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NatoozNatooz
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fixing cpp names camelCase + adding wheel actions
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‎.github/workflows/publish_pypi.yml

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name: Build wheel
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on:
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workflow_dispatch:
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release:
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types:
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- published
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permissions:
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contents: read
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jobs:
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build_wheels:
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name: Build wheel for ${{ matrix.python }}-${{ matrix.buildplat[1] }}
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runs-on: ${{ matrix.buildplat[0] }}
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strategy:
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matrix:
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# From wheel.yml of numpy (https://github.com/numpy/numpy/blob/main/.github/workflows/wheels.yml):
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# Github Actions doesn't support pairing matrix values together, let's improvise
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# https://github.com/github/feedback/discussions/7835#discussioncomment-1769026
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buildplat:
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- [ubuntu-22.04, manylinux_x86_64]
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- [ubuntu-22.04, musllinux_x86_64]
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- [ubuntu-22.04, manylinux_aarch64]
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- [ubuntu-22.04, musllinux_aarch64]
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- [macos-12, macosx_x86_64]
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- [macos-12, macosx_arm64]
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- [windows-2022, win_amd64]
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- [windows-2022, win32]
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python: ["cp38", "cp39", "cp310", "cp311", "cp312", "pp39"]
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exclude:
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- buildplat: [windows-2022, win32]
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python: "pp39"
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- buildplat: [ ubuntu-22.04, musllinux_x86_64 ]
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python: "pp39"
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- buildplat: [ ubuntu-22.04, musllinux_aarch64 ]
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python: "pp39"
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- buildplat: [macos-12, macosx_arm64]
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python: "pp39"
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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with:
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submodules: recursive
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- name: Set up QEMU
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if: ${{ contains(matrix.buildplat[1], 'linux_aarch64') }}
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uses: docker/setup-qemu-action@v3
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with:
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platforms: all
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- name: Setup MSVC (32-bit)
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if: ${{ matrix.buildplat[1] == 'win32' }}
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uses: bus1/cabuild/action/msdevshell@e22aba57d6e74891d059d66501b6b5aed8123c4d # v1
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with:
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architecture: 'x86'
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- name: Build wheels for manylinux x86_64
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if: ${{ matrix.buildplat[1] == 'manylinux_x86_64' }}
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uses: pypa/cibuildwheel@ce3fb7832089eb3e723a0a99cab7f3eaccf074fd # v2.16.5
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env:
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CIBW_PRERELEASE_PYTHONS: True
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CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
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CIBW_MANYLINUX_X86_64_IMAGE: quay.io/pypa/manylinux_2_28_x86_64
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CIBW_ARCHS: 'all'
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- name: Build wheels for manylinux aarch64
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if: ${{ matrix.buildplat[1] == 'manylinux_aarch64' }}
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uses: pypa/cibuildwheel@ce3fb7832089eb3e723a0a99cab7f3eaccf074fd # v2.16.5
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env:
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CIBW_PRERELEASE_PYTHONS: True
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CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
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CIBW_MANYLINUX_AARCH64_IMAGE: quay.io/pypa/manylinux_2_28_aarch64
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CIBW_ARCHS: 'all'
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- name: Build wheels for musllinux x86_64
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if: ${{ matrix.buildplat[1] == 'musllinux_x86_64' }}
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uses: pypa/cibuildwheel@ce3fb7832089eb3e723a0a99cab7f3eaccf074fd # v2.16.5
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env:
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CIBW_PRERELEASE_PYTHONS: True
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CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
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CIBW_MUSLLINUX_X86_64_IMAGE: quay.io/pypa/musllinux_1_2_x86_64
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CIBW_ARCHS: 'all'
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- name: Build wheels for musllinux aarch64
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if: ${{ matrix.buildplat[1] == 'musllinux_aarch64' }}
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uses: pypa/cibuildwheel@ce3fb7832089eb3e723a0a99cab7f3eaccf074fd # v2.16.5
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env:
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CIBW_PRERELEASE_PYTHONS: True
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CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
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CIBW_MUSLLINUX_AARCH64_IMAGE: quay.io/pypa/musllinux_1_2_aarch64
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CIBW_ARCHS: 'all'
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- name: Build wheels
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if: ${{ !contains(matrix.buildplat[1], 'linux') }}
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uses: pypa/cibuildwheel@ce3fb7832089eb3e723a0a99cab7f3eaccf074fd # v2.16.5
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env:
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CIBW_PRERELEASE_PYTHONS: True
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CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
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CIBW_ARCHS: 'all'
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- uses: actions/upload-artifact@v3
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with:
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path: ./wheelhouse/*.whl
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build_sdist:
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name: Build source distribution
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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with:
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submodules: recursive
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- name: Build sdist
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run: pipx run build --sdist
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- uses: actions/upload-artifact@v3
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with:
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path: dist/*.tar.gz
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upload_pypi:
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needs: [build_wheels, build_sdist]
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runs-on: ubuntu-latest
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environment:
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name: pypi
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url: https://pypi.org/p/lcsvec
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permissions:
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id-token: write
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steps:
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- uses: actions/download-artifact@v3
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with:
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# unpacks default artifact into dist/
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# if `name: artifact` is omitted, the action will create extra parent dir
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name: artifact
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path: dist
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- uses: pypa/gh-action-pypi-publish@release/v1
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#with:
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# To test: repository-url: https://test.pypi.org/legacy/

