👷 🔧 Configure and run Dependabot

.github/dependabot.yaml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    # Check for updates once a week
+    schedule:
+      interval: "weekly"
+    groups:
+      all-actions:
+        patterns: [ "*" ]

.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 }}

.github/workflows/build_and_test.yml

@@ -58,7 +58,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out C-PAC
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Set tag & see if it exists
@@ -80,17 +80,17 @@ jobs:
           sudo rm -rf "$AGENT_TOOLSDIRECTORY"
       - name: Set up Docker Buildx
         if: contains(fromJSON(env.REBUILD), matrix.Dockerfile) || steps.docker_tag.outputs.not_yet_exists == 1
-        uses: docker/setup-buildx-action@v2.2.1
+        uses: docker/setup-buildx-action@v3.9.0
       - name: Log in to GitHub Container Registry
         if: contains(fromJSON(env.REBUILD), matrix.Dockerfile) || steps.docker_tag.outputs.not_yet_exists == 1
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
       - name: Build and push Docker image
         if: contains(fromJSON(env.REBUILD), matrix.Dockerfile) || steps.docker_tag.outputs.not_yet_exists == 1
-        uses: docker/build-push-action@v4.0.0
+        uses: docker/build-push-action@v6.13.0
         with:
           file: .github/Dockerfiles/${{ matrix.Dockerfile }}.Dockerfile
           push: true
@@ -110,7 +110,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out C-PAC
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Set tag & see if it exists
@@ -140,17 +140,17 @@ jobs:
           sudo rm -rf "$AGENT_TOOLSDIRECTORY"
       - name: Set up Docker Buildx
         if: contains(fromJSON(env.REBUILD), matrix.Dockerfile) || steps.docker_tag.outputs.not_yet_exists == 1
-        uses: docker/setup-buildx-action@v2.2.1
+        uses: docker/setup-buildx-action@v3.9.0
       - name: Log in to GitHub Container Registry
         if: contains(fromJSON(env.REBUILD), matrix.Dockerfile) || steps.docker_tag.outputs.not_yet_exists == 1
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
       - name: Build and push Docker image
         if: contains(fromJSON(env.REBUILD), matrix.Dockerfile) || steps.docker_tag.outputs.not_yet_exists == 1
-        uses: docker/build-push-action@v4.0.0
+        uses: docker/build-push-action@v6.13.0
         with:
           context: .
           file: .github/Dockerfiles/${{ matrix.Dockerfile }}.Dockerfile
@@ -172,14 +172,14 @@ jobs:
         variant: ${{ fromJSON(inputs.phase_three) }}
     steps:
       - name: Maximize build space
-        uses: easimon/maximize-build-space@v6
+        uses: easimon/maximize-build-space@v10
         with:
           remove-dotnet: 'true'
           remove-android: 'true'
           remove-haskell: 'true'
           overprovision-lvm: 'true'
       - name: Check out C-PAC
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Prep source files
@@ -215,17 +215,17 @@ jobs:
           sudo rm -rf "$AGENT_TOOLSDIRECTORY"
       - name: Set up Docker Buildx
         if: contains(fromJSON(env.REBUILD), matrix.variant) || steps.docker_tag.outputs.not_yet_exists == 1
-        uses: docker/setup-buildx-action@v2.2.1
+        uses: docker/setup-buildx-action@v3.9.0
       - name: Log in to GitHub Container Registry
         if: contains(fromJSON(env.REBUILD), matrix.variant) || steps.docker_tag.outputs.not_yet_exists == 1
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
       - name: Build and push base image
         if: contains(fromJSON(env.REBUILD), matrix.variant) || steps.docker_tag.outputs.not_yet_exists == 1
-        uses: docker/build-push-action@v4.0.0
+        uses: docker/build-push-action@v6.13.0
         with:
           context: .
           file: .github/Dockerfiles/base-${{ matrix.variant }}.Dockerfile
@@ -244,14 +244,14 @@ jobs:
       REBUILD: ${{ inputs.rebuild_phase_three }}
     steps:
       - name: Maximize build space
-        uses: easimon/maximize-build-space@v6
+        uses: easimon/maximize-build-space@v10
         with:
           remove-dotnet: 'true'
           remove-android: 'true'
           remove-haskell: 'true'
           overprovision-lvm: 'true'
       - name: Check out C-PAC
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Prep source files
@@ -287,17 +287,17 @@ jobs:
           sudo rm -rf "$AGENT_TOOLSDIRECTORY"
       - name: Set up Docker Buildx
         if: contains(fromJSON(env.REBUILD), 'standard') || steps.docker_tag.outputs.not_yet_exists == 1
-        uses: docker/setup-buildx-action@v2.2.1
+        uses: docker/setup-buildx-action@v3.9.0
       - name: Log in to GitHub Container Registry
         if: contains(fromJSON(env.REBUILD), 'standard') || steps.docker_tag.outputs.not_yet_exists == 1
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
       - name: Build and push base image
         if: contains(fromJSON(env.REBUILD), 'standard') || steps.docker_tag.outputs.not_yet_exists == 1
-        uses: docker/build-push-action@v4.0.0
+        uses: docker/build-push-action@v6.13.0
         with:
           context: .
           file: .github/Dockerfiles/base-standard.Dockerfile
@@ -350,7 +350,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out C-PAC
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 2
       - name: Trigger CircleCI tests

