convert_genome 0.1.10

Convert DTC, VCF, or BCF genome files to VCF, BCF, or PLINK 1.9
Documentation
name: Build and Release

on:
  push:
    branches:
      - main
  workflow_dispatch:
    inputs:
      skip_tests:
        description: Skip test job
        type: boolean
        default: false

env:
  GNOMON_SKIP_LINT_CHECKS: "1"
  CARGO_TERM_COLOR: always
  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

permissions:
  contents: write

jobs:
  test:
    name: Run Tests
    if: ${{ github.event_name != 'workflow_dispatch' || !inputs.skip_tests }}
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Install Rust toolchain
        uses: dtolnay/rust-toolchain@nightly
        with:
          components: rustfmt, clippy

      - name: Cache dependencies
        uses: Swatinem/rust-cache@v2

      - name: Run tests
        run: cargo test --all-features

  build:
    name: Build ${{ matrix.target }}
    needs: test
    if: ${{ always() && (needs.test.result == 'success' || needs.test.result == 'skipped') }}
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        include:
          # MacOS ARM (Apple Silicon) - GH Actions uses M1
          - os: macos-14
            target: aarch64-apple-darwin
            artifact_name: convert_genome
            asset_name: convert_genome-macos-arm64
            cpu: apple-m1

          # MacOS Intel - use macos-15-intel which runs on Intel hardware
          - os: macos-15-intel
            target: x86_64-apple-darwin
            artifact_name: convert_genome
            asset_name: convert_genome-macos-intel
            cpu: x86-64-v3

          # Linux x86_64 (ubuntu-22.04 for wider glibc compatibility)
          - os: ubuntu-22.04
            target: x86_64-unknown-linux-gnu
            artifact_name: convert_genome
            asset_name: convert_genome-linux-x64
            cpu: x86-64-v3

          # Linux ARM64
          - os: ubuntu-22.04-arm
            target: aarch64-unknown-linux-gnu
            artifact_name: convert_genome
            asset_name: convert_genome-linux-arm64
            cpu: neoverse-n1

          # Windows x86_64
          - os: windows-latest
            target: x86_64-pc-windows-msvc
            artifact_name: convert_genome.exe
            asset_name: convert_genome-windows-x64
            cpu: x86-64-v3

          # Windows ARM64 (native ARM runner)
          - os: windows-11-arm
            target: aarch64-pc-windows-msvc
            artifact_name: convert_genome.exe
            asset_name: convert_genome-windows-arm64
            cpu: cortex-a76

    steps:
      - uses: actions/checkout@v4

      - name: Install Rust toolchain
        uses: dtolnay/rust-toolchain@nightly
        with:
          targets: ${{ matrix.target }}

      - name: Cache dependencies
        uses: Swatinem/rust-cache@v2
        with:
          key: ${{ matrix.target }}

      - name: Remove local cargo config
        shell: bash
        run: rm -f .cargo/config.toml

      - name: Build
        shell: bash
        env:
          GNOMON_SKIP_LINT_CHECKS: "1"
          RUSTFLAGS: "-C target-cpu=${{ matrix.cpu }}"
        run: cargo build --release --target ${{ matrix.target }}

      - name: Package (Unix)
        if: runner.os != 'Windows'
        shell: bash
        run: |
          cp target/${{ matrix.target }}/release/${{ matrix.artifact_name }} ${{ matrix.asset_name }}
          tar -czf ${{ matrix.asset_name }}.tar.gz ${{ matrix.asset_name }}

      - name: Package (Windows)
        if: runner.os == 'Windows'
        shell: pwsh
        run: |
          Copy-Item target/${{ matrix.target }}/release/${{ matrix.artifact_name }} -Destination ${{ matrix.asset_name }}.exe
          Compress-Archive -Path ${{ matrix.asset_name }}.exe -DestinationPath ${{ matrix.asset_name }}.zip

      - name: Upload Artifact
        uses: actions/upload-artifact@v4
        with:
          name: ${{ matrix.asset_name }}
          path: |
            ${{ matrix.asset_name }}.tar.gz
            ${{ matrix.asset_name }}.zip
          if-no-files-found: error

  release:
    name: Create Release
    needs: build
    runs-on: ubuntu-latest
    permissions:
      contents: write
    steps:
      - uses: actions/checkout@v4

      - name: Download artifacts
        uses: actions/download-artifact@v4
        with:
          path: artifacts

      - name: Display structure of downloaded files
        run: ls -R artifacts

      - name: Generate release tag
        id: tag
        run: echo "release_tag=v$(grep '^version' Cargo.toml | head -1 | sed 's/.*"\(.*\)"/\1/')-$(date +'%Y%m%d-%H%M%S')" >> $GITHUB_OUTPUT

      - name: Create Release
        uses: softprops/action-gh-release@v2
        with:
          tag_name: ${{ steps.tag.outputs.release_tag }}
          name: Release ${{ steps.tag.outputs.release_tag }}
          files: artifacts/**/*