fix #149 drugprot polishment (#150) #139
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| name: Test PIE Dataset | |
| on: | |
| push: | |
| branches: [main] | |
| paths: | |
| - "dataset_builders/pie/**" | |
| - "data/datasets/**" | |
| - "tests/dataset_builders/pie/**" | |
| - "tests/fixtures/dataset_builders/pie/**" | |
| - ".github/workflows/test_pie_datasets.yaml" | |
| pull_request: | |
| branches: [main, "release/*"] | |
| paths: | |
| - "dataset_builders/pie/**" | |
| - "data/datasets/**" | |
| - "tests/dataset_builders/pie/**" | |
| - "tests/fixtures/dataset_builders/pie/**" | |
| - ".github/workflows/test_pie_datasets.yaml" | |
| jobs: | |
| collect_modified_datasets: # Job that lists modified datasets | |
| runs-on: ubuntu-latest | |
| outputs: | |
| datasets: ${{ steps.set-datasets.outputs.datasets }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Get changed dataset files | |
| id: changed-files | |
| uses: tj-actions/changed-files@v44 | |
| with: | |
| files_yaml: | | |
| datasets: | |
| - 'dataset_builders/pie/**' | |
| - 'data/datasets/**' | |
| - 'tests/dataset_builders/pie/**' | |
| - 'tests/fixtures/dataset_builders/pie/**' | |
| - name: Determine modified datasets | |
| id: set-datasets # Give it an id to handle step outputs in the outputs key above | |
| # NOTE: Ensure all outputs are prefixed by the same key used above e.g. `datasets_(...)` | |
| # when trying to access the `any_changed` output. | |
| if: steps.changed-files.outputs.datasets_any_changed == 'true' | |
| env: | |
| DATASETS_ALL_CHANGED_FILES: ${{ steps.changed-files.outputs.datasets_all_changed_files }} | |
| run: | | |
| echo "all changed dataset files: $DATASETS_ALL_CHANGED_FILES" | |
| DATASETS=$(ls dataset_builders/pie) | |
| echo "collected datasets: $DATASETS" | tr '\n' ' ' | |
| echo "\n" | |
| PREFIXES="dataset_builders/pie/ data/datasets/ tests/dataset_builders/pie/ tests/fixtures/dataset_builders/pie/" | |
| echo "file paths to check for changes: $PREFIXES" | |
| # filter entries in DATASETS for which any prefix+dataset is in DATASETS_ALL_CHANGED_FILES | |
| DATASETS_FILTERED=$(for dataset in ${DATASETS}; do | |
| for prefix in ${PREFIXES}; do | |
| if [[ $DATASETS_ALL_CHANGED_FILES == *"$prefix$dataset"* ]]; then | |
| echo $dataset | |
| break | |
| fi | |
| done | |
| done) | |
| echo "filtered datasets: $DATASETS_FILTERED" | |
| # Define step output named dataset base on ls command transformed to JSON thanks to jq | |
| echo "datasets=$(echo "$DATASETS_FILTERED" | jq -R -s -c 'split("\n")[:-1]')" >> "$GITHUB_OUTPUT" | |
| test_dataset: | |
| runs-on: ubuntu-latest | |
| needs: [ collect_modified_datasets ] # Depends on previous job | |
| if: ${{ needs.collect_modified_datasets.outputs.datasets }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # List matrix strategy from datasets dynamically collected in the previous job | |
| dataset: ${{fromJson(needs.collect_modified_datasets.outputs.datasets)}} | |
| timeout-minutes: 15 | |
| steps: | |
| - run: echo "test dataset ${{matrix.dataset}}" | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Set up python | |
| id: setup-python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.9' | |
| cache: 'pip' # caching pip dependencies | |
| - name: Install dependencies | |
| run: | | |
| pip install --upgrade pip | |
| # install dataset requirements | |
| pip install -r dataset_builders/pie/${{matrix.dataset}}/requirements.txt | |
| # check if test requirements file exists and install it | |
| ADD_REQUIREMENTS_FILE=tests/dataset_builders/pie/${{matrix.dataset}}/additional-requirements.txt | |
| test -f $ADD_REQUIREMENTS_FILE && pip install -r $ADD_REQUIREMENTS_FILE | |
| # install pytest and pytest-cov | |
| pip install pytest pytest-cov | |
| - name: Run tests | |
| run: | | |
| pytest \ | |
| tests/dataset_builders/pie/${{matrix.dataset}} \ | |
| -k "not slow" \ | |
| --cov=dataset_builders/pie/${{matrix.dataset}} \ | |
| --cov-report=xml:coverage/${{matrix.dataset}}.xml | |
| - name: Upload coverage | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| file: coverage/${{matrix.dataset}}.xml | |
| name: ${{matrix.dataset}} | |
| fail_ci_if_error: true | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |