Develop

.github/workflows/ns_test.yml

@@ -7,10 +7,10 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
     - name: Set up java
-      uses: actions/setup-java@v4
+      uses: actions/setup-java@v5
       with:
         distribution: temurin
         java-version: '11'

.github/workflows/prep_release.yml

@@ -12,10 +12,10 @@ jobs:
 
     steps:
     - name: Checkout code
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
 
     - name: Set up JDK 17
-      uses: actions/setup-java@v4
+      uses: actions/setup-java@v5
       with:
         java-version: '17'
         distribution: 'temurin'
@@ -39,11 +39,13 @@ jobs:
       id: get_version
       run: |
         viash_version=$(bin/viash --version | cut -d ' ' -f 2)
+        viash_minor_version=$(echo $viash_version | cut -d. -f1,2)
         echo "Detected Viash version: $viash_version"
+        echo "Detected Viash minor version: $viash_minor_version"
         echo "viash_version=$viash_version" >> "$GITHUB_OUTPUT"
 
         # fetch relevant changelog section
-        changelog_section=$(awk "/# Viash ${viash_version}.*/{flag=1;next}/^# /{flag=0}flag" CHANGELOG.md)
+        changelog_section=$(awk "/# Viash ${viash_version}.*/{flag=1;print;next}/^# /{flag=0}flag" CHANGELOGS/CHANGELOG_${viash_minor_version}.md)
 
         echo "changelog_section<<GITHUB_EOF" >> "$GITHUB_OUTPUT"
         echo "$changelog_section" >> "$GITHUB_OUTPUT"

.github/workflows/sbt_test.yml

@@ -19,7 +19,7 @@ jobs:
           - { ver: '21', run_nextflow: true, run_coverage: false, nxf_ver: latest-edge }
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
     - uses: viash-io/viash-actions/project/update-docker-engine@v6
       if: runner.os == 'Linux'
@@ -37,7 +37,7 @@ jobs:
           testthat
 
     - name: Set up java
-      uses: actions/setup-java@v4
+      uses: actions/setup-java@v5
       with:
         distribution: temurin
         java-version: ${{ matrix.java.ver }}
@@ -55,7 +55,7 @@ jobs:
         fi
 
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.x'
 

