make sure to fix the CI/CD #24
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| name: Build package on different Os and Python versions | |
| on : | |
| pull_request: | |
| workflow_dispatch: | |
| inputs: | |
| testNotebooks: | |
| description: 'Enable notebook verification step' | |
| type: boolean | |
| required: false | |
| default: false | |
| # currently WIP | |
| jobs: | |
| build_package: | |
| name: Build ${{ github.event.repository.name }} on ${{ matrix.os }} for Python-${{ matrix.python-version }} | |
| runs-on: ${{ matrix.os }} | |
| timeout-minutes: 20 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, windows-latest, macos-latest] | |
| python-version: [3.8, 3.9, '3.10', '3.11'] | |
| include: | |
| - os: ubuntu-latest | |
| path: ~/.cache/pip | |
| papermill_timeout: 120 | |
| # ccache requires absolute path | |
| path_ccache: /home/runner/cache/ccache | |
| - os: macos-latest | |
| path: ~/Library/Caches/pip | |
| papermill_timeout: 240 | |
| # ccache requires absolute path | |
| path_ccache: /Users/runner/Library/Caches/ccache | |
| - os: windows-latest | |
| path: ~\AppData\Local\pip\Cache | |
| papermill_timeout: 300 | |
| # FIXME: ccache is currently not available on Windows | |
| # path_ccache: ~\AppData\Local\ccache\Cache | |
| env: | |
| BOOST_VERSION: 1.76.0 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: actions/setup-python@v2 | |
| name: Install Python-${{ matrix.python-version }} | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| ################### | |
| # Caching stuff # | |
| ################### | |
| - name: Activating Python cache | |
| uses: actions/cache@v2 | |
| id: cache_python | |
| continue-on-error: true | |
| with: | |
| path: ${{ matrix.path }} | |
| key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('**/requirements.txt') }} | |
| - name: Cache boost ${{env.BOOST_VERSION}} | |
| # FIXME For an unknow reason on windows runner, when the cache is hit | |
| # The compilation fails because it doesn't find some headers | |
| # I don't know if the cache is corrupted, for the moment hard to debug | |
| if: ${{ runner.os == 'Linux' || runner.os == 'macOS' }} | |
| uses: actions/cache@v2 | |
| id: cache-boost | |
| with: | |
| # Set the default path as the path to cache | |
| path: ${{ github.workspace }}/boost/boost | |
| # Use the version as the key to only cache the correct version | |
| key: boost-${{env.BOOST_VERSION}} | |
| # FIXME: This is quite costly but at the moment I don't have an alternative | |
| - name: Install ccache for Linux and Mac | |
| if: ${{ runner.os == 'Linux' || runner.os == 'macOS' }} | |
| run: | | |
| if [ "$RUNNER_OS" == "Linux" ]; then | |
| sudo apt -y install ccache | |
| elif [ "$RUNNER_OS" == "macOS" ]; then | |
| brew install ccache | |
| fi | |
| shell: bash | |
| # Windows does not support ccache with visual studio compiler | |
| - name: ccache cache files | |
| if: ${{ runner.os != 'Windows' }} | |
| uses: actions/cache@v2 | |
| id: cache_ccache | |
| continue-on-error: true | |
| with: | |
| path: ${{ matrix.path_ccache }} | |
| # TODO: When updating c++ backend, use new date (yy-mm-dd) | |
| key: ${{ runner.os }}-ccache-${{ matrix.python-version }}-22-01-11 | |
| - name: Upgrade pip and setuptools | |
| run: | | |
| python -m pip install --upgrade pip setuptools | |
| - name: Install boost ${{env.BOOST_VERSION}} | |
| uses: MarkusJx/install-boost@v2.1.0 | |
| id: install-boost | |
| if: steps.cache-boost.outputs.cache-hit != 'true' | |
| with: | |
| boost_version: ${{env.BOOST_VERSION}} | |
| ###################### | |
| # Building package # | |
| ###################### | |
| - name: Build ${{ github.event.repository.name }} on Linux and MacOs | |
| if: ${{ runner.os != 'Windows' }} | |
| run: | | |
| echo $BOOST_ROOT | |
| python -m pip install -e ".[dev]" | |
| env: | |
| CC: "ccache gcc" | |
| CXX: "ccache g++" | |
| CCACHE_DIR: ${{ matrix.path_ccache }} | |
| CCACHE_COMPRESS: 1 | |
| CCACHE_MAXSIZE: 4G | |
| BOOST_ROOT: ${{ github.workspace }}/boost/boost | |
| # Windows does not support ccache with visual studio compiler | |
| - name: Build ${{ github.event.repository.name }} on Windows | |
| if: ${{ runner.os == 'Windows' }} | |
| run: | | |
| python -m pip install -e ".[dev]" | |
| env: | |
| BOOST_ROOT: ${{ steps.install-boost.outputs.BOOST_ROOT }} | |
| - name: Install test tools | |
| run: | | |
| python -m pip install pandas pytest pytest-cov pytest-benchmark hypothesis | |
| ############# | |
| # Testing # | |
| ############# | |
| - name: Test package with pytest on Linux and Windows | |
| if: ${{ runner.os == 'Linux' || runner.os == 'Windows' }} | |
| run: | | |
| pytest --pyargs gtda --no-cov | |
| - name: Test package with pytest Mac with coverage | |
| if: ${{ runner.os == 'macOS' }} | |
| run: | | |
| pytest gtda --cov --cov-report xml:coverage.xml | |
| # FIXME: It does not use config.cfg, I don't know why ... | |
| - name: flake8 Lint on MacOS | |
| if: ${{ runner.os == 'macOS' }} | |
| uses: py-actions/flake8@v2 | |
| with: | |
| exclude: "boost,gtda/externals,doc,examples" | |
| - name: Test jupyter notebooks with papermill | |
| if: ${{ github.event.inputs.testNotebooks == true }} | |
| run: | | |
| python -m pip install openml matplotlib | |
| python -m pip install papermill | |
| cd examples | |
| # Get all .ipynb notebook but discard the MNIST_classification | |
| # Because it is too long | |
| # This command also removes the .pynb extension | |
| FILES_WITHOUT_EXT=`find . ! -name '*MNIST_classification*' -iname '*.ipynb' -exec bash -c 'printf "%s\n" "${@%.*}"' _ {} +` | |
| PAPERMILL_DIR=papermill_results | |
| mkdir -p $PAPERMILL_DIR | |
| for FILENAME in $FILES_WITHOUT_EXT | |
| do | |
| SAVE_FILE=$PAPERMILL_DIR/$FILENAME.txt | |
| papermill --execution-timeout ${{ matrix.papermill_timeout }} $FILENAME.ipynb $SAVE_FILE | |
| done | |
| shell: bash | |
| ###################### | |
| # Upload Artifacts # | |
| ###################### | |
| - name: Upload coverage for Mac | |
| if: ${{ runner.os == 'macOS' }} | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: ${{ runner.os }}-coverage | |
| path: coverage.xml | |
| if-no-files-found: warn | |