ci.yml

# This file was originally generated by maturin v0.14.17

name: CI3

on:
  push:
  schedule:
    - cron: '0 0 1 * *'
  pull_request:
  workflow_dispatch:
    
env:
  CARGO_TERM_COLOR: always

permissions:
  contents: read

jobs:

  test_rust:
    name: Test Rust
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
    runs-on: ${{ matrix.os }}
    steps:
      - name: Checkout
        uses: actions/checkout@v3
      - name: Set up Rust
        uses: actions-rs/toolchain@v1
        with:
          toolchain: 1.81
          override: true
      - name: Install Clippy (pinned version for this pinned version of Rust)
        run: rustup component add clippy
      - name: Run Clippy (strict for this pinned version of Rust)
        run: cargo clippy --all-targets --all-features -- -D warnings
      - name: Set up Rust (Latest Stable for Tests)
        uses: actions-rs/toolchain@v1
        with:
          toolchain: stable
          override: true
      - name: Install Clippy (Latest)
        run: rustup component add clippy
      - name: Run Clippy (lenient for latest version)
        run: cargo clippy --all-targets --all-features -- -A warnings || echo "Clippy warnings from the latest version"
      - name: Test Rust no-default-features
        run: cargo test --verbose --no-default-features
      - name: Test Rust default features
        run: cargo test --verbose
  
  
  macos:
    runs-on: macos-13
    strategy:
      matrix:
        target: [x86_64, aarch64]
    steps:
      - uses: actions/checkout@v3
      - uses: actions/setup-python@v4
        with:
          python-version: |
            3.10
            3.11
            3.12
            3.13
      - name: Build wheels
        uses: PyO3/maturin-action@v1
        with:
          target: ${{ matrix.target }}
          args: --release --out dist --find-interpreter
      - name: Upload wheels
        uses: actions/upload-artifact@v3
        with:
          name: wheels
          path: dist
          
  linux:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        target: [x86_64, aarch64]
    steps:
      - uses: actions/checkout@v3
      - uses: actions/setup-python@v4
        with:
          python-version: |
            3.10
            3.11
            3.12
            3.13

      - name: Install cross-compilation dependencies
        if: matrix.target == 'aarch64'
        run: |
          sudo apt-get update
          sudo apt-get install -y gcc-aarch64-linux-gnu
          
      - name: Build wheels for aarch64
        if: matrix.target == 'aarch64'
        env:
          CC: aarch64-linux-gnu-gcc
          CFLAGS: -march=armv8-a -D__ARM_ARCH=8
        uses: PyO3/maturin-action@v1
        with:
          target: ${{ matrix.target }}
          args: --release --out dist -i python3.10 -i python3.11 -i python3.12 -i python3.13
          manylinux: auto

      - name: Build wheels for x86_64
        if: matrix.target == 'x86_64'
        uses: PyO3/maturin-action@v1
        with:
          target: ${{ matrix.target }}
          args: --release --out dist -i -i python3.10 -i python3.11 -i python3.12 -i python3.13
          manylinux: auto

      - name: Upload wheels
        uses: actions/upload-artifact@v3
        with:
          name: wheels
          path: dist
          
  windows:
    runs-on: windows-latest
    strategy:
      matrix:
        target: [x64]
    steps:
      - uses: actions/checkout@v3
      - uses: actions/setup-python@v4
        with:
          python-version: |
            3.10
            3.11
            3.12
            3.13
          architecture: ${{ matrix.target }}
      - name: Build wheels
        uses: PyO3/maturin-action@v1
        with:
          target: ${{ matrix.target }}
          args: --release --out dist --find-interpreter
      - name: Upload wheels
        uses: actions/upload-artifact@v3
        with:
          name: wheels
          path: dist
        
  sdist:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - name: Build sdist
        uses: PyO3/maturin-action@v1
        with:
          command: sdist
          args: --out dist
      - name: Upload sdist
        uses: actions/upload-artifact@v3
        with:
          name: wheels
          path: dist

  test_python:
    name: Test Python
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.10", "3.11", "3.12", "3.13"]
        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
    runs-on: ${{ matrix.os }}
    steps:
    - name: Checkout
      uses: actions/checkout@v3
    - name: Install Rust
      uses: actions-rs/toolchain@v1
      with:
        toolchain: stable
        override: true
    - name: Install the latest version of uv
      uses: astral-sh/setup-uv@v3
    - name: Install Python ${{ matrix.python-version }}
      run: uv python install ${{ matrix.python-version }}
    - name: Setup, Lint, and Test Python (Linux/macOS)
      if: runner.os != 'Windows'
      run: |
        cd bed_reader
        uvx ruff@0.6.9 check .
        uvx ruff@latest check . || echo "Ignoring warnings from the latest version of ruff"
        uv sync --extra min_dev
        source ../.venv/bin/activate
        pytest tests/test_opt_dep.py
        uv sync --extra dev --extra sparse --extra samples
        source ../.venv/bin/activate
        pytest .
    - name: Setup, Lint, and Test Python (Windows)
      if: runner.os == 'Windows'
      run: |
        cd bed_reader
        uvx ruff@0.6.9 check .
        uvx ruff@latest check . || echo "Ignoring warnings from the latest version of ruff"
        uv sync --extra min_dev
        ../.venv/Scripts/activate
        pytest tests/test_opt_dep.py
        uv sync --extra dev --extra sparse --extra samples
        ../.venv/Scripts/activate
        pytest .