ci: refactor github actions for deprications

biorack · Sep 25, 2023 · 1cc4a17 · 1cc4a17
1 parent be8c235
commit 1cc4a17
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Showing 2 changed files with 18 additions and 18 deletions.
diff --git a/.github/workflows/cd.yaml b/.github/workflows/cd.yaml
@@ -9,12 +9,12 @@ jobs:
   build_push_metatlas_shifter_image:
     name: Build/push doejgi/metatlas_shifter docker image
     if: github.repository == 'biorack/metatlas' && (github.event.pull_request.merged || github.event_name == 'workflow_dispatch')
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
     - name: Checkout source
       uses: actions/checkout@v4
     - name: Login to DockerHub
-      uses: docker/login-action@v1
+      uses: docker/login-action@v3
       with:
         username: wjhjgi
         password: ${{ secrets.DOCKERHUB_TOKEN }}
@@ -24,10 +24,10 @@ jobs:
       id: timestamp
       run: |
         DATE_TIME=$(date -u +"%Y%m%d_%H%M%S")
-        echo "::set-output name=date_time::${DATE_TIME}"
+        echo "date_time=${DATE_TIME}" >> $GITHUB_OUTPUT
     - name: Build Docker images # This is for the targeted metatlas pipeline
       id: build
-      uses: docker/build-push-action@v2.7.0
+      uses: docker/build-push-action@v5
       with:
         context: ./docker
         file: ./docker/Dockerfile.shifter
@@ -43,24 +43,24 @@ jobs:
   build_push_metatlas_analysis_image:
     name: Build/push analysis docker image
     if: github.repository == 'biorack/metatlas' && (github.event.pull_request.merged || github.event_name == 'workflow_dispatch')
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
     - name: Checkout source
       uses: actions/checkout@v4
     - name: generate time based tag
       id: timestamp
       run: |
         DATE_TIME=$(date -u +"%Y%m%d_%H%M%S")
-        echo "::set-output name=date_time::${DATE_TIME}"
+        echo "date_time=${DATE_TIME}" >> $GITHUB_OUTPUT
     - name: Login to GHCR
-      uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
+      uses: docker/login-action@v3
       with:
         registry: ghcr.io
         username: ${{ github.repository_owner }}
         password: ${{ secrets.GITHUB_TOKEN }}
     - name: Build Docker images # This is for the boutique analysis tasks
       id: build_analysis
-      uses: docker/build-push-action@v2.7.0
+      uses: docker/build-push-action@v5
       with:
         context: ./docker
         file: ./docker/Dockerfile.analysis
@@ -74,24 +74,24 @@ jobs:
   build_push_metatlas_mzmine_image:
     name: Build/push mzmine docker image
     if: github.repository == 'biorack/metatlas' && (github.event.pull_request.merged || github.event_name == 'workflow_dispatch')
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
     - name: Checkout source
       uses: actions/checkout@v4
     - name: generate time based tag
       id: timestamp
       run: |
         DATE_TIME=$(date -u +"%Y%m%d_%H%M%S")
-        echo "::set-output name=date_time::${DATE_TIME}"
+        echo "date_time=${DATE_TIME}" >> $GITHUB_OUTPUT
     - name: Login to GHCR
-      uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
+      uses: docker/login-action@v3
       with:
         registry: ghcr.io
         username: ${{ github.repository_owner }}
         password: ${{ secrets.GITHUB_TOKEN }}
     - name: Build Docker images # This is for the mzmine container
       id: build_mzmine
-      uses: docker/build-push-action@v2.7.0
+      uses: docker/build-push-action@v5
       with:
         context: ./docker
         file: ./docker/Dockerfile.mzmine

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -6,7 +6,7 @@ on:
 jobs:
   unit_tests:
     name: Run unit tests suite
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
     - name: Checkout source
       uses: actions/checkout@v4
@@ -21,7 +21,7 @@ jobs:
       run: nox -s unit_tests-3.8
   system_test1:
     name: Run system test 1 - HILIC targeted
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
     - name: Checkout source
       uses: actions/checkout@v4
@@ -31,7 +31,7 @@ jobs:
       run: nox -s system_tests-3.8 -- -k test_targeted
   system_test2:
     name: Run system test 2 - RT alignment
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
     - name: Checkout source
       uses: actions/checkout@v4
@@ -41,7 +41,7 @@ jobs:
       run: nox -s system_tests-3.8 -- -k test_rt_alignment
   system_test3:
     name: Run system test 3 - add MSMS references
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
     - name: Checkout source
       uses: actions/checkout@v4
@@ -51,7 +51,7 @@ jobs:
       run: nox -s system_tests-3.8 -- -k test_add_msms_ref
   system_test4:
     name: Run system test 4 - C18 targeted
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
     - name: Checkout source
       uses: actions/checkout@v4
@@ -61,7 +61,7 @@ jobs:
       run: nox -s system_tests-3.8 -- -k test_c18
   system_test5:
     name: Run system test 5 - HILIC Targeted_hybrid
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     continue-on-error: true
     steps:
     - name: Checkout source