Replace pennbbl with pennlinc in package

.circleci/IntramodalTemplate.sh

@@ -34,7 +34,7 @@ TESTNAME=imtemplate
 setup_dir ${TESTDIR}/${TESTNAME}
 TEMPDIR=${TESTDIR}/${TESTNAME}/work
 OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives
-BIDS_INPUT_DIR=${TESTDIR}/data/twoses
+BIDS_INPUT_DIR=${TESTDIR}/data/twoses/twoses
 QSIPREP_CMD=$(run_qsiprep_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
 
 ${QSIPREP_CMD} \

.circleci/MultiT1w.sh

@@ -28,12 +28,12 @@ EDDY_CFG=${TESTDIR}/data/eddy_config.json
 setup_dir ${TESTDIR}/${TESTNAME}
 TEMPDIR=${TESTDIR}/${TESTNAME}/work
 OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives
-BIDS_INPUT_DIR=${TESTDIR}/data/DSDTI
+BIDS_INPUT_DIR=${TESTDIR}/data/DSDTI/DSDTI
 export FS_LICENSE=${TESTDIR}/data/license.txt
 QSIPREP_CMD=$(run_qsiprep_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
 
 # CRITICAL: delete the fieldmap data
-rm -rf data/DSDTI/sub-PNC/fmap
+rm -rf data/DSDTI/DSDTI/sub-PNC/fmap
 
 # Create a shifted version of the t1w
 if [[ "${IN_CI}" = 'true' ]]; then

.circleci/config.yml

@@ -4,7 +4,7 @@ orbs:
 
 .dockersetup: &dockersetup
   docker:
-    - image: pennbbl/qsiprep_build:24.7.4
+    - image: pennlinc/qsiprep_build:24.10.0
   working_directory: /tmp/src/qsiprep
 
 runinstall: &runinstall
@@ -33,10 +33,7 @@ runinstall: &runinstall
         ln -s /home/qsiprep/.dipy /root/.dipy
       fi
 
-
-
 jobs:
-
   build:
     resource_class: small
     docker:
@@ -133,15 +130,15 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: twoses-01
+          key: twoses-02
       - run: *runinstall
       - run:
           name: Download twoses test data
           command: |
             cd /tmp/src/qsiprep/.circleci
             python get_data.py $PWD/data twoses
       - save_cache:
-          key: twoses-01
+          key: twoses-02
           paths:
             - /tmp/src/qsiprep/.circleci/data/twoses
 
@@ -364,6 +361,8 @@ jobs:
       CIRCLE_CPUS: 4
     steps:
       - checkout
+      - restore_cache:
+          key: twoses-02
       - run: *runinstall
       - run:
           name: Test the intramodal template workflow
@@ -380,7 +379,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: twoses-01
+          key: DSDTI-01
       - run: *runinstall
       - run:
           name: Test the mri robust template for T1w images
@@ -465,9 +464,9 @@ jobs:
             # Build docker image
             e=1 && for i in {1..5}; do
               docker build \
-                --cache-from=pennbbl/qsiprep \
+                --cache-from=pennlinc/qsiprep \
                 --rm=false \
-                -t pennbbl/qsiprep:latest \
+                -t pennlinc/qsiprep:latest \
                 --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
                 --build-arg VCS_REF=`git rev-parse --short HEAD` \
                 --build-arg VERSION="${CIRCLE_TAG:-$THISVERSION}" . \
@@ -479,12 +478,12 @@ jobs:
           command: |
             if [[ -n "$DOCKER_PASS" ]]; then
               docker login -u $DOCKER_USER -p $DOCKER_PASS
-              docker tag pennbbl/qsiprep pennbbl/qsiprep:unstable
-              docker push pennbbl/qsiprep:unstable
+              docker tag pennlinc/qsiprep pennlinc/qsiprep:unstable
+              docker push pennlinc/qsiprep:unstable
               if [[ -n "$CIRCLE_TAG" ]]; then
-                docker push pennbbl/qsiprep:latest
-                docker tag pennbbl/qsiprep pennbbl/qsiprep:$CIRCLE_TAG
-                docker push pennbbl/qsiprep:$CIRCLE_TAG
+                docker push pennlinc/qsiprep:latest
+                docker tag pennlinc/qsiprep pennlinc/qsiprep:$CIRCLE_TAG
+                docker push pennlinc/qsiprep:$CIRCLE_TAG
               fi
             fi
 
@@ -591,14 +590,14 @@ workflows:
 
       - IntramodalTemplate:
           requires:
-            - build
+            - download_twoses
           filters:
             tags:
               only: /.*/
 
