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Merge branch 'develop' into coregistration_prep_vol
2 parents c38a1fd + 25d1bbd commit 233e932

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‎.github/dependabot.yaml‎

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

‎.github/workflows/build_C-PAC.yml‎

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

‎.github/workflows/build_and_test.yml‎

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runs-on: ubuntu-latest
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steps:
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- name: Check out C-PAC
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Set tag & see if it exists
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sudo rm -rf "$AGENT_TOOLSDIRECTORY"
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- name: Set up Docker Buildx
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if: contains(fromJSON(env.REBUILD), matrix.Dockerfile) || steps.docker_tag.outputs.not_yet_exists == 1
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uses: docker/setup-buildx-action@v2.2.1
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uses: docker/setup-buildx-action@v3.9.0
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- name: Log in to GitHub Container Registry
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if: contains(fromJSON(env.REBUILD), matrix.Dockerfile) || steps.docker_tag.outputs.not_yet_exists == 1
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uses: docker/login-action@v2
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uses: docker/login-action@v3
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with:
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registry: ghcr.io
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Build and push Docker image
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if: contains(fromJSON(env.REBUILD), matrix.Dockerfile) || steps.docker_tag.outputs.not_yet_exists == 1
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uses: docker/build-push-action@v4.0.0
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uses: docker/build-push-action@v6.13.0
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with:
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file: .github/Dockerfiles/${{ matrix.Dockerfile }}.Dockerfile
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push: true
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runs-on: ubuntu-latest
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steps:
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- name: Check out C-PAC
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Set tag & see if it exists
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sudo rm -rf "$AGENT_TOOLSDIRECTORY"
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- name: Set up Docker Buildx
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if: contains(fromJSON(env.REBUILD), matrix.Dockerfile) || steps.docker_tag.outputs.not_yet_exists == 1
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uses: docker/setup-buildx-action@v2.2.1
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uses: docker/setup-buildx-action@v3.9.0
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- name: Log in to GitHub Container Registry
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if: contains(fromJSON(env.REBUILD), matrix.Dockerfile) || steps.docker_tag.outputs.not_yet_exists == 1
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uses: docker/login-action@v2
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uses: docker/login-action@v3
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with:
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registry: ghcr.io
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Build and push Docker image
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if: contains(fromJSON(env.REBUILD), matrix.Dockerfile) || steps.docker_tag.outputs.not_yet_exists == 1
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uses: docker/build-push-action@v4.0.0
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uses: docker/build-push-action@v6.13.0
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with:
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context: .
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file: .github/Dockerfiles/${{ matrix.Dockerfile }}.Dockerfile
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variant: ${{ fromJSON(inputs.phase_three) }}
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steps:
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- name: Maximize build space
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uses: easimon/maximize-build-space@v6
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uses: easimon/maximize-build-space@v10
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with:
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remove-dotnet: 'true'
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remove-android: 'true'
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remove-haskell: 'true'
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overprovision-lvm: 'true'
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- name: Check out C-PAC
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Prep source files
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sudo rm -rf "$AGENT_TOOLSDIRECTORY"
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- name: Set up Docker Buildx
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if: contains(fromJSON(env.REBUILD), matrix.variant) || steps.docker_tag.outputs.not_yet_exists == 1
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uses: docker/setup-buildx-action@v2.2.1
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uses: docker/setup-buildx-action@v3.9.0
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- name: Log in to GitHub Container Registry
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if: contains(fromJSON(env.REBUILD), matrix.variant) || steps.docker_tag.outputs.not_yet_exists == 1
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uses: docker/login-action@v2
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uses: docker/login-action@v3
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with:
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registry: ghcr.io
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Build and push base image
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if: contains(fromJSON(env.REBUILD), matrix.variant) || steps.docker_tag.outputs.not_yet_exists == 1
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uses: docker/build-push-action@v4.0.0
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uses: docker/build-push-action@v6.13.0
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with:
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context: .
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file: .github/Dockerfiles/base-${{ matrix.variant }}.Dockerfile
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REBUILD: ${{ inputs.rebuild_phase_three }}
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steps:
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- name: Maximize build space
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uses: easimon/maximize-build-space@v6
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uses: easimon/maximize-build-space@v10
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with:
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remove-dotnet: 'true'
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remove-android: 'true'
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remove-haskell: 'true'
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overprovision-lvm: 'true'
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- name: Check out C-PAC
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Prep source files
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sudo rm -rf "$AGENT_TOOLSDIRECTORY"
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- name: Set up Docker Buildx
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if: contains(fromJSON(env.REBUILD), 'standard') || steps.docker_tag.outputs.not_yet_exists == 1
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uses: docker/setup-buildx-action@v2.2.1
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uses: docker/setup-buildx-action@v3.9.0
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- name: Log in to GitHub Container Registry
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if: contains(fromJSON(env.REBUILD), 'standard') || steps.docker_tag.outputs.not_yet_exists == 1
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uses: docker/login-action@v2
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uses: docker/login-action@v3
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with:
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registry: ghcr.io
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Build and push base image
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if: contains(fromJSON(env.REBUILD), 'standard') || steps.docker_tag.outputs.not_yet_exists == 1
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uses: docker/build-push-action@v4.0.0
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uses: docker/build-push-action@v6.13.0
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with:
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context: .
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file: .github/Dockerfiles/base-standard.Dockerfile
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runs-on: ubuntu-latest
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steps:
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- name: Check out C-PAC
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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with:
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fetch-depth: 2
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- name: Trigger CircleCI tests

