alphatesting.yml

name: AlphaX cross-projects tests

on:
  workflow_dispatch:
    inputs:
      alphabase_ref:
        description: "alphabase version: version of alphabase to use. Can be a commit hash, branch name or 'latest' for the latest release."
        default: latest
      alphatims_ref:
        description: "alphatims version"
        default: latest
      alpharaw_ref:
        description: "alpharaw version"
        default: development  # TODO: change to latest once properly tagged release is out
      alphaviz_ref:
        description: "alphaviz version"
        default: latest
      alphapeptdeep_ref:
        description: "alphapeptdeep version"
        default: latest
      directlfq_ref:
        description: "alphatims version"
        default: latest
      alphadia_ref:
        description: "alphadia version"
        default: latest

jobs:
  build_image:
    runs-on: AlphaDIA

    steps:
    - name: Print input parameters
      run: echo "${{ toJSON(github.event.inputs) }}"

    - name: Checkout repository
      uses: actions/checkout@v4

    - name: Set up Docker Buildx
      uses: docker/setup-buildx-action@v3

#    # avoid "no space left on device" error
#    # https://github.com/actions/runner-images/issues/2840#issuecomment-790492173
#    - name: cleanup
#      run: |
#        sudo rm -rf /usr/share/dotnet
#        sudo rm -rf /opt/ghc
#        sudo rm -rf "/usr/local/share/boost"
#        sudo rm -rf "$AGENT_TOOLSDIRECTORY"

    - name: Build and export
      uses: docker/build-push-action@v6
      with:
        tags: alphax:latest
        context: ./alphatesting
        outputs: type=docker,dest=/tmp/alphax.tar
#        cache-from: type=gha
#        cache-to: type=gha,mode=max
        no-cache: True
        build-args: |
          ALPHABASE_REF=${{ inputs.alphabase_ref }}
          ALPHATIMS_REF=${{ inputs.alphatims_ref }}
          ALPHARAW_REF=${{ inputs.alpharaw_ref }}
          ALPHAVIZ_REF=${{ inputs.alphaviz_ref }}
          ALPHAPEPTDEEP_REF=${{ inputs.alphapeptdeep_ref }}
          DIRECTLFQ_REF=${{ inputs.directlfq_ref }}
          ALPHADIA_REF=${{ inputs.alphadia_ref }}
    - name: Upload artifact
      uses: actions/upload-artifact@v4
      with:
        name: alphax
        path: /tmp/alphax.tar


  alphabase_tests:
    runs-on: AlphaDIA
    needs: [ build_image ]
    steps:
    - name: Download artifact
      uses: actions/download-artifact@v4
      with:
        name: alphax
        path: /tmp
    - name: Load image
      run: |
        docker load --input /tmp/alphax.tar
        docker image ls -a
    - name: Print pip freeze
      run: |
        docker run alphax bash -c "pip freeze"
    - name: alphabase tests
      id: alphabase_tests
      run: |
        docker run alphax bash -c "cd alphabase/tests && chmod +x run_tests.sh && ./run_tests.sh"

  alpharaw_tests:
    runs-on: AlphaDIA
    needs: [ build_image ]
    steps:
    - name: Download artifact
      uses: actions/download-artifact@v4
      with:
        name: alphax
        path: /tmp
    - name: Load image
      run: |
        docker load --input /tmp/alphax.tar
        docker image ls -a
    - name: Print pip freeze
      run: |
        docker run alphax bash -c "pip freeze"
    - name: alpharaw tests
      id: alpharaw_tests
      run: |
        docker run alphax bash -c "cd alpharaw/tests && ls && python -m download_test_data && chmod +x run_tests.sh && ./run_tests.sh"

  alphaviz_tests:
    runs-on: AlphaDIA
    needs: [ build_image ]
    steps:
    - name: Download artifact
      uses: actions/download-artifact@v4
      with:
        name: alphax
        path: /tmp
    - name: Load image
      run: |
        docker load --input /tmp/alphax.tar
        docker image ls -a
    - name: Print pip freeze
      run: |
        docker run alphax bash -c "pip freeze"
    - name: alphaviz tests
      id: alphaviz_tests
      run: |
        docker run alphax bash -c "cd alphaviz/tests && ls && python -m pytest test_io.py && python -m pytest test_preprocessing.py"


  alphapeptdeep_tests:
    runs-on: AlphaDIA
    needs: [ build_image ]
    steps:
    - name: Download artifact
      uses: actions/download-artifact@v4
      with:
        name: alphax
        path: /tmp
    - name: Load image
      run: |
        docker load --input /tmp/alphax.tar
        docker image ls -a
    - name: Print pip freeze
      run: |
        docker run alphax bash -c "pip freeze"
    - name: alphapeptdeep tests
      id: alphapeptdeep_tests
      run: |
        docker run alphax bash -c "cd alphapeptdeep/tests && chmod +x run_tests.sh && ./run_tests.sh"

  alphadia_tests:
    runs-on: AlphaDIA
    needs: [ build_image ]
    steps:
    - name: Download artifact
      uses: actions/download-artifact@v4
      with:
        name: alphax
        path: /tmp
    - name: Load image
      run: |
        docker load --input /tmp/alphax.tar
        docker image ls -a
    - name: Print pip freeze
      run: |
        docker run alphax bash -c "pip freeze"
    - name: alphadia unit tests ('not slow')
      id: alphadia_unit_tests
      run: |
        docker run alphax bash -c "cd alphadia/tests &&  python -m pytest -k 'not slow'"
    - name: alphadia unit tests ('slow')
      id: alphadia_slow_unit_tests
      run: |
        docker run alphax bash -c "cd alphadia/tests &&  python -m pytest -k 'slow'"
    - name: alphadia e2e test 'basic'
      id: alphadia_e2e_tests
      run: |
        TEST_CASE_NAME=basic
        docker run alphax bash -c "cd alphadia/tests/e2e_tests \
          &&  python prepare_test_data.py $TEST_CASE_NAME \
          &&  alphadia --config $TEST_CASE_NAME/config.yaml"