[ENH] add PermutationForests and FeatureImportanceForests to sktree #706
Workflow file for this run
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: "Build and unit tests" | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.type }} | |
| cancel-in-progress: true | |
| on: | |
| pull_request: | |
| paths: | |
| - "**" | |
| # - "**.py" | |
| # - "**.pxd" | |
| # - "**.pyx" | |
| push: | |
| branches: [main] | |
| paths: | |
| - "**.py" | |
| tags: | |
| - "v*.*.*" | |
| workflow_dispatch: | |
| env: | |
| INSTALLDIR: "build-install" | |
| CCACHE_DIR: "${{ github.workspace }}/.ccache" | |
| jobs: | |
| build_and_test: | |
| name: Meson build ${{ matrix.os }} - py${{ matrix.python-version }} | |
| timeout-minutes: 20 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-22.04, macos-latest] | |
| python-version: [3.9, "3.10", "3.11"] | |
| poetry-version: [1.5.0] | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash | |
| env: | |
| # to make sure coverage/test command builds cleanly | |
| FORCE_SUBMODULE: True | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/[email protected] | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| architecture: "x64" | |
| cache: "pip" | |
| cache-dependency-path: "requirements.txt" | |
| - name: show-gcc | |
| run: | | |
| gcc --version | |
| - name: Install Ccache for MacOSX | |
| if: ${{ matrix.os == 'macos-latest'}} | |
| run: | | |
| brew install ccache | |
| - name: Install packages for Ubuntu | |
| if: ${{ matrix.os == 'ubuntu-22.04'}} | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libopenblas-dev libatlas-base-dev liblapack-dev gfortran libgmp-dev libmpfr-dev libsuitesparse-dev ccache libmpc-dev | |
| - name: Install Python packages | |
| run: | | |
| python -m pip install -r build_requirements.txt | |
| python -m pip install spin | |
| python -m pip install -r test_requirements.txt | |
| - name: Prepare compiler cache | |
| id: prep-ccache | |
| shell: bash | |
| run: | | |
| mkdir -p "${CCACHE_DIR}" | |
| echo "dir=$CCACHE_DIR" >> $GITHUB_OUTPUT | |
| NOW=$(date -u +"%F-%T") | |
| echo "timestamp=${NOW}" >> $GITHUB_OUTPUT | |
| - name: Setup compiler cache | |
| uses: actions/cache@v3 | |
| id: cache-ccachev1 | |
| # Reference: https://docs.github.com/en/actions/guides/caching-dependencies-to-speed-up-workflows#matching-a-cache-key | |
| # NOTE: The caching strategy is modeled in a way that it will always have a unique cache key for each workflow run | |
| # (even if the same workflow is run multiple times). The restore keys are not unique and for a partial match, they will | |
| # return the most recently created cache entry, according to the GitHub Action Docs. | |
| with: | |
| path: ${{ steps.prep-ccache.outputs.dir }} | |
| # Restores ccache from either a previous build on this branch or on main | |
| key: ${{ github.workflow }}-${{ matrix.python-version }}-ccache-linux-${{ steps.prep-ccache.outputs.timestamp }} | |
| # This evaluates to `Linux Tests-3.9-ccache-linux-` which is not unique. As the CI matrix is expanded, this will | |
| # need to be updated to be unique so that the cache is not restored from a different job altogether. | |
| restore-keys: | | |
| ${{ github.workflow }}-${{ matrix.python-version }}-ccache-linux- | |
| - name: Setup build and install scikit-tree | |
| run: | | |
| ./spin build -j 2 --forcesubmodule | |
| - name: Ccache performance | |
| shell: bash -l {0} | |
| run: ccache -s | |
| - name: build-path | |
| run: | | |
| echo "$PWD/build-install/" | |
| export INSTALLED_PATH=$PWD/build-install/usr/lib/python${{matrix.python-version}}/site-packages | |
| - name: Run unit tests and coverage | |
| run: | | |
| ./spin --help | |
| ./spin coverage --help | |
| ./spin test --help | |
| ./spin coverage | |
| cp $PWD/build-install/usr/lib/python${{matrix.python-version}}/site-packages/coverage.xml ./coverage.xml | |
| - name: debug | |
| run: | | |
| ls $PWD/build-install/usr/lib/python${{matrix.python-version}}/site-packages/ | |
| echo "Okay..." | |
| ls $PWD/build | |
| ls ./ | |
| - name: Upload coverage stats to codecov | |
| if: ${{ matrix.os == 'ubuntu-22.04' && matrix.python-version == '3.10'}} | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| # python spin goes into the INSTALLED path in order to run pytest | |
| files: ./coverage.xml | |
| fail_ci_if_error: true | |
| verbose: true | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| - name: Save build | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: sktree-build | |
| path: $PWD/build | |
| # release is ran when a release is made on Github | |