‎.github/workflows/test_wheel.yml

+120
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name: Test build wheel
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on:
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workflow_dispatch:
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push:
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branches: [ main ]
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pull_request:
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branches: [ main ]
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jobs:
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build_wheels:
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name: Build wheel for ${{ matrix.python }}-${{ matrix.buildplat[1] }}
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runs-on: ${{ matrix.buildplat[0] }}
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strategy:
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matrix:
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# From wheel.yml of numpy (https://github.com/numpy/numpy/blob/main/.github/workflows/wheels.yml):
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# Github Actions doesn't support pairing matrix values together, let's improvise
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# https://github.com/github/feedback/discussions/7835#discussioncomment-1769026
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buildplat:
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- [ubuntu-22.04, manylinux_x86_64]
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- [ubuntu-22.04, musllinux_x86_64]
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- [ubuntu-22.04, manylinux_aarch64]
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- [ubuntu-22.04, musllinux_aarch64]
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- [macos-12, macosx_x86_64]
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- [macos-12, macosx_arm64]
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- [windows-2022, win_amd64]
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- [windows-2022, win32]
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python: ["cp38", "cp39", "cp310", "cp311", "cp312", "pp39"]
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exclude:
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- buildplat: [windows-2022, win32]
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python: "pp39"
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- buildplat: [ ubuntu-22.04, musllinux_x86_64 ]
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python: "pp39"
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- buildplat: [ ubuntu-22.04, musllinux_aarch64 ]
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python: "pp39"
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- buildplat: [macos-12, macosx_arm64]
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python: "pp39"
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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with:
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submodules: recursive
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- name: Set up QEMU
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if: ${{ contains(matrix.buildplat[1], 'linux_aarch64') }}
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uses: docker/setup-qemu-action@v3
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with:
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platforms: all
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- name: Setup MSVC (32-bit)
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if: ${{ matrix.buildplat[1] == 'win32' }}
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uses: bus1/cabuild/action/msdevshell@e22aba57d6e74891d059d66501b6b5aed8123c4d # v1
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with:
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architecture: 'x86'
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- name: Build wheels for manylinux x86_64
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if: ${{ matrix.buildplat[1] == 'manylinux_x86_64' }}
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uses: pypa/cibuildwheel@ce3fb7832089eb3e723a0a99cab7f3eaccf074fd # v2.16.5
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env:
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CIBW_PRERELEASE_PYTHONS: True
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CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
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CIBW_MANYLINUX_X86_64_IMAGE: quay.io/pypa/manylinux_2_28_x86_64
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CIBW_ARCHS: 'all'
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- name: Build wheels for manylinux aarch64
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if: ${{ matrix.buildplat[1] == 'manylinux_aarch64' }}
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uses: pypa/cibuildwheel@ce3fb7832089eb3e723a0a99cab7f3eaccf074fd # v2.16.5
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env:
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CIBW_PRERELEASE_PYTHONS: True
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CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
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CIBW_MANYLINUX_AARCH64_IMAGE: quay.io/pypa/manylinux_2_28_aarch64
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CIBW_ARCHS: 'all'
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- name: Build wheels for musllinux x86_64
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if: ${{ matrix.buildplat[1] == 'musllinux_x86_64' }}
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uses: pypa/cibuildwheel@ce3fb7832089eb3e723a0a99cab7f3eaccf074fd # v2.16.5
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env:
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CIBW_PRERELEASE_PYTHONS: True
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CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
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CIBW_MUSLLINUX_X86_64_IMAGE: quay.io/pypa/musllinux_1_2_x86_64
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CIBW_ARCHS: 'all'
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- name: Build wheels for musllinux aarch64
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if: ${{ matrix.buildplat[1] == 'musllinux_aarch64' }}
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uses: pypa/cibuildwheel@ce3fb7832089eb3e723a0a99cab7f3eaccf074fd # v2.16.5
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env:
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CIBW_PRERELEASE_PYTHONS: True
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CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
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CIBW_MUSLLINUX_AARCH64_IMAGE: quay.io/pypa/musllinux_1_2_aarch64
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CIBW_ARCHS: 'all'
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- name: Build wheels
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if: ${{ !contains(matrix.buildplat[1], 'linux') }}
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uses: pypa/cibuildwheel@ce3fb7832089eb3e723a0a99cab7f3eaccf074fd # v2.16.5
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env:
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CIBW_PRERELEASE_PYTHONS: True
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CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
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CIBW_ARCHS: 'all'
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- uses: actions/upload-artifact@v4
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with:
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name: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
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path: ./wheelhouse/*.whl
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build_sdist:
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name: Build source distribution
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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with:
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submodules: recursive
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- name: Build sdist
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run: pipx run build --sdist
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- uses: actions/upload-artifact@v3
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with:
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path: dist/*.tar.gz

