run_tests.yaml

name: Lint and Test

on:
    workflow_call:

jobs:
    run_unit_tests:
        runs-on: ubuntu-latest
        strategy:
            fail-fast: false

        steps:
            - name: Repo checkout
              uses: actions/checkout@main

            - name: Set up Python 3.12
              uses: actions/setup-python@main
              with:
                  python-version: 3.12

            - name: Install Poetry
              uses: snok/install-poetry@main

            - name: Install dependencies
              id: install_deps
              run: poetry install

            - name: poetry run pytest -rP tests/
              id: run_pytest
              run: |
                  poetry run pytest --cov=credit_engine --cov-report=xml -rP tests/
              continue-on-error: true

            - name: Send to Codecov
              id: send_to_codecov
              uses: codecov/codecov-action@main
              continue-on-error: true
              with:
                  files: ./coverage.xml
                  fail_ci_if_error: true
                  token: ${{ secrets.CODECOV_TOKEN }}

            - name: outcome failure
              if: steps.run_pytest.outcome != 'success' || steps.send_to_codecov.outcome != 'success'
              run: |
                  echo "Python tests: ${{ steps.run_pytest.outcome }}"
                  echo "upload coverage: ${{ steps.send_to_codecov.outcome }}"
                  exit 1

            - name: outcome success
              run: |
                  echo "Python tests: ${{ steps.run_pytest.outcome }}"
                  echo "upload coverage: ${{ steps.send_to_codecov.outcome }}"
                  exit 0

    run_linkml_tasks:
        runs-on: ubuntu-latest
        strategy:
            fail-fast: false

        steps:
            - name: Repo checkout
              uses: actions/checkout@main

            - name: Set up Python 3.12
              uses: actions/setup-python@main
              with:
                  python-version: 3.12

            - name: Install dependencies
              id: install_deps
              run: pip install linkml check-jsonschema 'jsonschema[format]'

            - name: Lint linkml file
              id: lint_linkml
              run: |
                  linkml-lint ./schema/kbase/linkml/credit_metadata.yaml --ignore-warnings
              continue-on-error: true

            - name: Validate kbase sample data against the schema
              id: validate_kbase_data
              run: |
                  linkml-validate -s schema/kbase/linkml/credit_metadata.yaml sample_data/kbase/**/*kbcms.json
              continue-on-error: true

            - name: Validate kbase sample data against JSONschema
              id: validate_kbase_data_against_jsonschema
              run: |
                  check-jsonschema --schemafile schema/kbase/jsonschema/credit_metadata.schema.json --verbose sample_data/kbase/**/*kbcms.json
              continue-on-error: true

            - name: outcome failure
              if: steps.lint_linkml.outcome != 'success' # || steps.validate_kbase_data.outcome != 'success'
              run: |
                  echo "linkml linting: ${{ steps.lint_linkml.outcome }}"
                  echo "KBase sample data validation: ${{ steps.validate_kbase_data.outcome }}"
                  exit 1

            - name: outcome success
              if: steps.lint_linkml.outcome == 'success' # || steps.validate_kbase_data.outcome != 'success'
              run: |
                  echo "linkml linting: ${{ steps.lint_linkml.outcome }}"
                  echo "KBase sample data validation: ${{ steps.validate_kbase_data.outcome }}"
                  exit 0