://neuro.debian.net>`_
 which provides the `heudiconv package <http://neuro.debian.net/pkgs/heudiconv.html>`_.
 
@@ -56,4 +53,4 @@ It also contains converted from Docker singularity images for stock heudiconv im
 <https://github.com/ReproNim/containers#a-typical-workflow>`_ section for a prototypical example of using
 `datalad-container <https://github.com/datalad/datalad-container/>`_ extension with this dataset, while fulfilling
 `YODA principles <https://github.com/myyoda/poster/blob/master/ohbm2018.pdf>`_.  **Note** that it should also work on
-OSX with ``///repronim/containers`` automagically taking care about running those Singularity containers via Docker.
+OSX with ``///repronim/containers`` automagically taking care about running those Singularity containers via Docker.

heudiconv/info.py

@@ -22,12 +22,13 @@
 PYTHON_REQUIRES = ">=3.7"
 
 REQUIRES = [
-    'nibabel',
-    'pydicom',
-    'nipype >=1.2.3',
+    'dcm2niix',
     'dcmstack>=0.8',
     'etelemetry',
     'filelock>=3.0.12',
+    'nibabel',
+    'nipype >=1.2.3',
+    'pydicom',
 ]
 
 TESTS_REQUIRES = [

utils/gen-docker-image.sh

@@ -8,7 +8,6 @@ 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=v1.0.20220720 method=source \
     --install git gcc pigz liblzma-dev libc-dev git-annex-standalone netbase \
     --copy . /src/heudiconv \
     --miniconda version="py39_4.12.0" conda_install="python=3.9 traits>=4.6.0 scipy numpy nomkl pandas" \