docs(mimic-iv): where to find Vitamin C / ascorbic acid (#1962) #79
Workflow file for this run
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| # Cheap, early equivalence signal for contributors on every PR. | |
| # | |
| # The authoritative build/equivalence chain (ci.yml) only runs after a | |
| # maintainer approves the PR, so contributors otherwise get no feedback on | |
| # whether their change keeps the PostgreSQL and DuckDB derived concepts in sync. | |
| # | |
| # This workflow does the same demo-data equivalence check, but consolidated into | |
| # a single job that runs on every PR push: | |
| # | |
| # * one runner instead of five (no per-job checkout / tooling install), | |
| # * both engines built locally, so there are no artifacts to upload/download | |
| # and no pg_dump / restore round-trip, | |
| # * path-filtered and concurrency-cancelled so unrelated pushes cost nothing. | |
| # | |
| # It uses the same composite actions as ci.yml, so the two stay in lock-step. | |
| name: PR equivalence | |
| on: | |
| pull_request: | |
| paths: | |
| - 'mimic-iv/concepts/**' | |
| - 'mimic-iv/concepts_postgres/**' | |
| - 'mimic-iv/concepts_duckdb/**' | |
| - 'mimic-iv/buildmimic/postgres/**' | |
| - 'mimic-iv/buildmimic/duckdb/**' | |
| - 'src/**' | |
| - 'pyproject.toml' | |
| - 'requirements-lock.txt' | |
| - '.github/actions/**' | |
| - '.github/workflows/pr-equivalence.yml' | |
| # Cancel superseded runs when a PR is pushed again, so only the latest commit | |
| # burns CI minutes. | |
| concurrency: | |
| group: pr-equivalence-${{ github.event.pull_request.number }} | |
| cancel-in-progress: true | |
| permissions: | |
| contents: read | |
| jobs: | |
| equivalence: | |
| runs-on: ubuntu-latest | |
| container: python:3.12 | |
| services: | |
| postgres: | |
| image: postgres:17 | |
| env: | |
| POSTGRES_PASSWORD: postgres | |
| # Force byte-order (C) collation so string ordering matches DuckDB's | |
| # binary sort. | |
| POSTGRES_INITDB_ARGS: "--encoding=UTF8 --lc-collate=C --lc-ctype=C" | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| env: | |
| PGHOST: postgres | |
| PGUSER: postgres | |
| PGPASSWORD: postgres | |
| PGDATABASE: postgres | |
| steps: | |
| - uses: actions/checkout@v7 | |
| - name: Install tooling | |
| run: | | |
| apt-get update | |
| apt-get install --yes --no-install-recommends postgresql-client wget unzip | |
| pip install -e ".[equivalence]" | |
| - uses: ./.github/actions/setup-duckdb | |
| - uses: ./.github/actions/download-demo | |
| # Load the demo into both engines locally, so the comparison can read them | |
| # directly without shuttling artifacts between jobs. | |
| - uses: ./.github/actions/load-mimic-psql | |
| - uses: ./.github/actions/load-mimic-duckdb | |
| - uses: ./.github/actions/create-derived-schemas | |
| with: | |
| engine: postgres | |
| - uses: ./.github/actions/create-derived-schemas | |
| with: | |
| engine: duckdb | |
| - uses: ./.github/actions/transpile-concepts | |
| with: | |
| dialect: postgres | |
| - uses: ./.github/actions/transpile-concepts | |
| with: | |
| dialect: duckdb | |
| - name: Build PostgreSQL concepts | |
| working-directory: ./mimic-iv/concepts_postgres | |
| run: | | |
| psql -q -v ON_ERROR_STOP=1 -f postgres-make-concepts.sql | |
| - name: Build DuckDB concepts | |
| working-directory: ./mimic-iv/concepts_duckdb | |
| run: | | |
| duckdb "$GITHUB_WORKSPACE/mimic4.db" -c ".read duckdb.sql" | |
| - uses: ./.github/actions/compare-concepts |