Prophage/provirus and plasmid geNomad output "Feature" example files #20
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| name: Lint and Test | |
| on: | |
| workflow_call: | |
| pull_request: | |
| jobs: | |
| run_linkml_tasks: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Repo checkout | |
| uses: actions/checkout@main | |
| - name: Set up Python 3. | |
| uses: actions/setup-python@main | |
| with: | |
| python-version: 3.13 | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v6 | |
| - name: Install dependencies | |
| id: install_deps | |
| run: uv sync | |
| - name: Validate linkml files | |
| id: validate_linkml | |
| run: | | |
| make lint-validate | |
| continue-on-error: true | |
| - name: Lint linkml file | |
| id: lint_linkml | |
| run: | | |
| make lint | |
| continue-on-error: true | |
| # - name: Validate sample data against the schema | |
| # id: test_sample_data | |
| # run: | | |
| # make test-sample-data | |
| # continue-on-error: true | |
| # - name: Validate sample data against JSONschema | |
| # id: test_sample_data_jsonschema | |
| # run: | | |
| # make test-sample-data-jsonschema | |
| # continue-on-error: true | |
| - name: Test documentation generation | |
| id: test_docgen | |
| run: | | |
| make gendoc | |
| continue-on-error: true | |
| - name: outcome failure | |
| if: steps.lint_linkml.outcome != 'success' || steps.validate_linkml.outcome != 'success' || steps.test_docgen.outcome != 'success' | |
| # steps.test_sample_data.outcome != 'success' || steps.test_sample_data_jsonschema.outcome != 'success' | |
| run: | | |
| echo "linkml linting: ${{ steps.lint_linkml.outcome }}" | |
| echo "linkml schema validation: ${{ steps.validate_linkml.outcome }}" | |
| echo "documentation generator: ${{ steps.test_docgen.outcome }}" | |
| exit 1 | |
| # echo "sample data validation: ${{ steps.test_sample_data.outcome }}" | |
| # echo "sample data JSON Schema validation: ${{ steps.test_sample_data_jsonschema.outcome }}" | |
| - name: outcome success | |
| if: steps.lint_linkml.outcome == 'success' && steps.validate_linkml.outcome == 'success' && steps.test_docgen.outcome == 'success' | |
| run: | | |
| echo All tests passed successfully! | |
| exit 0 |