Add safety check for masked loading of ROI tables to support ngio masked ROI tables #1441
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| name: CI (poetry) | |
| on: | |
| push: | |
| branches: ["main"] | |
| pull_request: | |
| branches: ["main"] | |
| jobs: | |
| tests_core: | |
| name: "Core, Python ${{ matrix.python-version }}" | |
| runs-on: ubuntu-22.04 | |
| timeout-minutes: 10 | |
| strategy: | |
| matrix: | |
| python-version: ["3.11", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| persist-credentials: false | |
| - name: Install poetry | |
| run: pipx install poetry==1.8.2 | |
| - name: Configure poetry | |
| run: poetry config virtualenvs.in-project true | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache poetry virtualenv | |
| uses: actions/cache@v4 | |
| with: | |
| path: ./.venv | |
| key: ${{ runner.os }}-python-${{ matrix.python-version }}-venv-${{ hashFiles('**/poetry.lock') }}-tests_core | |
| - name: Install dependencies (without extras) | |
| run: poetry install --with dev --without docs --no-interaction | |
| - name: Test core library with pytest | |
| env: | |
| COVERAGE_FILE: coverage-data-core-${{ matrix.python-version }} | |
| run: poetry run coverage run -m pytest tests --ignore tests/tasks --ignore tests/dev --ignore tests/tasks_v2 | |
| - name: Upload coverage data | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-data-core-${{ matrix.python-version }} | |
| path: coverage-data-core-${{ matrix.python-version }}* | |
| tests_tasks: | |
| name: "Tasks, Python ${{ matrix.python-version }}" | |
| runs-on: ubuntu-22.04 | |
| timeout-minutes: 30 | |
| strategy: | |
| matrix: | |
| python-version: ["3.11", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| persist-credentials: false | |
| - name: Install poetry | |
| run: pipx install poetry==1.8.2 | |
| - name: Configure poetry | |
| run: poetry config virtualenvs.in-project true | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache poetry virtualenv | |
| uses: actions/cache@v4 | |
| with: | |
| path: ./.venv | |
| key: ${{ runner.os }}-python-${{ matrix.python-version }}-venv-${{ hashFiles('**/poetry.lock') }}-tests_tasks | |
| - name: Install dependencies (including fractal-tasks extra) | |
| run: poetry install --with dev --without docs --no-interaction -E fractal-tasks | |
| - name: Check if manifest has changed | |
| run: poetry run fractal-manifest check --package fractal-tasks-core | |
| - name: Cache Pooch folder | |
| id: cache-pooch-folder | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/pooch | |
| key: pooch-cache | |
| - name: Test tasks with pytest | |
| env: | |
| COVERAGE_FILE: coverage-data-tasks-${{ matrix.python-version }} | |
| run: poetry run coverage run -m pytest tests/dev tests/tasks tests/tasks_v2 | |
| - name: Upload coverage data | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-data-tasks-${{ matrix.python-version }} | |
| path: coverage-data-tasks-${{ matrix.python-version }}* | |
| coverage: | |
| name: Coverage | |
| runs-on: ubuntu-22.04 | |
| needs: [tests_core, tests_tasks] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - run: pipx install poetry==1.8.2 | |
| - run: poetry config virtualenvs.in-project true | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install dependencies | |
| run: poetry install --with dev | |
| - name: Download data | |
| uses: actions/download-artifact@v4 | |
| with: | |
| pattern: coverage-data-* | |
| merge-multiple: true | |
| - name: Combine coverage | |
| # Combines all the downloaded coverage artifacts in a single `.coverage` file, | |
| # which will then be used by `py-cov-action/python-coverage-comment-action`. | |
| # We added this step to replace the variable `MERGE_COVERAGE_FILES: true` | |
| # in the next step, which had started to raise errors | |
| # (https://github.com/fractal-analytics-platform/fractal-server/pull/1725). | |
| run: poetry run coverage combine coverage-data-* | |
| - name: Add coverage comment to Pull Requests | |
| id: coverage_comment | |
| uses: py-cov-action/python-coverage-comment-action@v3 | |
| with: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| MINIMUM_GREEN: 90 | |
| MINIMUM_ORANGE: 60 | |
| ANNOTATE_MISSING_LINES: true | |
| ANNOTATION_TYPE: notice |