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Merge pull request #114 from jguhlin/minimappers2-update
minimappers2-update
2 parents 2fbf6d8 + 6229fdd commit ea69a01

16 files changed

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-3526
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‎.github/workflows/build-test-rust-minimappers2.yaml‎

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pull_request:
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branches: [ "main" ]
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paths:
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- 'minimappers2/src/'
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- 'minimappers2/Cargo.toml'
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- minimappers2/src/
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- minimappers2/Cargo.toml
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- minimappers2/**
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- .github/workflows/build-test-rust-minimappers2.yaml
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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env:
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RUSTFLAGS: -C debuginfo=0 # Do not produce debug symbols to keep memory usage down
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RUST_BACKTRACE: 1
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PYTHONUTF8: 1
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CARGO_TERM_COLOR: always
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defaults:
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run:
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working-directory: minimappers2
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shell: bash
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jobs:
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test:
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runs-on: ubuntu-latest
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test-python:
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest]
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python-version: ['3.9', '3.12', '3.13']
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: 'recursive'
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- run: cd minimappers2
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Create virtual environment
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env:
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BIN: ${{ matrix.os == 'windows-latest' && 'Scripts' || 'bin' }}
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run: |
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python -m venv .venv
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echo "$GITHUB_WORKSPACE/minimappers2/.venv/$BIN" >> $GITHUB_PATH
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echo "VIRTUAL_ENV=$GITHUB_WORKSPACE/minimappers2/.venv" >> $GITHUB_ENV
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- name: Set up Rust
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run: rustup show
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- name: Cache Rust
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uses: Swatinem/rust-cache@v2
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with:
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workspaces: minimappers2
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save-if: ${{ github.ref_name == 'main' }}
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- name: Install Python dependencies
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run: |
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pip install uv
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uv pip install maturin
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- name: Install minimappers2
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run: maturin develop
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- name: Build
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run: cargo build --verbose
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- name: Run tests
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run: cargo test --verbose
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build-manylinux-x64_64:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: 'recursive'
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- uses: actions/setup-python@v4
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with:
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python-version: '3.9'
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- name: Test build
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uses: messense/maturin-action@v1
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env:
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RUSTFLAGS: -C target-feature=+fxsr,+sse,+sse2,+sse3,+ssse3,+sse4.1,+sse4.2,+popcnt,+avx,+fma
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with:
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rust-toolchain: nightly-2025-01-08
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maturin-version: '1.8.0'
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command: build
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args: -m minimappers2/Cargo.toml
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run: cargo test --verbose

