Merge pull request #52 from KoslickiLab/sonarqube #164
Workflow file for this run
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| name: runTest | |
| on: [push] | |
| jobs: | |
| test-python-app: | |
| runs-on: ubuntu-20.04 | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: yacht_env | |
| environment-file: env/yacht_env.yml | |
| - name: make training data | |
| run: python make_training_data_from_sketches.py --ref_file 'tests/testdata/20_genomes_sketches.zip' --ksize 31 --prefix 'gtdb_ani_thresh_0.95' --ani_thresh 0.95 --outdir ./ --force | |
| - name: run YACHT | |
| run: python run_YACHT.py --json gtdb_ani_thresh_0.95_config.json --sample_file 'tests/testdata/sample.sig.zip' --significance 0.99 --min_coverage_list 1 0.6 0.2 0.1 | |
| - name: test-unit | |
| run: pytest tests/test_unit.py --cov=./ --cov-report xml:covunit.xml | |
| - name: test-utils | |
| run: pytest tests/test_utils.py --cov=./ --cov-report xml:covutils.xml | |
| - name: test-workflow | |
| run: pytest tests/test_workflow.py --cov=./ --cov-report xml:covworkflow.xml | |
| - name: integration-tests | |
| run: pytest -vv tests/integration_tests.py --cov=./ --cov-report xml:covntegration.xml | |
| - name: unit-tests | |
| run: pytest -vv tests/unittests.py --cov=./ --cov-report xml:covunittests.xml | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| files: ./covunit.xml,./covutils.xml,./covworkflow.xml,./covntegration.xml,./covunittests.xml | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| - name: Badge Action | |
| uses: emibcn/[email protected] | |