Merge pull request #244 from monarch-initiative/feature/mechanism-emb… #492
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| # Built from: | |
| # https://docs.github.com/en/actions/guides/building-and-testing-python | |
| --- | |
| name: Build and test | |
| on: # yamllint disable-line rule:truthy | |
| push: | |
| branches: [main] | |
| pull_request: | |
| env: | |
| FORCE_COLOR: "1" # Make tools pretty. | |
| permissions: {} | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.13"] | |
| fail-fast: false | |
| steps: | |
| # https://github.com/actions/checkout | |
| - name: Check out repository | |
| uses: actions/checkout@v6 | |
| with: | |
| persist-credentials: false | |
| - name: Check for changes | |
| uses: dorny/paths-filter@v3 | |
| id: changes | |
| with: | |
| list-files: shell | |
| filters: | | |
| src: | |
| - 'src/**' | |
| - 'tests/**' | |
| - 'pyproject.toml' | |
| - 'uv.lock' | |
| kb_disorders: | |
| - 'kb/disorders/**/*.yaml' | |
| - '!kb/disorders/**/*.history.yaml' | |
| kb_comorbidities: | |
| - 'kb/comorbidities/**/*.yaml' | |
| # https://github.com/astral-sh/setup-uv | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v7 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| enable-cache: true | |
| cache-dependency-glob: "uv.lock" | |
| # https://github.com/actions/setup-python | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v6.2.0 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install just | |
| run: | | |
| uv tool install rust-just | |
| - name: Install project | |
| run: uv sync --dev | |
| - name: Validate changed disorder KB files | |
| if: steps.changes.outputs.kb_disorders == 'true' | |
| run: | | |
| echo "Validating changed disorder KB files..." | |
| for f in ${{ steps.changes.outputs.kb_disorders_files }}; do | |
| if [[ "$f" == kb/disorders/* && "$f" == *.yaml && "$f" != *.history.yaml ]]; then | |
| echo "=== Validating disorder: $f ===" | |
| just validate "$f" | |
| else | |
| echo "Skipping non-disorder file: $f" | |
| fi | |
| done | |
| - name: Validate changed comorbidity KB files | |
| if: steps.changes.outputs.kb_comorbidities == 'true' | |
| run: | | |
| echo "Validating changed comorbidity KB files..." | |
| for f in ${{ steps.changes.outputs.kb_comorbidities_files }}; do | |
| if [[ "$f" == kb/comorbidities/* && "$f" == *.yaml ]]; then | |
| echo "=== Validating comorbidity: $f ===" | |
| just validate-comorbidity "$f" | |
| else | |
| echo "Skipping non-comorbidity file: $f" | |
| fi | |
| done | |
| - name: Run test suite | |
| if: steps.changes.outputs.src == 'true' | |
| run: just test |