.github/workflows/delete_images.yml

@@ -18,7 +18,7 @@ jobs:
       IMAGE: c-pac
     steps:
       - name: Check out C-PAC
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: 'Delete branch image'
         run: |
           OWNER=$(echo ${GITHUB_REPOSITORY} | cut -d '/' -f 1)
@@ -41,7 +41,7 @@ jobs:
             -X DELETE \
             https://api.github.com/${OWNER_TYPE}/${OWNER}/packages/container/c-pac/versions/${VERSION_ID}
       - name: Delete all containers from repository without tags
-        uses: Chizkiyahu/delete-untagged-ghcr-action@v2
+        uses: Chizkiyahu/delete-untagged-ghcr-action@v6
         with:
           token: ${GITHUB_TOKEN}
           repository_owner: ${{ github.repository_owner }}

.github/workflows/deploy_to_Docker_Hub.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Log in to Docker Hub
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USER }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}

.github/workflows/on_push.yml

@@ -32,11 +32,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out C-PAC
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 2
       - name: Get changed files since last commit
-        uses: tj-actions/changed-files@v41.0.0
+        uses: tj-actions/changed-files@v45.0.7
         id: changed-files
         with:
           since_last_remote_commit: "true"

.github/workflows/regression_test_full.yml

@@ -23,7 +23,7 @@ jobs:
           fi
 
       - name: Checkout Code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Clone reg-suite
         run: |
           git clone https://github.com/amygutierrez/reg-suite.git
@@ -34,7 +34,7 @@ jobs:
           echo "Running full regression test"
           echo "୧(๑•̀ヮ•́)૭ LET'S GO! ٩(^ᗜ^ )و "
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: always()
         with:
           name: logs

.github/workflows/regression_test_lite.yml

@@ -57,15 +57,15 @@ jobs:
           ssh-keyscan -H -t rsa "${{ env.SSH_HOST }}" > ~/.ssh/known_hosts
 
       - name: Initiate check
-        uses: guibranco/[email protected].7
+        uses: guibranco/[email protected].13
         with:
           authToken: ${{ secrets.GITHUB_TOKEN }}
           context: Launch lite regression test
           description: launching
           state: pending
 
       - name: Connect and Run Regression Test Lite
-        uses: appleboy/ssh-action@v1.0.0
+        uses: appleboy/ssh-action@v1.2.0
         with:
           host: ${{ secrets.SSH_HOST }}
           username: ${{ secrets.SSH_USER }}

.github/workflows/smoke_test_participant.yml

@@ -104,7 +104,7 @@ jobs:
             --participant_label ${{ matrix.participant }} \
             --preconfig ${{ matrix.preconfig }} \
             --n_cpus 2
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: ${{ always() }}
         with:
           name: expectedOutputs human ${{ matrix.preconfig }} ${{ matrix.variant }} ${{ matrix.participant }}
@@ -144,14 +144,13 @@ jobs:
           TAG=$TAG$VARIANT
           echo DOCKER_TAG=$(echo "ghcr.io/${{ github.repository }}" | tr '[:upper:]' '[:lower:]'):$TAG >> $GITHUB_ENV
           cat $GITHUB_ENV
+      - name: setup-conda
+        uses: s-weigand/[email protected]
       - name: Set up datalad-OSF
         run: |
           git config --global user.email "[email protected]"
           git config --global user.name "Theodore (Machine User)"
-          wget -O- http://neuro.debian.net/lists/jammy.us-tn.libre | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
-          sudo apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
-          sudo apt-get update
-          sudo apt-get install datalad git-annex-standalone
+          yes | conda install -c conda-forge datalad
           pip install datalad-osf
       - name: Get NHP test data
         run: |
@@ -168,7 +167,7 @@ jobs:
             --preconfig ${{ matrix.preconfig }} \
             --participant_label ${{ matrix.participant }} \
             --n_cpus 2
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: ${{ always() }}
         with:
           name: expectedOutputs nhp ${{ matrix.preconfig }} ${{ matrix.variant }} ${{ matrix.participant }}
@@ -203,14 +202,13 @@ jobs:
           TAG=$TAG$VARIANT
           echo DOCKER_TAG=$(echo "ghcr.io/${{ github.repository }}" | tr '[:upper:]' '[:lower:]'):$TAG >> $GITHUB_ENV
           cat $GITHUB_ENV
+      - name: setup-conda
+        uses: s-weigand/[email protected]
       - name: Set up datalad-OSF
         run: |
           git config --global user.email "[email protected]"
           git config --global user.name "Theodore (Machine User)"
-          wget -O- http://neuro.debian.net/lists/jammy.us-tn.libre | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
-          sudo apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
-          sudo apt-get update
-          sudo apt-get install datalad git-annex-standalone
+          yes | conda install -c conda-forge datalad
           pip install datalad-osf
       - name: Get rodent test data
         run: |
@@ -226,7 +224,7 @@ jobs:
             /test-data /outputs test_config \
             --preconfig rodent \
             --n_cpus 2
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: ${{ always() }}
         with:
           name: expectedOutputs rodent ${{ matrix.variant }}