python-test-conda-external.yml

name: Unit tests external tools

on:
  pull_request:
    branches: [ main, master ]

jobs:
  tests-external:
    strategy:
      matrix:
        platform: [ubuntu-latest]
        python-version: ['3.11', '3.12']
    runs-on: ${{ matrix.platform }}

    steps:
    - uses: actions/checkout@v4
      with:
        path: epytope
    - uses: actions/checkout@v4
      with:
        repository: kohlbacherlab/fred-tools
        token: ${{ secrets.FRED_CI_PAT }}
        path: epytope-tools
    - name: Install epytope-tools system dependencies
      run:
        apt-fast install -y tcsh
    - name: epytope-tools post scripts
      working-directory: ./epytope-tools/
      run: |
        ./post.runner
    - name: Activate epytope-tools
      run: |
        echo "$PWD/epytope-tools/bin" >> $GITHUB_PATH
        echo "PATH=$PATH"
    - name: Set up Miniconda
      uses: conda-incubator/setup-miniconda@v3
      with:
        python-version: ${{ matrix.python-version }}
        activate-environment: test
        auto-activate-base: false
    - name: Install epytope
      shell: bash -el {0}
      run: |
        pip install ./epytope/
    - name: Set up test environment
      shell: bash -el {0}
      run: |
        pip install pytest
    - name: Run Tests - Cleavage Prediction
      working-directory: ./epytope/
      shell: bash -el {0}
      continue-on-error: true
      run: pytest -v epytope/test/external/TestExternalCleavagePrediction.py || echo "Cleavage Prediction" >> FAILED_TESTS
    - name: Run Tests - Epitope Prediction
      working-directory: ./epytope/
      shell: bash -el {0}
      run: pytest -v epytope/test/external/TestExternalEpitopePrediction.py || echo "Epitope Prediction" >> FAILED_TESTS
    - name: Validate Test Results
      working-directory: ./epytope/
      run: |
        if [ -e FAILED_TESTS ]; then
          echo "FAILED TESTS:" >&2
          cat FAILED_TESTS
          exit 1
        fi