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| 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' |