unit.yml

name: unit test
on: [push, pull_request]

defaults:
  run:
    # This is needed for miniconda, see:
    # https://github.com/marketplace/actions/setup-miniconda#important.
    shell: bash -l {0}

jobs:
  miniwdl_check:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - name: Set up Python
      uses: actions/setup-python@v5
      with:
        python-version: 3.9
    - name: Install miniwdl
      run: |
        python -m pip install --upgrade pip
        pip3 install miniwdl
        pip3 install pytest-workflow
        mkdir ~/temp
    - name: Run unit tests
      # Use --symlink to limit disk usage.
      run: >- 
        pytest --keep-workflow-wd --git-aware
        --symlink tests/ --basetemp ~/temp
    - name: Check files 
      run: ls -ltr ~/temp/*
    - name: Check miniwdl log in case of failure.
      if: ${{ failure() }}
      # Get the last 1000 lines of the miniwdl log to catch the error.
      run: bash -c 'tail -n 1000 ~/temp/pytest_workflow_*/*/log.out'
    - name: Check job stderr messages in case of failure
      if: ${{ failure() }}
      run: >- 
        bash -c '
        for file in $(find ~/temp -name stderr); 
        do echo $file; cat $file; done'
    - name: Check job stdout messages in case of failure
      if: ${{ failure() }}
      run: >- 
        bash -c '
        for file in $(find ~/temp -name stdout); 
        do echo $file; cat $file; done'