Merge pull request #17 from PennLINC/pennlinc

Change pennbbl to pennlinc

Author: mattcieslak

.circleci/config.yml

@@ -43,11 +43,11 @@ build: &build
             --rm=false \
             -f ${BUILD_FILE} \
             --build-arg TAG_ANTS=${TAG_ANTS} \
-            -t pennbbl/${IMG_NAME}:${CIRCLE_TAG} .
+            -t pennlinc/${IMG_NAME}:${CIRCLE_TAG} .
 
           if [[ -n "$DOCKER_PASS" ]]; then
             docker login -u $DOCKER_USER -p $DOCKER_PASS
-            docker push pennbbl/${IMG_NAME}:$CIRCLE_TAG
+            docker push pennlinc/${IMG_NAME}:$CIRCLE_TAG
           fi
 
 jobs:
@@ -156,7 +156,7 @@ jobs:
               source setup_build.sh
               do_build build_fsl
               docker login -u $DOCKER_USER -p $DOCKER_PASS
-              docker push pennbbl/qsiprep_build:$CIRCLE_TAG
+              docker push pennlinc/qsiprep_build:$CIRCLE_TAG
             fi
 
   build_nofsl:
@@ -178,7 +178,7 @@ jobs:
               source setup_build.sh
               do_build no_fsl
               docker login -u $DOCKER_USER -p $DOCKER_PASS
-              docker push pennbbl/qsiprep_build:${CIRCLE_TAG}-nofsl
+              docker push pennlinc/qsiprep_build:${CIRCLE_TAG}-nofsl
             fi
 
   deployable:

Dockerfile

@@ -15,17 +15,17 @@ ARG TAG_SYNB0
 ARG FSL_BUILD
 
 # COPY can't handle variables, so here we go
-FROM pennbbl/qsiprep-fsl:${TAG_FSL} as build_fsl
-FROM pennbbl/qsiprep-freesurfer:${TAG_FREESURFER} as build_freesurfer
-FROM pennbbl/qsiprep-ants:${TAG_ANTS} as build_ants
-FROM pennbbl/qsiprep-mrtrix3:${TAG_MRTRIX3} as build_mrtrix3
-FROM pennbbl/qsiprep-3tissue:${TAG_3TISSUE} as build_3tissue
-FROM pennbbl/qsiprep-dsistudio:${TAG_DSISTUDIO} as build_dsistudio
-FROM pennbbl/qsiprep-micromamba:${TAG_MICROMAMBA} as build_micromamba
-FROM pennbbl/qsiprep-afni:${TAG_AFNI} as build_afni
-FROM pennbbl/qsiprep-drbuddi:${TAG_TORTOISE} as build_tortoise
-FROM pennbbl/qsiprep-drbuddicuda:${TAG_TORTOISE} as build_tortoisecuda
-FROM pennbbl/qsiprep-synb0:${TAG_SYNB0} as build_synb0
+FROM pennlinc/qsiprep-fsl:${TAG_FSL} as build_fsl
+FROM pennlinc/qsiprep-freesurfer:${TAG_FREESURFER} as build_freesurfer
+FROM pennlinc/qsiprep-ants:${TAG_ANTS} as build_ants
+FROM pennlinc/qsiprep-mrtrix3:${TAG_MRTRIX3} as build_mrtrix3
+FROM pennlinc/qsiprep-3tissue:${TAG_3TISSUE} as build_3tissue
+FROM pennlinc/qsiprep-dsistudio:${TAG_DSISTUDIO} as build_dsistudio
+FROM pennlinc/qsiprep-micromamba:${TAG_MICROMAMBA} as build_micromamba
+FROM pennlinc/qsiprep-afni:${TAG_AFNI} as build_afni
+FROM pennlinc/qsiprep-drbuddi:${TAG_TORTOISE} as build_tortoise
+FROM pennlinc/qsiprep-drbuddicuda:${TAG_TORTOISE} as build_tortoisecuda
+FROM pennlinc/qsiprep-synb0:${TAG_SYNB0} as build_synb0
 FROM pennlinc/atlaspack:0.1.0 as atlaspack
 FROM nvidia/cuda:11.1.1-runtime-ubuntu18.04 as ubuntu
 

Dockerfile_TORTOISE

@@ -1,6 +1,6 @@
 ARG TAG_ANTS
 
-FROM pennbbl/qsiprep-ants:${TAG_ANTS} as base
+FROM pennlinc/qsiprep-ants:${TAG_ANTS} as base
 FROM base as builder
 RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub
 

Dockerfile_TORTOISEcuda

@@ -1,6 +1,6 @@
 ARG TAG_ANTS
 
-FROM pennbbl/qsiprep-ants:${TAG_ANTS} as base
+FROM pennlinc/qsiprep-ants:${TAG_ANTS} as base
 FROM base as builder
 RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub
 

README.rst

@@ -1,14 +1,14 @@
 .. include:: links.rst
 
-QSIprep: Preprocessing and analysis of q-space images
-=======================================================
+QSIPrep: Preprocessing and analysis of q-space images
+=====================================================
 
-.. image:: https://readthedocs.org/projects/qsiprep/badge/?version=latest
-  :target: http://qsiprep.readthedocs.io/en/latest/?badge=latest
-  :alt: Documentation Status
+.. image:: https://circleci.com/gh/PennLINC/qsiprep_build/tree/master.svg?style=svg
+  :target: https://circleci.com/gh/PennLINC/qsiprep_build/tree/master
 
-.. image:: https://circleci.com/gh/PennLINC/qsiprep/tree/master.svg?style=svg
-  :target: https://circleci.com/gh/PennLINC/qsiprep/tree/master
+.. image:: https://img.shields.io/badge/docker-pennlinc/qsiprep_build-brightgreen.svg?logo=docker&style=flat
+  :target: https://hub.docker.com/r/pennlinc/qsiprep_build/tags/
+  :alt: Docker
 
 
 Full documentation at https://qsiprep.readthedocs.io
@@ -27,7 +27,7 @@ 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:

setup_build.sh

@@ -49,7 +49,7 @@ do_build() {
     DOCKER_BUILDKIT=1 \
     BUILDKIT_PROGRESS=plain \
     docker build -t \
-        pennbbl/qsiprep_build:${THIS_TAG} \
+        pennlinc/qsiprep_build:${THIS_TAG} \
         --build-arg TAG_FSL=${TAG_FSL} \
         --build-arg TAG_FREESURFER=${TAG_FREESURFER} \
         --build-arg TAG_ANTS=${TAG_ANTS} \