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sgiavasissgiavasis
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Merge branch 'develop' into merge/fsl-topup
2 parents a807cf4 + f401439 commit 7b2d975

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‎.circleci/main.yml‎

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@@ -56,23 +56,23 @@ commands:
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steps:
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- push-to-docker-hub:
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tag: nightly
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- when:
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condition:
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not:
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equal: [ << parameters.variant >>, fMRIPrep-LTS ]
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steps:
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- run:
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name: "Starting local registry"
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command: docker run -d -p 5000:5000 --restart=always --name registry registry:2
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- get-singularity
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- run:
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name: "Building Singularity image from Docker image"
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command: |
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docker load < ${DOCKER_TARBALL}.tar.gz
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docker tag fcpindi/c-pac:${DOCKER_TAG} localhost:5000/fcpindi/c-pac:${DOCKER_TAG}
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docker push localhost:5000/fcpindi/c-pac:${DOCKER_TAG}
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SINGULARITY_NOHTTPS=1 singularity build cpac-singularity-image${VARIANT}.simg docker://localhost:5000/fcpindi/c-pac:${DOCKER_TAG}
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no_output_timeout: 5h
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# - when:
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# condition:
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# not:
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# equal: [ << parameters.variant >>, fMRIPrep-LTS ]
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# steps:
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# - run:
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# name: "Starting local registry"
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# command: docker run -d -p 5000:5000 --restart=always --name registry registry:2
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# - get-singularity
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# - run:
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# name: "Building Singularity image from Docker image"
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# command: |
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# docker load < ${DOCKER_TARBALL}.tar.gz
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# docker tag fcpindi/c-pac:${DOCKER_TAG} localhost:5000/fcpindi/c-pac:${DOCKER_TAG}
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# docker push localhost:5000/fcpindi/c-pac:${DOCKER_TAG}
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# SINGULARITY_NOHTTPS=1 singularity build cpac-singularity-image${VARIANT}.simg docker://localhost:5000/fcpindi/c-pac:${DOCKER_TAG}
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# no_output_timeout: 5h
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check-updated:
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steps:
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- restore_cache:
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- run:
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name: "Configuring git user"
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command: |
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sudo apt-key adv --recv-keys --keyserver keyserver.ubuntu.com 78BD65473CB3BD13
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curl -L https://packagecloud.io/circleci/trusty/gpgkey | sudo apt-key add -
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sudo apt-get update
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sudo apt-get install git -y
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git config --global user.email "[email protected]"
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- build-images
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- store_artifacts:
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path: cpac-docker-image.tar.gz
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- store_artifacts:
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path: cpac-singularity-image.simg
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# - store_artifacts:
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# path: cpac-singularity-image.simg
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- persist_to_workspace:
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root: /home/circleci/
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paths:
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- project/cpac-docker-image.tar.gz
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- project/cpac-singularity-image.simg
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# - project/cpac-singularity-image.simg
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build-ABCD-HCP:
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machine:
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image: ubuntu-2004:202010-01
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variant: ABCD-HCP
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- store_artifacts:
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path: cpac-docker-image-ABCD-HCP.tar.gz
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- store_artifacts:
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path: cpac-singularity-image-ABCD-HCP.simg
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# - store_artifacts:
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# path: cpac-singularity-image-ABCD-HCP.simg
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- persist_to_workspace:
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root: /home/circleci/
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paths:
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- project/cpac-docker-image-ABCD-HCP.tar.gz
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- project/cpac-singularity-image-ABCD-HCP.simg
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# - project/cpac-singularity-image-ABCD-HCP.simg
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build-fMRIPrep-LTS:
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machine:
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image: ubuntu-2004:202010-01
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variant: fMRIPrep-LTS
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- store_artifacts:
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path: cpac-docker-image-fMRIPrep-LTS.tar.gz
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- store_artifacts:
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path: cpac-singularity-image-fMRIPrep-LTS.simg
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# - store_artifacts:
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# path: cpac-singularity-image-fMRIPrep-LTS.simg
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- persist_to_workspace:
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root: /home/circleci/
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paths:
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- project/cpac-docker-image-fMRIPrep-LTS.tar.gz
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- project/cpac-singularity-image-fMRIPrep-LTS.simg
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# - project/cpac-singularity-image-fMRIPrep-LTS.simg
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build-lite:
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machine:
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image: ubuntu-2004:202010-01
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variant: lite
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- store_artifacts:
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path: cpac-docker-image-lite.tar.gz
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- store_artifacts:
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path: cpac-singularity-image-lite.simg
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# - store_artifacts:
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# path: cpac-singularity-image-lite.simg
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- persist_to_workspace:
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root: /home/circleci/
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paths:
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- project/cpac-docker-image-lite.tar.gz
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- project/cpac-singularity-image-lite.simg
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# - project/cpac-singularity-image-lite.simg
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check-version:
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machine:
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image: ubuntu-2004:202010-01
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- check-updated
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- restore_cache:
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key: coverage-docker--{{ .Revision }}
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- restore_cache:
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key: coverage-singularity--{{ .Revision }}
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# - restore_cache:
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# key: coverage-singularity--{{ .Revision }}
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- restore_cache:
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key: coverage-docker-ABCD-HCP-{{ .Revision }}
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- restore_cache:
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key: coverage-singularity-ABCD-HCP-{{ .Revision }}
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# - restore_cache:
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# key: coverage-singularity-ABCD-HCP-{{ .Revision }}
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- restore_cache:
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key: coverage-docker-lite-{{ .Revision }}
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- restore_cache:
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key: coverage-singularity-lite-{{ .Revision }}
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# - restore_cache:
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# key: coverage-singularity-lite-{{ .Revision }}
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- set-python-version
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- combine-coverage
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- store_artifacts:
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name: "Build images"
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requires:
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- "Checking for updated version"
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- build-ABCD-HCP:
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name: "Build ABCD-HCP variant images"
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requires:
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- "Checking for updated version"
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- build-fMRIPrep-LTS:
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name: "Build fMRIPrep-LTS variant images"
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requires:
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- "Checking for updated version"
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# - build-ABCD-HCP:
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# name: "Build ABCD-HCP variant images"
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# requires:
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# - "Checking for updated version"
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# - build-fMRIPrep-LTS:
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# name: "Build fMRIPrep-LTS variant images"
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# requires:
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# - "Checking for updated version"
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- build-lite:
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name: "Build lite variant images"
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requires:
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name: "Combine coverage"
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requires:
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- "Test in Docker"
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- "Test in Singularity"
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# - "Test in Singularity"
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- "Test lite variant in Docker"
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- "Test lite variant in Singularity"
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- "Test ABCD-HCP variant in Docker"
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- "Test ABCD-HCP variant in Singularity"
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- "Test fMRIPrep-LTS variant in Docker"
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# - "Test lite variant in Singularity"
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# - "Test ABCD-HCP variant in Docker"
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# - "Test ABCD-HCP variant in Singularity"
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# - "Test fMRIPrep-LTS variant in Docker"
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- pytest-docker:
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name: "Test in Docker"
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requires:
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- "Build images"
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- pytest-docker:
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name: "Test ABCD-HCP variant in Docker"
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requires:
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- "Build ABCD-HCP variant images"
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variant: ABCD-HCP
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- pytest-docker:
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name: "Test fMRIPrep-LTS variant in Docker"
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requires:
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- "Build fMRIPrep-LTS variant images"
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variant: fMRIPrep-LTS
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# - pytest-docker:
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# name: "Test ABCD-HCP variant in Docker"
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# requires:
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# - "Build ABCD-HCP variant images"
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# variant: ABCD-HCP
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# - pytest-docker:
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# name: "Test fMRIPrep-LTS variant in Docker"
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# requires:
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# - "Build fMRIPrep-LTS variant images"
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# variant: fMRIPrep-LTS
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- pytest-docker:
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name: "Test lite variant in Docker"
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requires:
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- "Build lite variant images"
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variant: lite
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- pytest-singularity:
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name: "Test in Singularity"
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requires:
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- "Build images"
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- pytest-singularity:
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name: "Test ABCD-HCP variant in Singularity"
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requires:
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- "Build ABCD-HCP variant images"
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variant: ABCD-HCP
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- pytest-singularity:
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name: "Test lite variant in Singularity"
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requires:
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- "Build lite variant images"
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variant: lite
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# - pytest-singularity:
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# name: "Test in Singularity"
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# requires:
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# - "Build images"
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# - pytest-singularity:
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# name: "Test ABCD-HCP variant in Singularity"
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# requires:
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# - "Build ABCD-HCP variant images"
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# variant: ABCD-HCP
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# - pytest-singularity:
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# name: "Test lite variant in Singularity"
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# requires:
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# - "Build lite variant images"
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# variant: lite

