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| name: Test Aviary with Setup-Miniconda From Marketplace | |
| on: [push, pull_request] | |
| jobs: | |
| miniconda: | |
| name: Miniconda ${{ matrix.os }} | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| matrix: | |
| python-version: ["3.10"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up environment with Python ${{ matrix.python-version }} | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: test | |
| environment-file: aviary.yml | |
| python-version: ${{ matrix.python-version }} | |
| auto-activate-base: false | |
| channels: conda-forge,bioconda | |
| channel-priority: true | |
| - run: | | |
| conda info | |
| conda list | |
| conda config --set channel_priority strict | |
| - name: Install Aviary | |
| run: | | |
| pip install -e . | |
| - name: Run unit tests | |
| run: | | |
| aviary -h | |
| python test/test_assemble.py | |
| python test/test_recover.py | |
| python test/test_run_checkm.py -b |