       - MultiT1w:
           requires:
-            - download_twoses
+            - download_DSDTI
           filters:
             tags:
               only: /.*/

.circleci/get_data.sh

@@ -1,4 +1,4 @@
-IMAGE=pennbbl/qsiprep:unstable
+IMAGE=pennlinc/qsiprep:unstable
 
 # Set this to be comfortable on the testing machine
 MAX_CPUS=18

.github/config.yml

@@ -5,15 +5,15 @@ newPRWelcomeComment: >
   Thanks for opening this pull request!
   We have detected this is the first time for you to contribute
   to *qsiprep*.
-  Please check out our [contributing guidelines](https://github.com/pennbbl/qsiprep/blob/master/CONTRIBUTING.md).
+  Please check out our [contributing guidelines](https://github.com/pennlinc/qsiprep/blob/master/CONTRIBUTING.md).
 
   These are guidelines intended to make communication easier by describing a
   consistent process, but don't worry if you don't get it everything exactly
   "right" on the first try.
 
   We invite you to list yourself as a *qsiprep* contributor, so if your name
   is not already mentioned, please modify the
-  [``.zenodo.json``](https://github.com/pennbbl/qsiprep/blob/master/.zenodo.json)
+  [``.zenodo.json``](https://github.com/pennlinc/qsiprep/blob/master/.zenodo.json)
   file with your data. If you do so, your name will be listed as an author
   at the next release. Please add yourself to the list in alphabetical order,
   keeping Cieslak, Matthew as first and Satterthwaite, Theodore D. as last

Dockerfile

@@ -6,7 +6,7 @@ RUN apt-get update && \
 COPY . /src/qsiprep
 RUN python -m build /src/qsiprep
 
-FROM pennbbl/qsiprep_build:24.7.4
+FROM pennlinc/qsiprep_build:24.10.0
 
 # Install qsiprep wheel
 COPY --from=wheelstage /src/qsiprep/dist/*.whl .
@@ -30,6 +30,6 @@ LABEL org.label-schema.build-date=$BUILD_DATE \
       org.label-schema.description="qsiprep - q Space Images preprocessing tool" \
       org.label-schema.url="http://qsiprep.readthedocs.io" \
       org.label-schema.vcs-ref=$VCS_REF \
-      org.label-schema.vcs-url="https://github.com/pennbbl/qsiprep" \
+      org.label-schema.vcs-url="https://github.com/pennlinc/qsiprep" \
       org.label-schema.version=$VERSION \
       org.label-schema.schema-version="1.0"

README.rst

@@ -11,8 +11,8 @@ QSIprep: Preprocessing and analysis of q-space images
   :target: http://qsiprep.readthedocs.io/en/latest/?badge=latest
   :alt: Documentation Status
 
-.. image:: https://img.shields.io/badge/docker-pennbbl/qsiprep-brightgreen.svg?logo=docker&style=flat
-  :target: https://hub.docker.com/r/pennbbl/qsiprep/tags/
+.. image:: https://img.shields.io/badge/docker-pennlinc/qsiprep-brightgreen.svg?logo=docker&style=flat
+  :target: https://hub.docker.com/r/pennlinc/qsiprep/tags/
   :alt: Docker
 
 .. image:: https://circleci.com/gh/PennLINC/qsiprep/tree/master.svg?style=svg
@@ -44,7 +44,7 @@ The main features of this software are
      from Dipy_, MRTrix_, `DSI Studio`_  and others.
   4. A novel motion correction algorithm that works on DSI and random q-space sampling schemes
 
-.. image:: https://github.com/PennBBL/qsiprep/raw/master/docs/_static/workflow_full.png
+.. image:: https://github.com/PennLINC/qsiprep/raw/master/docs/_static/workflow_full.png
 
 
 .. _preprocessing_def:

docs/contributors.rst

@@ -9,8 +9,8 @@ update an existing environment, as necessary.
 
 Development in Docker is encouraged, for the sake of consistency and
 portability.
-By default, work should be built off of `pennbbl/qsiprep:latest
-<https://hub.docker.com/r/pennbbl/qsiprep/>`_ (see the
+By default, work should be built off of `pennlinc/qsiprep:latest
+<https://hub.docker.com/r/pennlinc/qsiprep/>`_ (see the
 installation_ guide for the basic procedure for running).
 
