CI: Run nbval with python 3.12, matplotlib 3.9, seaborn 0.13 #705
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| 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 | |
| - py313 | |
| 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: ${{ steps.coverage.outputs.do == 'true' && github.event_name != 'pull_request' }} | |
| nbval: | |
| runs-on: ubuntu-latest | |
| name: Build and check notebooks | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| submodules: true | |
| - name: Set dependencies | |
| id: dependencies | |
| env: | |
| DEPS_CONFIG: py312 | |
| run: | | |
| source ci/deps/${DEPS_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" >> $GITHUB_ENV | |
| echo "requirements=ci/deps/${DEPS_CONFIG}.sh" >> $GITHUB_OUTPUT | |
| - name: Cache downloaded packages | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.CONDA_PKGS_DIRS }} | |
| key: ${{ runner.os }}-${{ runner.arch }}-conda-3.11-${{ hashFiles(steps.dependencies.outputs.requirements, 'pyproject.toml', 'ci/deps/requirements.yaml.tmpl') }} | |
| - name: Create Conda Environment | |
| run: | | |
| source ci/setup_conda.sh "${{ runner.os }}" "${{ runner.arch }}" "${{ env.CONDA_PKGS_DIRS }}" | |
| ci/setup_env.sh "${{ runner.os }}" | |
| - name: Configure matplotlib | |
| run: | | |
| mkdir -p ${XDG_CONFIG_HOME}/matplotlib | |
| echo 'figure.figsize: 6.0, 4.0' > ${XDG_CONFIG_HOME}/matplotlib/matplotlibrc | |
| echo 'figure.facecolor: white' >> ${XDG_CONFIG_HOME}/matplotlib/matplotlibrc | |
| echo 'figure.edgecolor: white' >> ${XDG_CONFIG_HOME}/matplotlib/matplotlibrc | |
| echo 'figure.dpi: 72' >> ${XDG_CONFIG_HOME}/matplotlib/matplotlibrc | |
| echo 'font.size: 10' >> ${XDG_CONFIG_HOME}/matplotlib/matplotlibrc | |
| - 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: Test notebooks | |
| run: | | |
| source activate sksurv-test | |
| pytest --nbval doc/user_guide/*.ipynb --nbval-sanitize-with ci/nb_sanitize.cfg |