Implement machine learning workflow #1584
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: "Run Tests" | |
| on: | |
| push: | |
| branches: | |
| - "main" | |
| pull_request: | |
| branches: | |
| - "*" | |
| concurrency: | |
| group: testing-${{ github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| PYTEST_COMMON_ARGS: --cov-append --cov-report=xml --cov=nimare nimare | |
| PYTEST_UNIT_MARKERS: not performance_estimators and not performance_correctors and not performance_smoke and not cbmr_importerror | |
| PYTEST_PERFORMANCE_ESTIMATORS_MARKERS: performance_estimators | |
| PYTEST_PERFORMANCE_CORRECTORS_MARKERS: performance_correctors | |
| PYTEST_PERFORMANCE_SMOKE_MARKERS: performance_smoke | |
| PYTEST_CBMR_IMPORTERROR_MARKERS: cbmr_importerror | |
| jobs: | |
| # Determine if tests should be run based on commit message. | |
| check_skip: | |
| name: Determine if CI should be skipped | |
| runs-on: ubuntu-latest | |
| outputs: | |
| skip: ${{ steps.result_step.outputs.ci-skip }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - id: result_step | |
| uses: mstachniuk/ci-skip@master | |
| with: | |
| commit-filter: "[skip ci];[ci skip];[skip github]" | |
| commit-filter-separator: ";" | |
| run_unit_tests: | |
| name: Unit tests | |
| needs: check_skip | |
| if: ${{ needs.check_skip.outputs.skip == 'false' }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest", "macos-latest", "windows-latest"] | |
| python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: "Set up python" | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: "Install NiMARE" | |
| shell: bash {0} | |
| run: python -m pip install -e .[tests,cbmr] | |
| - name: "Run tests" | |
| shell: bash {0} | |
| run: python -m pytest -m "${PYTEST_UNIT_MARKERS}" ${PYTEST_COMMON_ARGS} | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: unit_${{ matrix.os }}_${{ matrix.python-version }} | |
| path: coverage.xml | |
| if: success() | |
| run_unit_tests_with_minimum_dependencies: | |
| name: Unit tests with minimum dependency versions | |
| needs: check_skip | |
| if: ${{ needs.check_skip.outputs.skip == 'false' }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.10"] | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: "Set up python" | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: "Install NiMARE" | |
| shell: bash {0} | |
| run: python -m pip install -e .[minimum,tests,cbmr] | |
| - name: "Run tests" | |
| shell: bash {0} | |
| run: python -m pytest -m "${PYTEST_UNIT_MARKERS}" ${PYTEST_COMMON_ARGS} | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: unit_minimum | |
| path: coverage.xml | |
| if: success() | |
| test_performance_estimators: | |
| name: Estimator performance tests | |
| needs: check_skip | |
| if: ${{ needs.check_skip.outputs.skip == 'false' }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.13"] | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: "Set up python" | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: "Install NiMARE" | |
| shell: bash {0} | |
| run: python -m pip install -e .[tests,cbmr] | |
| - name: "Run tests" | |
| shell: bash {0} | |
| run: python -m pytest -m "${PYTEST_PERFORMANCE_ESTIMATORS_MARKERS}" ${PYTEST_COMMON_ARGS} | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: performance_estimator | |
| path: coverage.xml | |
| if: success() | |
| test_performance_correctors: | |
| name: Corrector performance tests | |
| needs: check_skip | |
| if: ${{ needs.check_skip.outputs.skip == 'false' }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.13"] | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: "Set up python" | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: "Install NiMARE" | |
| shell: bash {0} | |
| run: python -m pip install -e .[tests,cbmr] | |
| - name: "Run tests" | |
| shell: bash {0} | |
| run: python -m pytest -m "${PYTEST_PERFORMANCE_CORRECTORS_MARKERS}" ${PYTEST_COMMON_ARGS} | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: performance_corrector | |
| path: coverage.xml | |
| if: success() | |
| test_performance_smoke: | |
| name: Smoke performance tests | |
| needs: check_skip | |
| if: ${{ needs.check_skip.outputs.skip == 'false' }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.13"] | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: "Set up python" | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: "Install NiMARE" | |
| shell: bash {0} | |
| run: python -m pip install -e .[tests,cbmr] | |
| - name: "Run tests" | |
| shell: bash {0} | |
| run: python -m pytest -m "${PYTEST_PERFORMANCE_SMOKE_MARKERS}" ${PYTEST_COMMON_ARGS} | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: performance_smoke | |
| path: coverage.xml | |
| if: success() | |
| test_cbmr_importerror: | |
| name: CBMR ImportError tests | |
| needs: check_skip | |
| if: ${{ needs.check_skip.outputs.skip == 'false' }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.13"] | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: "Set up python" | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: "Install NiMARE" | |
| shell: bash {0} | |
| run: python -m pip install -e .[tests] | |
| - name: "Run tests" | |
| shell: bash {0} | |
| run: python -m pytest -m "${PYTEST_CBMR_IMPORTERROR_MARKERS}" ${PYTEST_COMMON_ARGS} | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: cbmr_importerror | |
| path: coverage.xml | |
| if: success() | |
| upload_to_codecov: | |
| name: Upload coverage | |
| needs: | |
| [ | |
| run_unit_tests, | |
| run_unit_tests_with_minimum_dependencies, | |
| test_performance_estimators, | |
| test_performance_correctors, | |
| test_performance_smoke, | |
| test_cbmr_importerror, | |
| ] | |
| runs-on: "ubuntu-latest" | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: Download artifacts | |
| uses: actions/download-artifact@v4 | |
| - name: Upload to CodeCov | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| fail_ci_if_error: true | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |