Merge WP2: ontology discipline (ROBOT default + markers + budget + op… #1
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| name: Ontology build (ROBOT/ELK) | |
| # WP2 §4.A: ROBOT/ELK is the canonical ontology verifier; CI runs it | |
| # on every push to main/staging and on every PR so contributions can't | |
| # land without passing the integration story. | |
| on: | |
| push: | |
| branches: [main, staging] | |
| pull_request: | |
| branches: [main, staging] | |
| workflow_dispatch: | |
| permissions: | |
| contents: read | |
| jobs: | |
| build: | |
| name: Python assembly + ROBOT/ELK verification | |
| runs-on: ubuntu-latest | |
| env: | |
| ROBOT_VERSION: "1.9.5" | |
| ROBOT: obo-robot | |
| steps: | |
| - name: Check out the repo | |
| uses: actions/checkout@v4 | |
| - name: Set up Java 17 (Temurin) | |
| uses: actions/setup-java@v4 | |
| with: | |
| distribution: temurin | |
| java-version: '17' | |
| - name: Cache the ROBOT jar | |
| id: cache-robot | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.local/lib/robot | |
| key: robot-${{ env.ROBOT_VERSION }} | |
| - name: Download ROBOT jar if not cached | |
| if: steps.cache-robot.outputs.cache-hit != 'true' | |
| run: | | |
| mkdir -p "$HOME/.local/lib/robot" | |
| curl -fsSL -o "$HOME/.local/lib/robot/robot.jar" \ | |
| "https://github.com/ontodev/robot/releases/download/v${ROBOT_VERSION}/robot.jar" | |
| - name: Install the obo-robot wrapper on PATH | |
| run: | | |
| mkdir -p "$HOME/.local/bin" | |
| cat > "$HOME/.local/bin/obo-robot" <<'EOF' | |
| #!/usr/bin/env bash | |
| exec java -jar "${HOME}/.local/lib/robot/robot.jar" "$@" | |
| EOF | |
| chmod +x "$HOME/.local/bin/obo-robot" | |
| echo "${HOME}/.local/bin" >> "$GITHUB_PATH" | |
| - name: Confirm toolchain | |
| run: | | |
| java -version | |
| obo-robot --version | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v6 | |
| with: | |
| enable-cache: true | |
| - name: Sync Python dependencies | |
| run: uv sync | |
| - name: Run canonical ontology build (preflight + Python + ROBOT/ELK) | |
| run: make ontology | |
| - name: Confirm rtm.ttl is committed in-sync with rebuild | |
| # If the rebuild produced a different artifact than what's | |
| # committed, the contributor forgot to commit the regenerated | |
| # rtm.ttl + manifest. Fail the build with a clear diff. | |
| run: | | |
| if ! git diff --quiet --exit-code -- ontology/rtm.ttl ontology/assembly_manifest.json; then | |
| echo "::error::Built ontology artifacts differ from committed copies." | |
| echo "Run 'make ontology' locally and commit ontology/rtm.ttl + ontology/assembly_manifest.json." | |
| git --no-pager diff --stat -- ontology/rtm.ttl ontology/assembly_manifest.json | |
| exit 1 | |
| fi | |
| - name: Run unit tests (live + network markers skipped by default) | |
| run: uv run pytest -v |