viash/.github/workflows/sbt_test.yml at 5ae6c745b3352637e1fa9bd6001ea35bde99297b · viash-io/viash · GitHub

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name: Scala CI

on:
  pull_request:
  push:
    branches:
      - main
      - 'develop_**'

jobs:
  scala-ci:
    runs-on: ${{ matrix.config.os }}
    if: "!contains(github.event.head_commit.message, 'ci skip')"

    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 }

    steps:
    - uses: actions/checkout@v6

    - 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 (via Coursier)
      uses: coursier/setup-action@v2
      with:
        apps: sbt scala

    - name: Set up .NET SDK
      if: ${{ runner.os == 'Linux' }}
      uses: actions/setup-dotnet@v4
      with:
        dotnet-version: '9.0.x'

    - name: Set up dotnet-script
      if: ${{ runner.os == 'Linux' }}
      run: dotnet tool install -g dotnet-script

    - 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
      run: bash <(curl -s https://codecov.io/bash)

    - name: Upload check results on fail
      if: failure()
      uses: actions/upload-artifact@v6
      with:
        name: ${{ matrix.config.name }}_results
        path: check