Merge bids2table integration for BIDS ingress and RPool creation from main C-PAC repo

.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.dev1
-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
@@ -45,7 +45,8 @@ RUN rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/* \
     && chmod 777 $(ls / | grep -v sys | grep -v proc)
 ENV PYTHONUSERBASE=/home/c-pac_user/.local
 ENV PATH=$PATH:/home/c-pac_user/.local/bin \
-    PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages
+    PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages \
+    _SHELL=/bin/bash
 
 # set user
 WORKDIR /home/c-pac_user

.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.dev1
-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
@@ -46,7 +46,8 @@ RUN rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/* \
     && chmod 777 $(ls / | grep -v sys | grep -v proc)
 ENV PYTHONUSERBASE=/home/c-pac_user/.local
 ENV PATH=$PATH:/home/c-pac_user/.local/bin \
-    PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages
+    PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages \
+    _SHELL=/bin/bash
 
 # set user
 WORKDIR /home/c-pac_user

.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 \

.github/Dockerfiles/base-lite.Dockerfile

@@ -22,9 +22,9 @@ FROM ghcr.io/fcp-indi/c-pac/fsl:6.0.6.5-jammy as FSL
 FROM ghcr.io/fcp-indi/c-pac/ica-aroma:0.4.4-beta-jammy as ICA-AROMA
 
 FROM ghcr.io/fcp-indi/c-pac/ubuntu: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 \
 Standard software dependencies for C-PAC standard and lite images"
-LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
+LABEL org.opencontainers.image.source=https://github.com/FCP-INDI/C-PAC
 USER root
 
 # Installing connectome-workbench

.github/Dockerfiles/base-standard.Dockerfile

@@ -17,9 +17,9 @@
 FROM ghcr.io/fcp-indi/c-pac/freesurfer:6.0.0-min.neurodocker-jammy as FreeSurfer
 
 FROM ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.8.dev1
-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 \
 Standard software dependencies for C-PAC standard images"
-LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
+LABEL org.opencontainers.image.source=https://github.com/FCP-INDI/C-PAC
 USER root
 
 # Installing FreeSurfer

.github/Dockerfiles/c3d.1.0.0-jammy.Dockerfile

@@ -36,7 +36,7 @@ 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 \
 c3d 1.0.0 (Jammy) 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=c3d /opt/c3d/ /opt/c3d/

.github/Dockerfiles/connectome-workbench.1.5.0.neurodebian-jammy.Dockerfile

@@ -24,9 +24,9 @@ RUN apt-get update \
 USER c-pac_user
 
 # 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 \
 # connectome-workbench 1.5.0 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=base /lib/x86_64-linux-gnu/ld-linux-x86-64.so.2 /lib/x86_64-linux-gnu/ld-linux-x86-64.so.2
 # COPY --from=base /lib/x86_64-linux-gnu/libGL.so.1 /lib/x86_64-linux-gnu/libGL.so.1
 # COPY --from=base /lib/x86_64-linux-gnu/libGLU.so.1 /lib/x86_64-linux-gnu/libGLU.so.1

.github/Dockerfiles/neuroparc.1.0-human-bionic.Dockerfile

@@ -1,8 +1,8 @@
 # using neurodebian runtime as parent image
 FROM neurodebian:bionic-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 \
 neuroparc v1.0-human 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
 
 ARG DEBIAN_FRONTEND=noninteractive
 

.github/README/README.md

@@ -46,7 +46,7 @@ flowchart LR
       subgraph build_C-PAC.yml
         bCPAC[[C-PAC]]
       end
-      subgraph build_and_test.yml
+      subgraph build_and_test.yaml
         ubuntu[[Ubnutu]]-->stages[[stages]]-->build-base[[build-base]]-->build-base-standard[[build-base-standard]]
 
         Circle_tests[[Circle_tests]]
@@ -65,7 +65,7 @@ flowchart LR
         smoke-tests-participant[[smoke-tests-participant]]
       end
 
-      on_push.yml-->build_and_test.yml
+      on_push.yaml-->build_and_test.yaml
 
       delete_images.yml
     end
@@ -79,8 +79,8 @@ flowchart LR
 
     Circle_tests-->CircleCI((Run tests on Circle CI))
 
-    on_push.yml<-->get_pr_base_shas
-    on_push.yml-->update_all_preconfigs
+    on_push.yaml<-->get_pr_base_shas
+    on_push.yaml-->update_all_preconfigs
 
     cpacdockerfiles<-->C-PAC
 
@@ -94,7 +94,7 @@ flowchart LR
     bCPAC<-->local_ghcr
     stages<-->local_ghcr
 
-    push>git push]-->on_push.yml
+    push>git push]-->on_push.yaml
 
     smoke-tests-participant-->smoke_test_human
     smoke-tests-participant-->smoke_test_nhp

.github/dependabot.yaml

@@ -0,0 +1,20 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: /
+    # Check for updates once a week
+    schedule:
+      interval: weekly
+    groups:
+      all-actions:
+        patterns: [ "*" ]
+  - package-ecosystem: pip
+    directory: /
+    schedule:
+      interval: weekly
+    groups:
+      production dependencies:
+        dependency-type: production
+      development dependencies:
+        dependency-type: development
+    target-branch: develop

.github/workflows/build_C-PAC.yml

@@ -13,20 +13,20 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Maximize build space
-        uses: easimon/maximize-build-space@v6
+        uses: easimon/maximize-build-space@v10
         with:
           remove-dotnet: 'true'
           remove-android: 'true'
           remove-haskell: 'true'
           overprovision-lvm: 'true'
       - name: Check out C-PAC
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 2
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2.2.1
+        uses: docker/setup-buildx-action@v3.9.0
       - name: Log in to GitHub Container Registry
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
@@ -87,7 +87,7 @@ jobs:
           echo $DOCKERFILE
           cat $DOCKERFILE
       - name: Build and push Docker image
-        uses: docker/build-push-action@v4.0.0
+        uses: docker/build-push-action@v6.13.0
         with:
           context: .
           file: ${{ env.DOCKERFILE }}