‎.github/workflows/create-python-release.yaml‎

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# Taken from Polar-rs github action
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name: Create Python release
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# This file is autogenerated by maturin v1.8.1
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# To update, run
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#
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# maturin generate-ci github
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#
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name: CI
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on:
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push:
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branches:
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- main
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- master
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tags:
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- py-*
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- '*'
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pull_request:
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workflow_dispatch:
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defaults:
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run:
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shell: bash
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permissions:
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contents: read
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jobs:
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manylinux-x64_64:
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runs-on: ubuntu-latest
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linux:
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runs-on: ${{ matrix.platform.runner }}
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strategy:
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matrix:
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platform:
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- runner: ubuntu-22.04
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target: x86_64
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- runner: ubuntu-22.04
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target: x86
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- runner: ubuntu-22.04
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target: aarch64
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- runner: ubuntu-22.04
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target: armv7
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- runner: ubuntu-22.04
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target: s390x
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- runner: ubuntu-22.04
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target: ppc64le
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: 'recursive'
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- run: cd minimappers2
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- uses: actions/setup-python@v5
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with:
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python-version: '3.7'
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- name: Publish wheel
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python-version: 3.x
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- name: Build wheels
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uses: PyO3/maturin-action@v1
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env:
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MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
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RUSTFLAGS: -C target-feature=+fxsr,+sse,+sse2,+sse3,+ssse3,+sse4.1,+sse4.2,+popcnt,+avx,+fma
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with:
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rust-toolchain: nightly-2024-02-04
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maturin-version: '1.6.0'
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command: publish
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args: -m minimappers2/Cargo.toml --skip-existing -o wheels -u jguhlin
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# Needed for Docker on Apple M1
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# manylinux-aarch64:
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# runs-on: ubuntu-latest
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# steps:
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# - uses: actions/checkout@v3
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# - uses: actions/setup-python@v4
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# with:
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# python-version: '3.7'
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#
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# - name: Publish wheel
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# uses: messense/maturin-action@v1
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# env:
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# MATURIN_PASSWORD: ${{ secrets.PYPI_PASS }}
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# with:
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# rust-toolchain: nightly-2023-01-19
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# target: aarch64-unknown-linux-gnu
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# maturin-version: '0.14.10'
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# command: publish
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# args: -m minimappers2/Cargo.toml --skip-existing -o wheels -u jguhlin
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target: ${{ matrix.platform.target }}
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args: --release --out dist
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sccache: 'true'
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manylinux: auto
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- name: Build free-threaded wheels
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uses: PyO3/maturin-action@v1
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with:
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target: ${{ matrix.platform.target }}
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args: --release --out dist -i python3.13t
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sccache: 'true'
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manylinux: auto
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- name: Upload wheels
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uses: actions/upload-artifact@v4
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with:
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name: wheels-linux-${{ matrix.platform.target }}
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path: dist
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# uncomment to build a universal2 wheel
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# we don't run it because it is twice as big and not needed because we build for both architectures separately
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# macos-aarch64-universal:
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# runs-on: macos-latest
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# steps:
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# - uses: actions/checkout@v3
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# - uses: actions/setup-python@v4
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# with:
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# python-version: '3.7'
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musllinux:
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runs-on: ${{ matrix.platform.runner }}
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strategy:
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matrix:
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platform:
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- runner: ubuntu-22.04
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target: x86_64
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- runner: ubuntu-22.04
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target: x86
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- runner: ubuntu-22.04
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target: aarch64
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- runner: ubuntu-22.04
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target: armv7
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steps:
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- uses: actions/checkout@v4
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- run: cd minimappers2
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- uses: actions/setup-python@v5
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with:
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python-version: 3.x
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- name: Build wheels
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uses: PyO3/maturin-action@v1
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with:
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target: ${{ matrix.platform.target }}
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args: --release --out dist
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sccache: 'true'
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manylinux: musllinux_1_2
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- name: Build free-threaded wheels
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uses: PyO3/maturin-action@v1
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with:
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target: ${{ matrix.platform.target }}
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args: --release --out dist -i python3.13t
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sccache: 'true'
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manylinux: musllinux_1_2
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- name: Upload wheels
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uses: actions/upload-artifact@v4
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with:
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name: wheels-musllinux-${{ matrix.platform.target }}
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path: dist
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# - name: Fix README symlink
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# run: |
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# rm py-polars/README.md
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# cp README.md py-polars/README.md
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# No support for minimap2 for windows
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# - name: Set up Rust
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# uses: dtolnay/rust-toolchain@master
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# with:
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# toolchain: nightly-2023-01-19
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macos:
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runs-on: ${{ matrix.platform.runner }}
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strategy:
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matrix:
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platform:
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- runner: macos-13
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target: x86_64
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- runner: macos-14
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target: aarch64
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steps:
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- uses: actions/checkout@v4
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- run: cd minimappers2
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- uses: actions/setup-python@v5
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with:
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python-version: 3.x
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- name: Build wheels
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uses: PyO3/maturin-action@v1
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with:
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target: ${{ matrix.platform.target }}
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args: --release --out dist
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sccache: 'true'
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- name: Build free-threaded wheels
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uses: PyO3/maturin-action@v1
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with:
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target: ${{ matrix.platform.target }}
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args: --release --out dist -i python3.13t
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sccache: 'true'
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- name: Upload wheels
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uses: actions/upload-artifact@v4
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with:
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name: wheels-macos-${{ matrix.platform.target }}
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path: dist
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# - name: Set up Rust targets
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# run: rustup target add aarch64-apple-darwin
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sdist:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- run: cd minimappers2
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- name: Build sdist
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uses: PyO3/maturin-action@v1
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with:
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command: sdist
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args: --out dist
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- name: Upload sdist
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uses: actions/upload-artifact@v4
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with:
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name: wheels-sdist
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path: dist
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# - name: Publish wheel
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# uses: messense/maturin-action@v1
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# env:
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# MATURIN_PASSWORD: ${{ secrets.PYPI_PASS }}
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# with:
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# maturin-version: '0.14.10'
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# command: publish
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# args: -m py-polars/Cargo.toml --no-sdist --universal2 -o wheels -i python -u ritchie46
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release:
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name: Release
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runs-on: ubuntu-latest
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if: ${{ startsWith(github.ref, 'refs/tags/py-') || github.event_name == 'workflow_dispatch' }}
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needs: [linux, musllinux, macos, sdist]
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permissions:
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# Use to sign the release artifacts
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id-token: write
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# Used to upload release artifacts
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contents: write
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# Used to generate artifact attestation
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attestations: write
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steps:
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- uses: actions/download-artifact@v4
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- run: cd minimappers2
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- name: Generate artifact attestation
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uses: actions/attest-build-provenance@v1
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with:
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subject-path: 'wheels-*/*'
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- name: Publish to PyPI
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if: ${{ startsWith(github.ref, 'refs/tags/') }}
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uses: PyO3/maturin-action@v1
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env:
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MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
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with:
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command: upload
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args: --non-interactive --skip-existing wheels-*/*

‎minimappers2/.gitattributes‎

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# GitHub syntax highlighting
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pixi.lock linguist-language=YAML linguist-generated=true

‎minimappers2/.gitignore‎

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# pixi environments
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.pixi
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*.egg-info

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