runTest.yml

name: runTest
on: [push]
jobs:
  test-python-app:
    runs-on: ubuntu-20.04
    defaults:
      run:
        shell: bash -el {0}
    steps:
    - uses: actions/checkout@v4

    - name: Python Linter
      uses: chartboost/ruff-action@v1
      with:
        src: "src"
        # args: --select ALL 
    - uses: conda-incubator/setup-miniconda@v3
      with:
        miniconda-version: "latest"
        activate-environment: yacht_env
        environment-file: env/yacht_env.yml

    - name: install YACHT locally
      run: pip install .

    - name: List contents of 'yacht' in site-packages
      run: |
        SITE_PACKAGES=$(python -c "import site; print(site.getsitepackages()[0])")
        ls -R $SITE_PACKAGES/yacht

    - name: make training data
      run: yacht train --ref_file './tests/testdata/20_genomes_sketches.zip' --ksize 31 --prefix 'gtdb_ani_thresh_0.95' --ani_thresh 0.95 --outdir ./ --force

    - name: run YACHT
      run: yacht run --json ./gtdb_ani_thresh_0.95_config.json --sample_file './tests/testdata/sample.sig.zip' --significance 0.99 --min_coverage_list 1 0.6 0.2 0.1
    
    - name: unit-tests
      run: pytest tests/ --cov-report term-missing --cov-report xml:tests.xml --cov=yacht
    
    - name: Upload coverage reports to Codecov
      uses: codecov/codecov-action@v4
      with:
        files: ./tests.xml
      env:
        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}