Update test_opentargets.json #1981
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: CI - tests and reporting | |
| on: | |
| # Scheduled runs twice weekly. | |
| # These runs execute tests on both Python versions, save the pytest output to a file, | |
| # upload the file as an artifact, and commit the 3.12 report back to main. | |
| schedule: | |
| - cron: "0 16 * * 1,4" | |
| # Push runs only when package code or tests change. | |
| # These runs execute tests normally and fail immediately on test failure. | |
| push: | |
| paths: | |
| - "gget/**" | |
| - "tests/**" | |
| # Avoid recursively triggering on committed pytest result files. | |
| - "!tests/pytest_results_py*.txt" | |
| # Manual runs behave like scheduled runs: | |
| # save output, upload artifact, and optionally commit report back to main. | |
| workflow_dispatch: | |
| permissions: | |
| contents: write | |
| jobs: | |
| build: | |
| name: Test on Python ${{ matrix.python }} | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python: ["3.11", "3.12"] | |
| steps: | |
| - name: Checkout branch | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Setup python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install -r requirements.txt | |
| python -m pip install -r dev-requirements.txt | |
| # Push behavior: | |
| # run pytest normally and let this step fail the job immediately if tests fail. | |
| - name: Run tests on push | |
| if: github.event_name == 'push' | |
| run: | | |
| pytest -ra -v --tb=long --maxfail=5 --durations=10 \ | |
| --cov=gget --cov-report=term-missing tests | |
| # Scheduled/manual behavior: | |
| # run pytest, save full output to a file, and capture the real pytest exit code. | |
| # | |
| # Important: | |
| # - GitHub bash shells may stop on non-zero commands before later lines run. | |
| # - We temporarily disable errexit with "set +e" so failed tests do not prevent | |
| # us from recording PIPESTATUS[0] and writing it to GITHUB_OUTPUT. | |
| # - continue-on-error keeps later artifact/commit steps running. | |
| - name: Run tests and save output for scheduled/manual runs | |
| id: pytest_saved | |
| if: github.event_name == 'schedule' || github.event_name == 'workflow_dispatch' | |
| continue-on-error: true | |
| shell: bash | |
| run: | | |
| set -o pipefail | |
| OUT="tests/pytest_results_py${{ matrix.python }}.txt" | |
| echo "Pytest results (Python ${{ matrix.python }}) - $(date -u +"%Y-%m-%dT%H:%M:%SZ")" > "$OUT" | |
| echo "" >> "$OUT" | |
| set +e | |
| pytest -ra -v --tb=long --maxfail=5 --durations=10 \ | |
| --cov=gget --cov-report=term-missing tests 2>&1 | tee -a "$OUT" | |
| code=${PIPESTATUS[0]} | |
| set -e | |
| echo "exit_code=$code" >> "$GITHUB_OUTPUT" | |
| echo "pytest exit code: $code" | |
| # Do not fail here; a later step fails the job after artifacts/report handling. | |
| exit 0 | |
| # Upload the saved pytest report as an artifact. | |
| # Only do this once (3.12) to avoid duplicate artifacts from the matrix. | |
| - name: Upload pytest results artifact | |
| if: always() && matrix.python == '3.12' && (github.event_name == 'schedule' || github.event_name == 'workflow_dispatch') | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: pytest-results-py${{ matrix.python }} | |
| path: tests/pytest_results_py${{ matrix.python }}.txt | |
| # Commit the saved pytest report back to the repository. | |
| # Safety guards: | |
| # - only on scheduled/manual runs | |
| # - only once (3.12) to avoid matrix push races | |
| # - commits back to the branch that the run was triggered from | |
| # Retry logic helps if the branch moved while this job was running. | |
| - name: Commit and push pytest results | |
| if: > | |
| always() && | |
| matrix.python == '3.12' && | |
| (github.event_name == 'schedule' || github.event_name == 'workflow_dispatch') | |
| shell: bash | |
| run: | | |
| set -euo pipefail | |
| BRANCH="${GITHUB_REF#refs/heads/}" | |
| echo "Current branch: $BRANCH" | |
| git config user.name "github-actions[bot]" | |
| git config user.email "github-actions[bot]@users.noreply.github.com" | |
| git add tests/pytest_results_py*.txt | |
| if git diff --cached --quiet; then | |
| echo "No changes to commit." | |
| exit 0 | |
| fi | |
| git commit -m "CI: update pytest results ($BRANCH)" | |
| for attempt in 1 2 3 4 5; do | |
| echo "Push attempt $attempt..." | |
| git pull --rebase --autostash origin "$BRANCH" || true | |
| if git push origin "$BRANCH"; then | |
| exit 0 | |
| fi | |
| sleep $((attempt * 5)) | |
| done | |
| echo "Push failed after retries." | |
| exit 1 | |
| # After scheduled/manual runs, explicitly fail the job if pytest failed. | |
| # This step is separate so that artifact upload and report commit can still happen | |
| # even when tests fail. | |
| - name: Fail job if pytest failed | |
| if: always() && (github.event_name == 'schedule' || github.event_name == 'workflow_dispatch') | |
| shell: bash | |
| run: | | |
| code="${{ steps.pytest_saved.outputs.exit_code }}" | |
| echo "Captured pytest exit code: ${code:-<missing>}" | |
| # Missing output means something went wrong before exit code capture. | |
| if [ -z "${code:-}" ]; then | |
| echo "pytest exit code was not captured" | |
| exit 1 | |
| fi | |
| if [ "$code" != "0" ]; then | |
| exit "$code" | |
| fi |