add debug flag #505
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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 | |
| - name: Python Linter | |
| uses: chartboost/ruff-action@v1 | |
| with: | |
| src: "src" | |
| # args: --select ALL | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniconda-version: "latest" | |
| activate-environment: yacht_env | |
| environment-file: env/yacht_env.yml | |
| - name: install YACHT locally | |
| run: pip install . | |
| - name: List contents of 'yacht' in site-packages | |
| run: | | |
| SITE_PACKAGES=$(python -c "import site; print(site.getsitepackages()[0])") | |
| ls -R $SITE_PACKAGES/yacht | |
| - name: make training data | |
| run: yacht train --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: yacht run --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: unit-tests | |
| run: pytest tests/ --cov-report term-missing --cov-report xml:tests.xml --cov=yacht | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| files: ./tests.xml | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |