Add Harbor benchmark runner scripts and document k=1/k=3 sweeps #3
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| name: ci | |
| on: | |
| pull_request: | |
| push: | |
| branches: [main] | |
| # Only the lint job runs in GitHub Actions. Building the `bioterm-*:v1` | |
| # Docker images pulls multi-GB of bioinformatics tool chains and can | |
| # chew through a private account's runner quota in a single push, so | |
| # image builds and the oracle-all sweep are intentionally kept local | |
| # (see scripts/build_images.sh and scripts/run_oracle_all.sh). | |
| jobs: | |
| lint: | |
| name: lint tasks | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: install helper deps | |
| run: pip install click | |
| - name: syntax-check shell scripts | |
| run: | | |
| bash -n scripts/build_images.sh | |
| bash -n scripts/run_oracle_all.sh | |
| bash -n scripts/refresh_db_golds.sh | |
| bash -n scripts/new_task.sh | |
| - name: validate task directories | |
| run: python scripts/validate_task.py | |
| - name: scaffolder smoke test | |
| run: | | |
| bash scripts/new_task.sh ci-smoke-stub --category metadata | |
| # scaffolded tasks intentionally fail validation until filled in | |
| if python scripts/validate_task.py --only ci-smoke-stub; then | |
| echo "scaffolder regression: placeholder task passed validation" >&2 | |
| exit 1 | |
| fi | |
| rm -rf tasks/ci-smoke-stub |