python-test-conda-external.yml

name: Unit tests external tools

on:
  push:
    branches: [ main, develop ]
  pull_request:
    branches: [ main, develop ]

jobs:
  tests-external:
    strategy:
      matrix:
        platform: [ubuntu-latest]
        python-version: [3.7]
    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: Set conda package directory
      run: |
        mkdir /tmp/condapkgs
        echo "CONDA_PKGS_DIRS=/tmp/condapkgs" >> $GITHUB_ENV
    - name: Activate epytope-tools
      run: |
        echo "$PWD/epytope-tools/bin" >> $GITHUB_PATH
        echo "PATH=$PATH"
    - name: Set up Python ${{ matrix.python-version }}
      run: |
        $CONDA/bin/conda create -p /tmp/condaenv python==${{ matrix.python-version }}'.*' setuptools"==52.0" protobuf"<=3.20.1"
    - name: Activate conda environment
      run: |
        echo "/tmp/condaenv/bin" >> $GITHUB_PATH
        export PATH="/tmp/condaenv/bin:$PATH"
    - name: Install epytope
      run: |
        pip install ./epytope/
    - name: Set up test environment
      run: |
        conda install -p /tmp/condaenv -c conda-forge -c bioconda nose
    - name: Run Tests - Cleavage Prediction
      working-directory: ./epytope/
      continue-on-error: true
      run: nosetests -v epytope/test/external/TestExternalCleavagePrediction.py || echo "Cleavage Prediction" >> FAILED_TESTS
    - name: Run Tests - Epitope Prediction
      working-directory: ./epytope/
      run: nosetests -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