ci: update gha #1
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| name: sourcepredict_ci | |
| on: [push, pull_request] | |
| jobs: | |
| pydamage_ci: | |
| name: sourcepredict_testing | |
| runs-on: 'ubuntu-latest' | |
| if: "!contains(github.event.head_commit.message, '[skip_ci]')" | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| mamba-version: "*" | |
| channels: conda-forge,bioconda,defaults | |
| channel-priority: true | |
| environment-file: conda_env.yaml | |
| activate-environment: sourcepredict_test | |
| - name: Test with pytest | |
| shell: bash -l {0} | |
| run: | | |
| pip install -e . | |
| pip install pytest | |
| pytest | |
| - name: Check sourcepredict help message | |
| shell: bash -l {0} | |
| run: | | |
| sourcepredict --help | |
| - name: Check sourcepredict on test data | |
| shell: bash -l {0} | |
| run: | | |
| sourcepredict -s data/modern_gut_microbiomes_sources.csv -l data/modern_gut_microbiomes_labels.csv data/test/dog_test_sink_sample.cs |