Added Custom Headers to fix User-Agent based rate limiting #641
Workflow file for this run
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| name: runTest | |
| on: [push, pull_request] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test-python-app: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4.1.4 | |
| - name: Set up Python | |
| uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5.0.0 | |
| with: | |
| python-version: '3.11' | |
| - name: Python Linter | |
| run: | | |
| pip install ruff | |
| ruff check src | |
| - uses: conda-incubator/setup-miniconda@23dfbf7fc77cdca3333feeb1986f2e47b50ff610 # v3.0.3 | |
| 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@a8f56627de17dc7572799226327276b2b8d8e959 # v4.1.0 | |
| with: | |
| files: ./tests.xml | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |