add MANIFEST.in #473
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 | |
| - 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 }} | |