 
@@ -30,15 +30,15 @@ For example, ::
 
     $ docker run --rm -v $HOME/fullds005:/data:ro -v $HOME/dockerout:/out \
         -v $HOME/projects/qsiprep/qsiprep:/usr/local/miniconda/lib/python3.10/site-packages/qsiprep:ro \
-        pennbbl/qsiprep:latest /data /out/out participant \
+        pennlinc/qsiprep:latest /data /out/out participant \
         -w /out/work/
 
 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 \
         -v $HOME/projects/qsiprep/qsiprep:/usr/local/miniconda/lib/python3.10/site-packages/qsiprep:ro --entrypoint=bash \
-        pennbbl/qsiprep:latest
+        pennlinc/qsiprep:latest
 
 Patching containers can be achieved in Apptainer analogous to ``docker``
 using the ``--bind`` (``-B``) option: ::
@@ -65,14 +65,14 @@ dependency changes.
 
 Python dependencies should generally be included in the ``REQUIRES``
 list in `qsiprep/info.py
-<https://github.com/pennbbl/qsiprep/blob/29133e5e9f92aae4b23dd897f9733885a60be311/qsiprep/info.py#L46-L61>`_.
+<https://github.com/pennlinc/qsiprep/blob/29133e5e9f92aae4b23dd897f9733885a60be311/qsiprep/info.py#L46-L61>`_.
 If the latest version in `PyPI <https://pypi.org/>`_ is sufficient,
 then no further action is required.
 
 For large Python dependencies where there will be a benefit to
 pre-compiled binaries, `conda <https://github.com/conda/conda>`_ packages
 may also be added to the ``conda install`` line in the `Dockerfile
-<https://github.com/pennbbl/qsiprep/blob/29133e5e9f92aae4b23dd897f9733885a60be311/Dockerfile#L46>`_.
+<https://github.com/pennlinc/qsiprep/blob/29133e5e9f92aae4b23dd897f9733885a60be311/Dockerfile#L46>`_.
 
 Non-Python dependencies must also be installed in the Dockerfile, via a
 ``RUN`` command.
@@ -89,7 +89,7 @@ repository, located in ``~/projects/qsiprep``: ::
 
     ~/projects/qsiprep$ docker build -t qsiprep .
 
-To work in this image, replace ``pennbbl/qsiprep:latest`` with
+To work in this image, replace ``pennlinc/qsiprep:latest`` with
 ``qsiprep`` in any of the above commands.
 
 

docs/installation.rst

@@ -32,7 +32,7 @@ You may invoke ``docker`` directly::
         -v /filepath/to/data/dir \
         -v /filepath/to/output/dir \
         -v ${FREESURFER_HOME}/license.txt:/opt/freesurfer/license.txt \
-        pennbbl/qsiprep:latest \
+        pennlinc/qsiprep:latest \
         /filepath/to/data/dir /filepath/to/output/dir participant \
         --fs-license-file /opt/freesurfer/license.txt
 
@@ -42,7 +42,7 @@ For example: ::
         -v $HOME/fullds005 \
         -v $HOME/dockerout \
         -v ${FREESURFER_HOME}/license.txt:/opt/freesurfer/license.txt \
-        pennbbl/qsiprep:latest \
+        pennlinc/qsiprep:latest \
         $HOME/fullds005 $HOME/dockerout participant \
         --ignore fieldmaps \
         --fs-license-file /opt/freesurfer/license.txt
@@ -54,7 +54,7 @@ you will need to mount your Freesurfer license.txt file when invoking ``docker``
         -v $HOME/fullds005 \
         -v $HOME/dockerout \
         -v ${FREESURFER_HOME}/license.txt:/opt/freesurfer/license.txt \
-        pennbbl/qsiprep:latest \
+        pennlinc/qsiprep:latest \
         $HOME/fullds005 -v $HOME/dockerout participant \
         --fs-license-file /opt/freesurfer/license.txt
 
@@ -69,7 +69,7 @@ Apptainer Container
 
 The easiest way to get an Apptainer (formerly Singularity) image is to run::
 
-    $ apptainer build qsiprep-<version>.sif docker://pennbbl/qsiprep:<version>
+    $ apptainer build qsiprep-<version>.sif docker://pennlinc/qsiprep:<version>
 
 Where ``<version>`` should be replaced with the desired version of qsiprep that you want to download.
 Do not use ``latest`` or ``unstable`` unless you are performing limited testing.

docs/license.rst

@@ -2,10 +2,10 @@ License information
 -------------------
 
 We use the 3-clause BSD license; the full license may be found in the
-`LICENSE <https://github.com/pennbbl/qsiprep/blob/master/LICENSE>`_ file
+`LICENSE <https://github.com/pennlinc/qsiprep/blob/master/LICENSE>`_ file
 in the ``qsiprep`` distribution.
 