‎README.md

+3-2
Original file line numberDiff line numberDiff line change
@@ -21,7 +21,7 @@ You can install the package with pip: `pip install lcsvec`.
2121
Here we will use numpy, the usage for other deep learning libraries is the same.
2222

2323
```Python
24-
from lcsvec import lcs, lcs_length, lccs_length
24+
from lcsvec import lccs, lccs_length, lcs, lcs_length
2525
import numpy as np
2626

2727
seq1 = np.arange(0, 12)
@@ -30,7 +30,8 @@ seq2 = np.array([8, 0, 1, 2, 8, 2, 3, 4, 5, 6], dtype=np.int64)
3030
lcs_ = lcs(seq1, seq2) # [0, 1, 2, 3, 4, 5, 6]
3131
lcs_len = lcs_length(seq1, seq2) # 7, more efficient than calling len(lcs(seq1, seq2))
3232

33-
lccs_len = lccs_length(seq1, seq2) # 5, [2, 3, 4, 5, 6]
33+
lccs = lccs(seq1, seq2) # [2, 3, 4, 5, 6]
34+
lccs_len = lccs_length(seq1, seq2) # 5, more efficient than calling len(lccs(seq1, seq2))
3435
```
3536

3637
## TODOs

‎src/cpu/lccs_cpu_dyn.cpp

+9-9
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@ using namespace nb::literals;
77

88

99
// Returns the length of the longest common subsequence and the idx of its end in s1
10-
std::vector<int> lccs_length_idx(
10+
std::vector<int> lccsLengthIdx(
1111
const nb::ndarray<double, nb::ndim<1>>& s1,
1212
const nb::ndarray<double, nb::ndim<1>>& s2
1313
) {
@@ -33,18 +33,18 @@ std::vector<int> lccs_length_idx(
3333
}
3434
}
3535
}
36-
std::vector<int> lccs_len_idx = {max_length, imax};
37-
return lccs_len_idx;
36+
std::vector<int> lccsLenIdx = {max_length, imax};
37+
return lccsLenIdx;
3838
}
3939

4040

4141
// Calculating the length of the longest common contiguous subsequence with dynamic programming
42-
int lccs_length(
42+
int lccsLength(
4343
const nb::ndarray<double, nb::ndim<1>>& s1,
4444
const nb::ndarray<double, nb::ndim<1>>& s2
4545
) {
46-
std::vector<int> lccs_len_idx = lccs_length_idx(s1, s2);
47-
return lccs_len_idx[0];
46+
std::vector<int> lccsLenIdx = lccsLengthIdx(s1, s2);
47+
return lccsLenIdx[0];
4848
}
4949

5050

@@ -53,12 +53,12 @@ std::vector<int> lccs(
5353
const nb::ndarray<double, nb::ndim<1>>& s1,
5454
const nb::ndarray<double, nb::ndim<1>>& s2
5555
) {
56-
std::vector<int> lccs_len_idx = lccs_length_idx(s1, s2);
56+
std::vector<int> lccsLenIdx = lccsLengthIdx(s1, s2);
5757

5858
// Extract the longest common substring from s1
59-
std::vector<int> longestSubseq(lccs_len_idx[0]);
59+
std::vector<int> longestSubseq(lccsLenIdx[0]);
6060
int idx = 0;
61-
for (int i = lccs_len_idx[1] - lccs_len_idx[0] + 1; i <= lccs_len_idx[1]; ++i)
61+
for (int i = lccsLenIdx[1] - lccsLenIdx[0] + 1; i <= lccsLenIdx[1]; ++i)
6262
longestSubseq[idx++] = s1(i);
6363

6464
return longestSubseq;

‎src/lcs.cpp

+1-1
Original file line numberDiff line numberDiff line change
@@ -15,6 +15,6 @@ NB_MODULE(lcsvec_ext, m) {
1515

1616
m.def("lccs", &lccs, "seq1"_a, "seq2"_a,
1717
"Returns the longest common contiguous subsequence (lccs) from `seq1` and `seq2`.");
18-
m.def("lccs_length", &lccs_length, "seq1"_a, "seq2"_a,
18+
m.def("lccs_length", &lccsLength, "seq1"_a, "seq2"_a,
1919
"Returns the length of the longest common contiguous subsequence (lccs) from `seq1` and `seq2`.");
2020
}

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