Add end-to-end test to GHAs #10
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| name: test | |
| on: [push] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| conda-solver: "libmamba" | |
| python-version: "3.11" | |
| channels: bioconda,conda-forge,defaults | |
| - name: Conda install | |
| shell: bash -el {0} | |
| run: conda install 'python >=3.6' 'biopython >=1.79' 'reportlab ==3.4.0' 'prodigal >=2.6.1' 'blast >=2.2.28' | |
| - name: Unit tests | |
| shell: bash -el {0} | |
| run: python3 -m unittest | |
| - name: End-to-end test | |
| shell: bash -el {0} | |
| run: mkdir -p output/ && ./hicap-runner.py --query_fp example/Hi75.fasta --output_dir output/ |