🔀 Merge 'develop' into prep_for/mri_robust_template

Author: shnizzedy

.circleci/main.yml

@@ -45,10 +45,6 @@ commands:
       - run:
           name: "Configuring git user"
           command: |
-            sudo apt-key adv --recv-keys --keyserver keyserver.ubuntu.com 78BD65473CB3BD13
-            curl -L https://packagecloud.io/circleci/trusty/gpgkey | sudo apt-key add -
-            sudo apt-get update
-            sudo apt-get install git -y
             git config --global user.email "[email protected]"
             git config --global user.name "Theodore (machine user) @ CircleCI"
   create-docker-test-container:
@@ -64,11 +60,6 @@ commands:
             mkdir -p ~/project/test-results
             docker pull ${DOCKER_TAG}
             docker run -v /etc/passwd:/etc/passwd --user=$(id -u):c-pac -dit -P -e COVERAGE_FILE=<< parameters.coverage-file >> -v /home/circleci/project/test-results:/code/test-results -v /home/circleci:/home/circleci -v /home/circleci/project/CPAC/resources/configs/test_configs:/test_configs -v $PWD:/code -v $PWD/dev/circleci_data:$PWD/dev/circleci_data --workdir=/home/circleci/project --entrypoint=/bin/bash --name docker_test ${DOCKER_TAG}
-  get-sample-bids-data:
-    steps:
-      - run:
-          name: Getting Sample BIDS Data
-          command: git clone https://github.com/bids-standard/bids-examples.git
   get-singularity:
     parameters:
       version:
@@ -231,7 +222,6 @@ jobs:
       - set-up-variant:
           variant: "<< parameters.variant >>"
       - set-python-version
-      - get-sample-bids-data
       - run-pytest-docker
       - store_test_results:
           path: test-results

.github/Dockerfiles/AFNI.23.3.09-jammy.Dockerfile

@@ -155,9 +155,9 @@ RUN apt-get clean \
     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/*
 
 FROM scratch
-LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
+LABEL org.opencontainers.image.description="NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
 AFNI ${AFNI_VERSION} (${VERSION_NAME}) stage"
-LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
+LABEL org.opencontainers.image.source=https://github.com/FCP-INDI/C-PAC
 COPY --from=AFNI /lib/x86_64-linux-gnu/ld* /lib/x86_64-linux-gnu/
 COPY --from=AFNI /lib/x86_64-linux-gnu/lib*so* /lib/x86_64-linux-gnu/
 COPY --from=AFNI /lib64/ld* /lib64/

.github/Dockerfiles/ANTs.2.4.3-jammy.Dockerfile

@@ -30,8 +30,8 @@ RUN curl -sL https://github.com/ANTsX/ANTs/releases/download/v2.4.3/ants-2.4.3-u
 
 # Only keep what we need
 FROM scratch
-LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
+LABEL org.opencontainers.image.description="NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
 ANTs 2.4.3 stage"
-LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
+LABEL org.opencontainers.image.source=https://github.com/FCP-INDI/C-PAC
 COPY --from=ANTs /usr/lib/ants/ /usr/lib/ants/
 COPY --from=ANTs /ants_template/ /ants_template/

.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile

@@ -15,8 +15,8 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.8.dev2
-LABEL org.opencontainers.image.description "Full C-PAC image"
-LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
+LABEL org.opencontainers.image.description="Full C-PAC image"
+LABEL org.opencontainers.image.source=https://github.com/FCP-INDI/C-PAC
 USER root
 
 # install C-PAC

.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile

@@ -15,8 +15,8 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.8.dev2
-LABEL org.opencontainers.image.description "Full C-PAC image without FreeSurfer"
-LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
+LABEL org.opencontainers.image.description="Full C-PAC image without FreeSurfer"
+LABEL org.opencontainers.image.source=https://github.com/FCP-INDI/C-PAC
 USER root
 
 # install C-PAC

.github/Dockerfiles/FSL.6.0.6.5-jammy.Dockerfile

@@ -101,9 +101,9 @@ ENTRYPOINT ["/bin/bash"]
 
 # # Only keep what we need
 FROM scratch
-LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
+LABEL org.opencontainers.image.description="NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
 FSL 6.0.6.5 stage"
-LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
+LABEL org.opencontainers.image.source=https://github.com/FCP-INDI/C-PAC
 COPY --from=FSL /lib/x86_64-linux-gnu /lib/x86_64-linux-gnu
 COPY --from=FSL /usr/lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu
 COPY --from=FSL /usr/bin /usr/bin

.github/Dockerfiles/FSL.data.Dockerfile

@@ -18,9 +18,9 @@ RUN mkdir -p /fsl_data/atlases/HarvardOxford fsl_data/standard/tissuepriors \
     && chmod -R ugo+r /fsl_data/atlases
 
 FROM scratch
-LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
+LABEL org.opencontainers.image.description="NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
 FSL data"
-LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
+LABEL org.opencontainers.image.source=https://github.com/FCP-INDI/C-PAC
 
 COPY --from=FSL /fsl_data/standard fsl_data/standard
 COPY --from=FSL /fsl_data/atlases fsl_data/atlases

.github/Dockerfiles/FreeSurfer.6.0.0-min.neurodocker-jammy.Dockerfile

@@ -32,7 +32,7 @@ RUN apt-get clean && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 FROM scratch
-LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
+LABEL org.opencontainers.image.description="NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
 FreeSurfer 6.0.0-min stage"
-LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
+LABEL org.opencontainers.image.source=https://github.com/FCP-INDI/C-PAC
 COPY --from=FreeSurfer6 /usr/lib/freesurfer/ /usr/lib/freesurfer/

.github/Dockerfiles/ICA-AROMA.0.4.4-beta-jammy.Dockerfile

@@ -24,6 +24,6 @@ USER c-pac_user
 
 # Only keep what we need
 FROM scratch
-LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
+LABEL org.opencontainers.image.description="NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
 ICA-AROMA 0.4.4-beta stage"
 COPY --from=ICA-AROMA /opt/ICA-AROMA/ /opt/ICA-AROMA/

.github/Dockerfiles/Ubuntu.jammy-non-free.Dockerfile

@@ -26,9 +26,9 @@ RUN apt-get update \
 
 # use neurodebian runtime as parent image
 FROM neurodebian:jammy-non-free
-LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
+LABEL org.opencontainers.image.description="NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
 Ubuntu Jammy base image"
-LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
+LABEL org.opencontainers.image.source=https://github.com/FCP-INDI/C-PAC
 ARG BIDS_VALIDATOR_VERSION=1.14.6 \
     DEBIAN_FRONTEND=noninteractive
 ENV TZ=America/New_York \