| release: | |
| name: Release | |
| runs-on: ubuntu-latest | |
| needs: [build_and_test] | |
| if: startsWith(github.ref, 'refs/tags/') | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/[email protected] | |
| with: | |
| python-version: 3.9 | |
| architecture: "x64" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --progress-bar off --upgrade pip setuptools wheel | |
| python -m pip install --progress-bar off build twine | |
| - name: Prepare environment | |
| run: | | |
| echo "RELEASE_VERSION=${GITHUB_REF#refs/tags/v}" >> $GITHUB_ENV | |
| echo "TAG=${GITHUB_REF#refs/tags/}" >> $GITHUB_ENV | |
| - name: Download package distribution files | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: package | |
| path: dist | |
| # TODO: refactor scripts to generate release notes from `whats_new.rst` file instead | |
| # - name: Generate release notes | |
| # run: | | |
| # python scripts/release_notes.py > ${{ github.workspace }}-RELEASE_NOTES.md | |
| - name: Publish package to PyPI | |
| run: | | |
| twine upload -u ${{ secrets.PYPI_USERNAME }} -p ${{ secrets.PYPI_PASSWORD }} dist/* | |
| - name: Publish GitHub release | |
| uses: softprops/action-gh-release@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| # body_path: ${{ github.workspace }}-RELEASE_NOTES.md | |
| prerelease: ${{ contains(env.TAG, 'rc') }} | |
| files: | | |
| dist/* | |
| # build-windows: | |
| # name: Meson build Windows | |
| # runs-on: windows-2019 | |
| # steps: | |
| # - name: Checkout | |
| # uses: actions/checkout@v4 | |
| # with: | |
| # submodules: recursive | |
| # - name: Setup Python | |
| # uses: actions/[email protected] | |
| # with: | |
| # python-version: "3.10" | |
| # architecture: "x64" | |
| # cache: "pip" | |
| # cache-dependency-path: "requirements.txt" | |
| # - name: install-rtools | |
| # run: | | |
| # choco install rtools -y --no-progress --force --version=4.0.0.20220206 | |
| # echo "c:\rtools40\ucrt64\bin;" >> $env:GITHUB_PATH | |
| # - name: show-gcc | |
| # run: | | |
| # gcc --version | |
| # - name: Install system dependencies | |
| # run: | | |
| # # Download and install Miniconda | |
| # Invoke-WebRequest -Uri https://repo.anaconda.com/miniconda/Miniconda3-latest-Windows-x86_64.exe -OutFile miniconda.exe | |
| # Start-Process -Wait -FilePath miniconda.exe -ArgumentList '/S', '/AddToPath=1' | |
| # # Add Miniconda to the PATH | |
| # $env:Path += ";C:\Users\runneradmin\Miniconda3\Scripts;C:\Users\runneradmin\Miniconda3" | |
| # # Update conda | |
| # conda update -y conda | |
| # # Add conda-forge channel and install openblas | |
| # conda config --add channels conda-forge | |
| # conda install -y openblas | |
| # - name: pip-packages | |
| # run: | | |
| # pip install -r build_requirements.txt | |
| # pip install -r test_requirements.txt | |
| # pip install spin | |
| # pip install numpy==1.22.4 | |
| # # - name: Download cibw_before_build_win.sh for openblas-libs | |
| # # shell: bash | |
| # # run: | | |
| # # # mkdir tools | |
| # # # mkdir tools/wheels | |
| # # # curl -L https://raw.githubusercontent.com/scipy/scipy/main/tools/wheels/cibw_before_build_win.sh -o cibw_before_build_win.sh | |
| # # # curl -L https://raw.githubusercontent.com/scipy/scipy/main/tools/openblas_support.py -o tools/openblas_support.py | |
| # # # curl -L https://raw.githubusercontent.com/scipy/scipy/main/tools/wheels/LICENSE_win32.txt -o tools/wheels/LICENSE_win32.txt | |
| # # - name: Run cibw_before_build_win.sh for openblas-libs | |
| # # shell: bash | |
| # # run: | | |
| # # set -xe | |
| # # ls | |
| # # bash ./tools/setup_windows.sh | |
| # # - name: Set PKG_CONFIG_PATH for openblas-libs | |
| # # run: echo "PKG_CONFIG_PATH=c:\opt\64\lib\pkgconfig;" >> $GITHUB_ENV | |
| # # - name: Install system dependencies like openblas | |
| # # run: | | |
| # # choco install openblas -y | |
| # - name: Build | |
| # run: | | |
| # echo "SCIPY_USE_PROPACK=1" >> $env:GITHUB_ENV | |
| # echo "FORCE_SUBMODULE=True" >> $env:GITHUB_ENV | |
| # python spin setup_submodule --forcesubmodule | |
| # python spin build -j 2 | |
| # # Necessary because GitHub Actions checks out the repo to D:\ while OpenBLAS | |
| # # got installed to C:\ higher up. The copying with `--win-cp-openblas` fails | |
| # # when things are split over drives. | |
| # # cp C:\opt\64\bin\*.dll $pwd\build-install\Lib\site-packages\scikit-tree\.libs\ | |
| # # python tools\openblas_support.py --write-init $PWD\build-install\Lib\site-packages\scikit-tree\ | |
| # - name: test | |
| # run: | | |
| # python spin test | |