 All trademarks referenced herein are property of their respective holders.
 
-Copyright (c) 2018-2019 PennBBL
+Copyright (c) 2018-2019 PennLINC
 All rights reserved.

docs/preprocessing.rst

@@ -738,7 +738,7 @@ Configuring ``eddy``
 options, you can specify them in a JSON file and pass that to ``qsiprep``
 using the ``--eddy-config`` option. An example (default) eddy config json can
 be viewed or downloaded `here
-<https://github.com/PennBBL/qsiprep/blob/master/qsiprep/data/eddy_params.json>`__
+<https://github.com/PennLINC/qsiprep/blob/master/qsiprep/data/eddy_params.json>`__
 
 
 

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "hatchling.build"
 name = "qsiprep"
 description = "qsiprep builds workflows for preprocessing and reconstructing q-space images"
 readme = "long_description.rst"
-authors = [{name = "The PennBBL developers"}]
+authors = [{name = "The PennLINC developers"}]
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Intended Audience :: Science/Research",
@@ -47,10 +47,10 @@ dependencies = [
 dynamic = ["version"]
 
 [project.urls]
-Homepage = "https://github.com/pennbbl/qsiprep"
+Homepage = "https://github.com/pennlinc/qsiprep"
 Documentation = "https://www.qsiprep.readthedocs.io"
 Paper = "https://doi.org/10.1038/s41592-022-01458-7"
-"Docker Images" = "https://hub.docker.com/r/pennbbl/qsiprep/tags/"
+"Docker Images" = "https://hub.docker.com/r/pennlinc/qsiprep/tags/"
 
 [project.optional-dependencies]
 doc = [

qsiprep/cli/run.py

@@ -30,7 +30,6 @@
 def main():
     """Entry point."""
     import gc
-    import os
     import sys
     from multiprocessing import Manager, Process
     from os import EX_SOFTWARE
@@ -42,31 +41,6 @@ def main():
 
     parse_args()
 
-    # Raise a warning about PennBBL/QSIPrep being deprecated
-    in_container = False
-    # Check for Docker
-    if os.path.exists("/.dockerenv"):
-        in_container = True
-
-    # Check for Apptainer/Singularity
-    if os.path.exists("/.singularity.d") or os.path.exists("/.apptainer.d"):
-        in_container = True
-
-    # Check for environment variables
-    if os.getenv("SINGULARITY_NAME") or os.getenv("APPTAINER_NAME"):
-        in_container = True
-
-    if in_container:
-        print(
-            """\
-**************************************************************
-WARNING: The pennbbl/qsiprep Docker image has been DEPRECATED.
-Please use the pennlinc/qsiprep image instead.
-**************************************************************
-""",
-            file=sys.stderr,
-        )
-
     if "pdb" in config.execution.debug:
         from qsiprep.utils.debug import setup_exceptionhook
 

qsiprep/cli/version.py

@@ -66,12 +66,12 @@ def check_latest():
 
 def is_flagged():
     """Check whether current version is flagged."""
-    # https://raw.githubusercontent.com/pennbbl/qsiprep/master/.versions.json
+    # https://raw.githubusercontent.com/pennlinc/qsiprep/master/.versions.json
     flagged = tuple()
     try:
         response = requests.get(
             url="""\
-https://raw.githubusercontent.com/pennbbl/qsiprep/master/.versions.json""",
+https://raw.githubusercontent.com/pennlinc/qsiprep/master/.versions.json""",
             timeout=1.0,
         )
     except Exception:

qsiprep/tests/run_local_tests.py

@@ -70,7 +70,7 @@ def run_tests(test_regex, test_mark):
     run_str = "docker run --rm -ti "
     run_str += f"-v {local_patch}:{mounted_code} "
     run_str += "--entrypoint pytest "
-    run_str += "pennbbl/qsiprep:unstable "
+    run_str += "pennlinc/qsiprep:unstable "
     run_str += (
         f"{mounted_code}/qsiprep "
         f"--data_dir={mounted_code}/qsiprep/tests/test_data "

qsiprep/utils/bids.py

@@ -243,7 +243,7 @@ def write_derivative_description(bids_dir, deriv_dir):
                 "CodeURL": DOWNLOAD_URL,
             }
         ],
-        "CodeURL": "https://github.com/pennbbl/qsiprep",
+        "CodeURL": "https://github.com/pennlinc/qsiprep",
         "HowToAcknowledge": "Please cite our paper "
         "(https://www.nature.com/articles/s41592-021-01185-5#citeas), and "
         "include the generated citation boilerplate within the Methods "