tests.yml

name: Run unit tests

on: [push, pull_request]

jobs:
  build:
    runs-on: ubuntu-latest
    steps:
    - name: Check out repo
      uses: actions/checkout@v2
    - uses: actions/cache@v2
      with:
        path: ~/.cache/pip
        key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }}
        restore-keys: |
          ${{ runner.os }}-pip-
    - name: Set up Python
      uses: actions/setup-python@v2
      with:
        python-version: 3.8
    - name: Install without INDRA
      run: |
        pip install nose coverage
        pip install .
    - name: Run unit tests
      run: nosetests genewalk/tests -v
    - name: Install with INDRA
      run: |
        pip install .[indra]
    - name: Run unit tests again
      run: nosetests genewalk -v --with-coverage --cover-inclusive --cover-package=genewalk
    - name: Run CLI smoke tests
      run: |
        genewalk --project test_custom_genes --genes genewalk/tests/resources/custom_gene_list.txt --id_type custom --network_source sif_annot --network_file genewalk/tests/resources/test_sif_custom.sif --base_folder ~/genewalk/.test