‎CHANGELOG.md‎

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@@ -11,18 +11,23 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- Added FSL-TOPUP as an option for distortion correction.
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- Added changelog
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- Added CHD8 mouse template (`/cpac_templates/chd8_functional_template_noise_mask_ag.nii.gz`)
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- Added commandline flags `--T1w_label` and `--bold_label`
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### Changed
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- Expanded meta-data ingress for EPI field maps to include more fields when parsing BIDS sidecar JSONs.
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- Updated possible inputs for T2w processing and ACPC-alignment blocks to increase the modularity of these pipeline options.
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- `master` branch renamed `main`
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- Packaged templates in https://github.com/FCP-INDI/C-PAC_templates
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### Deprecated
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- `master` branch name (renamed `main`)
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### Fixed
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- Fixed [bug](https://github.com/FCP-INDI/C-PAC/issues/1620) in which the preprocessed T2w data would not be found in the resource pool when expected.
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- Fixed [bug](https://github.com/FCP-INDI/C-PAC/issues/1582) in which distortion correction-related field map ingress would raise `IndexError: list index out of range` when ingressing the field maps.
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- Fixed [bug](https://github.com/FCP-INDI/C-PAC/issues/1572) in which some nodes would raise `KeyError: 'in_file'` when estimating memory allocation
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- Improved memory management for multi-core node allocation.

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