‎.github/workflows/delete_images.yml‎

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IMAGE: c-pac
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steps:
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- name: Check out C-PAC
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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- name: 'Delete branch image'
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run: |
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OWNER=$(echo ${GITHUB_REPOSITORY} | cut -d '/' -f 1)
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-X DELETE \
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https://api.github.com/${OWNER_TYPE}/${OWNER}/packages/container/c-pac/versions/${VERSION_ID}
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- name: Delete all containers from repository without tags
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uses: Chizkiyahu/delete-untagged-ghcr-action@v2
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uses: Chizkiyahu/delete-untagged-ghcr-action@v6
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with:
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token: ${GITHUB_TOKEN}
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repository_owner: ${{ github.repository_owner }}

‎.github/workflows/deploy_to_Docker_Hub.yml‎

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runs-on: ubuntu-latest
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steps:
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- name: Log in to Docker Hub
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uses: docker/login-action@v2
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uses: docker/login-action@v3
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with:
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username: ${{ secrets.DOCKERHUB_USER }}
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password: ${{ secrets.DOCKERHUB_TOKEN }}

‎.github/workflows/on_push.yml‎

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runs-on: ubuntu-latest
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steps:
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- name: Check out C-PAC
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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with:
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fetch-depth: 2
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- name: Get changed files since last commit
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uses: tj-actions/changed-files@v41.0.0
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uses: tj-actions/changed-files@v45.0.7
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id: changed-files
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with:
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since_last_remote_commit: "true"

‎.github/workflows/regression_test_full.yml‎

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fi
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- name: Checkout Code
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uses: actions/checkout@v4
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- name: Clone reg-suite
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run: |
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git clone https://github.com/amygutierrez/reg-suite.git
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echo "Running full regression test"
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echo "୧(๑•̀ヮ•́)૭ LET'S GO! ٩(^ᗜ^ )و "
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- uses: actions/upload-artifact@v3
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- uses: actions/upload-artifact@v4
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if: always()
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with:
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name: logs

‎.github/workflows/regression_test_lite.yml‎

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ssh-keyscan -H -t rsa "${{ env.SSH_HOST }}" > ~/.ssh/known_hosts
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- name: Initiate check
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uses: guibranco/[email protected].7
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uses: guibranco/[email protected].13
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authToken: ${{ secrets.GITHUB_TOKEN }}
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context: Launch lite regression test
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description: launching
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state: pending
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- name: Connect and Run Regression Test Lite
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uses: appleboy/ssh-action@v1.0.0
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uses: appleboy/ssh-action@v1.2.0
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with:
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host: ${{ secrets.SSH_HOST }}
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username: ${{ secrets.SSH_USER }}

