[ENH] Fix patch sampling for discontiguous case #1180
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| name: "Build and unit tests" | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.type }} | |
| cancel-in-progress: true | |
| on: | |
| pull_request: | |
| paths: | |
| - "**" | |
| push: | |
| branches: [main] | |
| paths: | |
| - "**.py" | |
| tags: | |
| - "v*.*.*" | |
| workflow_dispatch: | |
| env: | |
| INSTALLDIR: "build-install" | |
| CCACHE_DIR: "${{ 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"] | |
| 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/setup-python@v5 | |
| 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@v4 | |
| 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 | |
| - 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 test | |
| - name: debug | |
| run: | | |
| ls $PWD/build-install/usr/lib/python${{matrix.python-version}}/site-packages/ | |
| echo "Okay..." | |
| ls $PWD/build | |
| ls ./ | |
| - name: Save build | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: sktree-build | |
| path: $PWD/build | |
| build_and_test_slow: | |
| name: Slow Meson build ${{ matrix.os }} - py${{ matrix.python-version }} | |
| timeout-minutes: 20 | |
| needs: [build_and_test] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-22.04] | |
| python-version: ["3.11"] | |
| 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/setup-python@v5 | |
| 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@v4 | |
| 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 | |
| uses: codecov/codecov-action@v4 | |
| 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@v4 | |
| with: | |
| name: sktree-build | |
| path: $PWD/build | |
| # 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/setup-python@v5 | |
| # 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 |