protein validaiton on by default #2
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| name: GMB CI | |
| on: | |
| push: | |
| paths: | |
| - 'support_scripts/gmb/**' | |
| - '.github/workflows/ci.yml' | |
| pull_request: | |
| paths: | |
| - 'support_scripts/gmb/**' | |
| - '.github/workflows/ci.yml' | |
| jobs: | |
| lint: | |
| name: Lint (ruff) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install ruff | |
| run: pip install "ruff>=0.4" | |
| - name: Run ruff | |
| working-directory: support_scripts/gmb | |
| run: ruff check . | |
| test-default: | |
| name: Unit + synthetic integration tests | |
| runs-on: ubuntu-latest | |
| needs: lint | |
| strategy: | |
| matrix: | |
| python-version: ['3.9', '3.11'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| working-directory: support_scripts/gmb | |
| run: | | |
| pip install -r requirements.txt | |
| pip install -r requirements-dev.txt | |
| - name: Run unit + synthetic tests (exclude real-data integration) | |
| working-directory: support_scripts/gmb | |
| run: python -m pytest tests/ -v -m "not integration" --tb=short | |
| test-integration-subset: | |
| name: Real-data integration test (z_tritici region fixtures, ~8 s) | |
| runs-on: ubuntu-latest | |
| needs: lint | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install dependencies | |
| working-directory: support_scripts/gmb | |
| run: | | |
| pip install -r requirements.txt | |
| pip install -r requirements-dev.txt | |
| - name: Run z_tritici region integration tests (pre-subsetted fixtures) | |
| working-directory: support_scripts/gmb | |
| # Pre-subsetted fixtures run in ~8 seconds; allow 5 minutes for CI overhead | |
| timeout-minutes: 5 | |
| run: python -m pytest tests/test_z_tritici_subset.py -v -m integration --tb=short | |
| test-compat: | |
| name: Compat (pandas 3.0 + pyranges 0.1.4) | |
| runs-on: ubuntu-latest | |
| needs: lint | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install compat dependencies | |
| working-directory: support_scripts/gmb | |
| run: | | |
| pip install -r requirements-compat.txt | |
| pip install pytest | |
| - name: Run unit + synthetic tests (compat env) | |
| working-directory: support_scripts/gmb | |
| run: python -m pytest tests/ -v -m "not integration" --tb=short |