Drop Docker wrapper

.circleci/config.yml

@@ -391,7 +391,6 @@ jobs:
               echo "the command ``git fetch --tags --verbose`` and push"
               echo "them to your fork with ``git push origin --tags``"
             fi
-            sed -i -E "s/(__version__ = )'[A-Za-z0-9.-]+'/\1'${CIRCLE_TAG:-$THISVERSION}'/" wrapper/qsirecon_container/qsirecon_docker.py
             sed -i -E "s/(var version = )'[A-Za-z0-9.-]+'/\1'${CIRCLE_TAG:-$THISVERSION}'/" docs/citing.rst
             sed -i "s/title = {qsirecon}/title = {qsirecon ${CIRCLE_TAG:-$THISVERSION}}/" qsirecon/data/boilerplate.bib
             # Build docker image

docs/contributors.rst

@@ -19,21 +19,6 @@ Patching working repositories
 In order to test new code without rebuilding the Docker image, it is
 possible to mount working repositories as source directories within the
 container.
-The ``qsirecon-docker`` script simplifies this for the most common repositories::
-
-    -f PATH, --patch-qsirecon PATH
-                          working qsirecon repository (default: None)
-    -p PATH, --patch-nipype PATH
-                          working nipype repository (default: None)
-
-For instance, if your repositories are contained in ``$HOME/projects``::
-
-    $ qsirecon-docker -f $HOME/projects/qsirecon/qsirecon \
-                      -p $HOME/projects/nipype/nipype \
-                      -i pennlinc/qsirecon:latest \
-                      $HOME/fullds005 $HOME/dockerout participant
-
-Note the ``-i`` flag allows you to specify an image.
 
 When invoking ``docker`` directly, the mount options must be specified
 with the ``-v`` flag::
@@ -48,12 +33,7 @@ For example, ::
         pennlinc/qsirecon:latest /data /out/out participant \
         -w /out/work/
 
-In order to work directly in the container, pass the ``--shell`` flag to
-``qsirecon-docker``::
-
-    $ qsirecon-docker --shell $HOME/fullds005 $HOME/dockerout participant
-
-This is the equivalent of using ``--entrypoint=bash`` and omitting the qsirecon
+In order to work directly in the container, use ``--entrypoint=bash`` and omit the qsirecon
 arguments in a ``docker`` command::
 
     $ docker run --rm -v $HOME/fullds005:/data:ro -v $HOME/dockerout:/out \
@@ -111,10 +91,6 @@ repository, located in ``~/projects/qsirecon``: ::
 
 To work in this image, replace ``pennlinc/qsirecon:latest`` with
 ``qsirecon`` in any of the above commands.
-This image may be accessed by the ``qsirecon-docker`` wrapper via the
-``-i`` flag, e.g. ::
-
-    $ qsirecon-docker -i qsirecon --shell
 
 
 Adding new features to the citation boilerplate

docs/installation.rst

@@ -20,24 +20,12 @@ Docker Container
 
 In order to run qsirecon in a Docker container, Docker must be `installed
 <https://docs.docker.com/engine/installation/>`_.
-Once Docker is installed, the recommended way to run qsirecon is to use the
-``qsirecon-docker`` wrapper, which requires Python and an Internet connection
-and that you install the ``qsirecon-container`` package with ``pip``.
 
 .. note:: If running Docker Desktop on MacOS (or via Docker Desktop), be sure to set
     the memory to 6 or more GB. Too little memory assigned to Docker Desktop can result
     in a message like ``Killed.``
 
-When run, ``qsirecon-docker`` will generate a Docker command line for you,
-print it out for reporting purposes, and then run the command, e.g.::
-
-    $ qsirecon-docker /path/to/data/dir /path/to/output/dir participant
-    RUNNING: docker run --rm -it -v /path/to/data/dir:/data \
-        -v /path/to_output/dir:/out pennlinc/qsirecon:latest \
-        /data /out participant
-    ...
-
-You may also invoke ``docker`` directly::
+You may invoke ``docker`` directly::
 
     $ docker run -ti --rm \
         -v /filepath/to/data/dir \

docs/reconstruction.rst

@@ -63,7 +63,7 @@ information about how to customize these, see :ref:`custom_reconstruction`.
 To use a pre-packaged workflow, simply provide the name from the leftmost column above for the
 ``--recon-spec`` argument. For example::
 
-  $ qsirecon-docker \
+  $ qsirecon \
       /output/from/qsiprep \
       /path/for/reconstruction/outputs \
       participant \
@@ -163,7 +163,7 @@ and from ``qsirecon``::
 
 You can run::
 
-  $ qsirecon-docker \
+  $ qsirecon \
       derivatives/qsiprep derivatives participant \
       --recon_spec mrtrix_multishell_msmt_ACT-hsvs \
       --freesurfer-input derivatives/freesurfer \
@@ -518,7 +518,7 @@ Executing the reconstruction pipeline
 Assuming this file is called ``qgi_scalar_export.json`` and you've installed
 ``qsirecon-container`` you can execute this pipeline with::
 
-  $ qsirecon-docker \
+  $ qsirecon \
       /output/from/qsiprep \
       /where/my/reconstructed/data/goes \
       participant \
@@ -601,9 +601,8 @@ Where ``"node_names"`` are the text names of the regions in ``"my_custom_atlas"`
 section.
 
 The directory containing ``atlas_config.json`` and the atlas nifti files should be mounted in
-the container at ``/atlas/qsirecon_atlases``. If using ``qsirecon-docker`` or
-``qsirecon-singularity`` this can be done with ``--custom-atlases /path/to/my/atlases`` or
-if you're running on your own system (not recommended) you can set the environment variable
+the container at ``/atlas/qsirecon_atlases``.
+If you're running on your own system (not recommended) you can set the environment variable
 ``QSIRECON_ATLAS=/path/to/my/atlases``.
 
 The nifti images should be registered to the

docs/usage.rst

@@ -31,25 +31,6 @@ Command-Line Arguments
    :nodefaultconst:
 
 
-The docker wrapper CLI
-======================
-
-.. argparse::
-   :ref: qsirecon_docker.get_parser
-   :prog: qsirecon-docker
-   :nodefault:
-   :nodefaultconst:
-
-
-The singularity wrapper CLI
-=============================
-
-.. argparse::
-   :ref: qsirecon_singularity.get_parser
-   :prog: qsirecon-docker
-   :nodefault:
-   :nodefaultconst:
-
 Note on using CUDA
 ==================
 

qsirecon/cli/run.py

@@ -157,7 +157,6 @@ def main():
             if config.environment.exec_env in (
                 "singularity",
                 "docker",
-                "qsirecon-docker",
             ):
                 boiler_file = Path("<OUTPUT_PATH>") / boiler_file.relative_to(
                     config.execution.output_dir

qsirecon/config.py

@@ -165,8 +165,7 @@
     _exec_env = "singularity"
     _cgroup = Path("/proc/1/cgroup")
     if _cgroup.exists() and "docker" in _cgroup.read_text():
-        _docker_ver = os.getenv("DOCKER_VERSION_8395080871")
-        _exec_env = "qsirecon-docker" if _docker_ver else "docker"
+        _exec_env = "docker"
     del _cgroup
 
 _fs_license = os.getenv("FS_LICENSE")