test.yml

name: Test Kingfisher with Setup-Miniconda From Marketplace
on: [push, pull_request]

jobs:
  miniconda:
    name: Miniconda ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    defaults:
      run:
        shell: bash -l {0}
    strategy:
        matrix:
            os: ["ubuntu-latest"]
    steps:
      - uses: actions/checkout@v2
      - uses: conda-incubator/setup-miniconda@v2
        with:
          activate-environment: test
          environment-file: kingfisher.yml
          python-version: 3.9
          auto-activate-base: false
          mamba-version: "*"
          channels: conda-forge,defaults,bioconda,masonite
      - run: |
          conda info
          conda list
      - name: Run tests
        env:
          NCBI_API_KEY: ${{ secrets.NCBI_API_KEY }}
        run: |
            # ascp does not work in bare conda env, so don't run those tests. AWS cp also fails here (because it has not been setup, I think).
            echo key is $NCBI_API_KEY && \
            rm test/test_ena.py && \
            pytest -v --timeout=600 -m 'not aws_cp'