imports from module #186
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 srcs/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 srcs/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/badge-action@v2.0.2 | |