.github/workflows/weekly_branch_tests.yml

@@ -0,0 +1,111 @@
+name: Weekly Branch Tests
+
+on:
+  schedule:
+    # Run every Sunday at 02:30 UTC (30 minutes after download test)
+    - cron: '30 2 * * 0'
+  workflow_dispatch: # Allow manual triggering
+
+jobs:
+  weekly-test:
+    runs-on: ${{ matrix.config.os }}
+    if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/develop'
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { name: 'ubuntu_latest', os: ubuntu-latest }
+          - { name: 'macos_latest', os: macos-latest }
+        java:
+          - { ver: '11', run_nextflow: true, run_coverage: false, nxf_ver: "22.04.5" }
+          - { ver: '17', run_nextflow: true, run_coverage: true, nxf_ver: latest }
+          - { ver: '21', run_nextflow: true, run_coverage: false, nxf_ver: latest-edge }
+        branch:
+          - main
+          - develop_0_9
+
+    steps:
+    - name: Checkout ${{ matrix.branch }} branch
+      uses: actions/checkout@v5
+      with:
+        ref: ${{ matrix.branch }}
+
+    - uses: viash-io/viash-actions/project/update-docker-engine@v6
+      if: runner.os == 'Linux'
+
+    - name: Set up R
+      uses: r-lib/actions/setup-r@v2
+      with:
+        use-public-rspm: true
+
+    - name: Set up R dependencies
+      uses: r-lib/actions/setup-r-dependencies@v2
+      with:
+        packages: |
+          processx
+          testthat
+
+    - name: Set up java
+      uses: actions/setup-java@v5
+      with:
+        distribution: temurin
+        java-version: ${{ matrix.java.ver }}
+
+    - name: Set up sbt
+      uses: sbt/setup-sbt@v1
+
+    - name: Set up Scala
+      run: |
+        if [[ "${{ matrix.config.os }}" =~ ^macos.*$ ]]; then
+          brew install scala
+        else
+          sudo apt-get update
+          sudo apt-get install -y scala
+        fi
+
+    - name: Set up Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: '3.x'
+
+    - name: Set up Nextflow
+      if: ${{ runner.os == 'Linux' && matrix.java.run_nextflow }}
+      uses: nf-core/setup-nextflow@v2
+      with:
+        version: ${{ matrix.java.nxf_ver }}
+
+    - name: Run tests
+      run: |
+        if [[ "${{ matrix.config.name }}" =~ ^ubuntu.*$ ]] && [[ "${{ matrix.java.run_coverage }}" == "true" ]]; then
+          # only run coverage on main runner
+          sbt clean coverage test coverageReport
+        elif [[ "${{ matrix.config.name }}" =~ ^ubuntu.*$ ]] && [[ "${{ matrix.java.run_nextflow }}" == "false" ]]; then
+          sbt 'testOnly -- -l io.viash.NextflowTest'
+        elif [[ "${{ matrix.config.os }}" =~ ^macos.*$ ]]; then
+          # macOS on github actions does not have Docker, so skip those
+          sbt 'testOnly -- -l io.viash.DockerTest -l io.viash.NextflowTest'
+        else
+          sbt test
+        fi
+
+    - name: Upload coverage on success
+      if: ${{ matrix.java.run_coverage }}
+      run: bash <(curl -s https://codecov.io/bash)
+
+    - name: Upload check results on fail
+      if: failure()
+      uses: actions/upload-artifact@master
+      with:
+        name: ${{ matrix.config.name }}_${{ matrix.branch }}_${{ matrix.java.ver }}_results
+        path: check
+
+    - name: Notify on failure
+      if: failure()
+      run: |
+        curl -X POST \
+          -H 'Content-Type: application/json' \
+          -d '{
+            "text": "🚨 *Weekly Tests Failed*\n\n• **Branch**: ${{ matrix.branch }}\n• **OS**: ${{ matrix.config.name }}\n• **Java**: ${{ matrix.java.ver }}\n• **Repository**: ${{ github.repository }}\n• **Run**: <${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}|View Logs>"
+          }' \
+          "${{ secrets.GOOGLE_CHAT_WEBHOOK_URL }}"

.github/workflows/weekly_download_test.yml

@@ -0,0 +1,52 @@
+name: Weekly Download Test
+
+on:
+  schedule:
+    # Run every Sunday at 02:00 UTC
+    - cron: '0 2 * * 0'
+  workflow_dispatch: # Allow manual triggering
+
+jobs:
+  download-install-test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+
+    steps:
+    - name: Test viash download and installation
+      run: |
+        echo "Testing viash download from https://dl.viash.io"
+
+        # Download viash
+        if [[ "${{ matrix.os }}" =~ ^ubuntu.*$ ]]; then
+          curl -fsSL https://dl.viash.io | bash
+        elif [[ "${{ matrix.os }}" =~ ^macos.*$ ]]; then
+          curl -fsSL https://dl.viash.io | bash
+        fi
+
+        # Verify installation
+        if command -v viash &> /dev/null; then
+          echo "✅ viash command is available"
+          viash --version
+          echo "✅ viash version check successful"
+        else
+          echo "❌ viash command not found after installation"
+          exit 1
+        fi
+
+        # Test basic functionality
+        echo "Testing basic viash functionality..."
+        viash --help > /dev/null
+        echo "✅ viash help command works"
+
+    - name: Notify download test failure
+      if: failure()
+      run: |
+        curl -X POST \
+          -H 'Content-Type: application/json' \
+          -d '{
+            "text": "🚨 *Viash Download Test Failed*\n\n• **OS**: ${{ matrix.os }}\n• **Issue**: Failed to download/install viash from https://dl.viash.io\n• **Repository**: ${{ github.repository }}\n• **Run**: <${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}|View Logs>"
+          }' \
+          "${{ secrets.GOOGLE_CHAT_WEBHOOK_URL }}"