Drop mentions of the qsiprep-docker wrapper (#807)

* Drop mentions of the docker CLI.

* Update docs/contributors.rst

---------

Co-authored-by: Matt Cieslak <[email protected]>

.circleci/config.yml

@@ -420,7 +420,6 @@ 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/qsiprep_container/qsiprep_docker.py
             sed -i -E "s/(var version = )'[A-Za-z0-9.-]+'/\1'${CIRCLE_TAG:-$THISVERSION}'/" docs/citing.rst
             sed -i "s/title = {qsiprep}/title = {qsiprep ${CIRCLE_TAG:-$THISVERSION}}/" qsiprep/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 ``qsiprep-docker`` script simplifies this for the most common repositories::
-
-    -f PATH, --patch-qsiprep PATH
-                          working qsiprep repository (default: None)
-    -p PATH, --patch-nipype PATH
-                          working nipype repository (default: None)
-
-For instance, if your repositories are contained in ``$HOME/projects``::
-
-    $ qsiprep-docker -f $HOME/projects/qsiprep/qsiprep \
-                      -p $HOME/projects/nipype/nipype \
-                      -i pennbbl/qsiprep: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, ::
         pennbbl/qsiprep:latest /data /out/out participant \
         -w /out/work/
 
-In order to work directly in the container, pass the ``--shell`` flag to
-``qsiprep-docker``::
-
-    $ qsiprep-docker --shell $HOME/fullds005 $HOME/dockerout participant
-
-This is the equivalent of using ``--entrypoint=bash`` and omitting the qsiprep
+In order to work directly in the container, use ``--entrypoint=bash`` 
 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/qsiprep``: ::
 
 To work in this image, replace ``pennbbl/qsiprep:latest`` with
 ``qsiprep`` in any of the above commands.
-This image may be accessed by the ``qsiprep-docker`` wrapper via the
-``-i`` flag, e.g. ::
-
-    $ qsiprep-docker -i qsiprep --shell
 
 
 Adding new features to the citation boilerplate

docs/installation.rst

@@ -20,24 +20,13 @@ Docker Container
 
 In order to run qsiprep in a Docker container, Docker must be `installed
 <https://docs.docker.com/engine/installation/>`_.
-Once Docker is installed, the recommended way to run qsiprep is to use the
-``qsiprep-docker`` wrapper, which requires Python and an Internet connection
-and that you install the ``qsiprep-container`` package with ``pip``.
 
-.. note:: If running Docker Desktop on MacOS (or via Docker Desktop), be sure to set
+.. 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, ``qsiprep-docker`` will generate a Docker command line for you,
-print it out for reporting purposes, and then run the command, e.g.::
-
-    $ qsiprep-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 pennbbl/qsiprep: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/usage.rst

@@ -30,25 +30,6 @@ Command-Line Arguments
    :nodefaultconst:
 
 
-The docker wrapper CLI
-======================
-
-.. argparse::
-   :ref: qsiprep_docker.get_parser
-   :prog: qsiprep-docker
-   :nodefault:
-   :nodefaultconst:
-
-
-The singularity wrapper CLI
-=============================
-
-.. argparse::
-   :ref: qsiprep_singularity.get_parser
-   :prog: qsiprep-docker
-   :nodefault:
-   :nodefaultconst:
-
 Note on using CUDA
 ==================
 

qsiprep/cli/run.py

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

qsiprep/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 = "qsiprep-docker" if _docker_ver else "docker"
+        _exec_env = "docker"
     del _cgroup
 
 _fs_license = os.getenv("FS_LICENSE")