‎.github/workflows/smoke_test_participant.yml‎

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--participant_label ${{ matrix.participant }} \
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--preconfig ${{ matrix.preconfig }} \
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--n_cpus 2
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- uses: actions/upload-artifact@v3
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- uses: actions/upload-artifact@v4
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if: ${{ always() }}
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with:
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name: expectedOutputs human ${{ matrix.preconfig }} ${{ matrix.variant }} ${{ matrix.participant }}
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TAG=$TAG$VARIANT
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echo DOCKER_TAG=$(echo "ghcr.io/${{ github.repository }}" | tr '[:upper:]' '[:lower:]'):$TAG >> $GITHUB_ENV
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cat $GITHUB_ENV
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- name: setup-conda
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uses: conda-incubator/[email protected]
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- name: Set up datalad-OSF
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run: |
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sudo apt-get update && sudo apt-get install -y git-annex
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git config --global user.email "[email protected]"
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git config --global user.name "Theodore (Machine User)"
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wget -O- http://neuro.debian.net/lists/jammy.us-tn.libre | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
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sudo apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
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sudo apt-get update
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sudo apt-get install datalad git-annex-standalone
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yes | conda install -c conda-forge datalad
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pip install datalad-osf
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- name: Get NHP test data
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run: |
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--preconfig ${{ matrix.preconfig }} \
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--participant_label ${{ matrix.participant }} \
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--n_cpus 2
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- uses: actions/upload-artifact@v3
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- uses: actions/upload-artifact@v4
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if: ${{ always() }}
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with:
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name: expectedOutputs nhp ${{ matrix.preconfig }} ${{ matrix.variant }} ${{ matrix.participant }}
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TAG=$TAG$VARIANT
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echo DOCKER_TAG=$(echo "ghcr.io/${{ github.repository }}" | tr '[:upper:]' '[:lower:]'):$TAG >> $GITHUB_ENV
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cat $GITHUB_ENV
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- name: setup-conda
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uses: conda-incubator/[email protected]
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with:
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activate-environment: datalad-osf
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channels: conda-forge
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conda-remove-defaults: "true"
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python-version: 3.12
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- name: Set up datalad-OSF
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run: |
215+
sudo apt-get update && sudo apt-get install -y git-annex
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git config --global user.email "[email protected]"
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git config --global user.name "Theodore (Machine User)"
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wget -O- http://neuro.debian.net/lists/jammy.us-tn.libre | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
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sudo apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
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sudo apt-get update
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sudo apt-get install datalad git-annex-standalone
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yes | conda install -c conda-forge datalad
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pip install datalad-osf
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- name: Get rodent test data
216221
run: |
222+
export GIT_TRACE=1
223+
export DATALAD_LOG_LEVEL=DEBUG
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datalad clone osf://uya3r test-data
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- name: Run rodent smoke test
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run: |
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/test-data /outputs test_config \
227234
--preconfig rodent \
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--n_cpus 2
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- uses: actions/upload-artifact@v3
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- uses: actions/upload-artifact@v4
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if: ${{ always() }}
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with:
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name: expectedOutputs rodent ${{ matrix.variant }}

‎CHANGELOG.md‎

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@@ -33,6 +33,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- Automatically tag untagged `subject_id` and `unique_id` as `!!str` when loading data config files.
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- Made orientation configurable (was hard-coded as "RPI").
3535
- Input `desc-brain_bold` to `desc-preproc_bold` for `sbref` generation nodeblock `coregistration_prep_vol`.
36+
- Moved `ref_mask_res_2` and `T1w_template_res-2` fields from registration into surface under `abcd_prefreesurfer_prep`.
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### Fixed
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@@ -47,6 +48,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
4748
- `ABCD-HCP`
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- `fMRIPrep-LTS`
4950
- Typehinting support for Python < 3.10.
51+
- Extra outputs listed in `freesurfer_abcd_preproc`.
52+
- Resource `space-template_desc-T1w_mask`
53+
- as output from FNIRT registration.
54+
- as inputs from Nodeblocks requesting it and, replaced with `space-template_desc-brain_mask`.
55+
- from outputs tsv.
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## [1.8.7] - 2024-05-03
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