CI: Test notebooks using pixi #656
This file contains 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: Tests | |
| on: | |
| push: | |
| pull_request: | |
| schedule: | |
| - cron: '0 6 1 * *' | |
| jobs: | |
| pytest: | |
| name: Build and check | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - py39 | |
| - py310 | |
| - py311 | |
| - py312 | |
| runner: | |
| - ubuntu-latest | |
| - macos-14 | |
| runs-on: ${{ matrix.runner }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| submodules: true | |
| - name: Set dependencies | |
| id: dependencies | |
| run: | | |
| source ci/deps/${{ matrix.config }}.sh | |
| echo "CI_PYTHON_VERSION=${CI_PYTHON_VERSION}" >> $GITHUB_ENV | |
| echo "CI_PANDAS_VERSION=${CI_PANDAS_VERSION}" >> $GITHUB_ENV | |
| echo "CI_NUMPY_VERSION=${CI_NUMPY_VERSION}" >> $GITHUB_ENV | |
| echo "CI_SKLEARN_VERSION=${CI_SKLEARN_VERSION}" >> $GITHUB_ENV | |
| echo "CI_NO_SLOW=${CI_NO_SLOW}" >> $GITHUB_ENV | |
| echo "CONDA_PKGS_DIRS=${{ runner.temp }}/conda_pkgs_dir" >> $GITHUB_ENV | |
| echo "py_version=$(cut -d'.' -f 1-2 <<< ${CI_PYTHON_VERSION})" >> $GITHUB_OUTPUT | |
| echo "requirements=ci/deps/${{ matrix.config }}.sh" >> $GITHUB_OUTPUT | |
| - name: Cache downloaded packages | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.CONDA_PKGS_DIRS }} | |
| key: ${{ runner.os }}-${{ runner.arch }}-conda-${{ steps.dependencies.outputs.py_version }}-${{ hashFiles(steps.dependencies.outputs.requirements, 'pyproject.toml', 'ci/deps/requirements.yaml.tmpl') }} | |
| restore-keys: | | |
| ${{ runner.os }}-${{ runner.arch }}-conda-${{ steps.dependencies.outputs.py_version }}- | |
| - name: Create Conda Environment | |
| run: | | |
| source ci/setup_conda.sh "${{ runner.os }}" "${{ runner.arch }}" "${{ env.CONDA_PKGS_DIRS }}" | |
| ci/setup_env.sh "${{ runner.os }}" | |
| - name: Configure Xcode | |
| run: | | |
| sudo xcode-select -s "/Applications/Xcode_15.0.1.app" | |
| if: runner.os == 'macOS' | |
| - name: Build package | |
| run: | | |
| source activate sksurv-test | |
| python -m build . | |
| pip install --exists-action=w --pre --no-index --find-links dist/ scikit-survival | |
| rm -fr build dist sksurv | |
| - name: Run Tests | |
| run: | | |
| source activate sksurv-test | |
| ci/run_tests.sh | |
| - name: Check whether to create coverage report | |
| id: coverage | |
| run: | | |
| if [ ${{ env.CI_NO_SLOW }} = 'false' ] && [ ${{ runner.os }} = 'Linux' ] && [ ${{ github.actor }} != 'dependabot[bot]' ]; then | |
| echo "do=true" >> $GITHUB_OUTPUT | |
| else | |
| echo "do=false" >> $GITHUB_OUTPUT | |
| fi | |
| - name: Submit Coverage to Codecov | |
| uses: codecov/codecov-action@v4 | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| with: | |
| file: coverage.xml | |
| fail_ci_if_error: true | |
| disable_file_fixes: true | |
| if: steps.coverage.outputs.do == 'true' | |
| - name: Submit Coverage to Codacy | |
| uses: codacy/codacy-coverage-reporter-action@master | |
| with: | |
| project-token: ${{ secrets.CODACY_PROJECT_TOKEN }} | |
| coverage-reports: coverage.xml | |
| if: ${{ steps.coverage.outputs.do == 'true' && github.event_name != 'pull_request' }} |