linux-build.yml

name: Linux CI
on: [push, pull_request]

concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

jobs:
  build-linux:
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        # Fully declare each matrix entry here, as otherwise it's possible
        # to get unexpected results due to the way the entries get expanded
        # (See https://magmanu.github.io/blog/tech/matrices-github-actions/)
        include:
          # x86-64, clang, configure
          - os: ubuntu-latest
            use-configure: use-configure
            htssrc: hidden-htslib
            compiler: clang
            sanitize: no-sanitize

          # x86-64, gcc, configure, sanitize
          - os: ubuntu-latest
            use-configure: use-configure
            htssrc: hidden-htslib
            compiler: gcc
            sanitize: sanitize

          # x86-64, gcc, no configure, run extra checks
          - os: ubuntu-latest
            use-configure: no-configure
            htssrc: htslib
            compiler: gcc
            sanitize: no-sanitize

          # arm, gcc, configure
          - os: ubuntu-24.04-arm
            use-configure: use-configure
            htssrc: hidden-htslib
            compiler: gcc
            sanitize: no-sanitize

    defaults:
      run:
        working-directory: ./bcftools

    steps:
    - name: Checkout
      # This is actions/checkout@v6.0.2
      uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
      with:
        persist-credentials: false
        path: bcftools

    - name: Run apt
      working-directory: .
      run: |
        sudo apt-get update
        sudo apt-get install -y --no-install-suggests --no-install-recommends autoconf automake make ${{ matrix.compiler }} perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev libdeflate-dev libperl-dev libgsl0-dev libio-pty-perl

    - name: Clone htslib
      working-directory: .
      run: |
        mkdir -p ${{ matrix.htssrc }}
        htslib_pr=`git log -2 --format='%s' | sed -n 's/.*htslib#\([0-9]*\).*/\1/p'`
        ./bcftools/.ci_helpers/clone ${GITHUB_REPOSITORY_OWNER} htslib ${{ matrix.htssrc }} ${GITHUB_HEAD_REF:-$GITHUB_REF_NAME} $htslib_pr

    - name: Set build options
      run: |
        cc='clang'
        configure_opts='--enable-werror --enable-perl-filters --enable-libgsl'
        cflags='-g -O3'
        ldflags=''

        if [ '${{ matrix.sanitize }}' = 'sanitize' ] ; then
          cflags="-g -Og -fsanitize=address,undefined -Wno-format-truncation -Wno-format-overflow -DHTS_ALLOW_UNALIGNED=0"
          ldflags='-fsanitize=address,undefined'
        fi

        echo "cc=${cc}" >> "$GITHUB_ENV"
        echo "configure_opts=${configure_opts}" >> "$GITHUB_ENV"
        echo "cflags=${cflags}" >> "$GITHUB_ENV"
        echo "ldflags=${ldflags}" >> "$GITHUB_ENV"

    - name: Build htslib
      working-directory: ${{ matrix.htssrc }}
      run: |
        htsdir="`realpath ..`/installed-htslib"
        echo "htsdir=${htsdir}" >> "$GITHUB_ENV"

        autoreconf -i
        { ./configure --prefix="$htsdir" ${configure_opts} ${cc:+CC="$cc"} ${cflags:+CFLAGS="$cflags"} ${ldflags:+LDFLAGS="$ldflags"} ||
          { cat config.log ; false ; } ; } &&
        make -j 5 &&
        make install

    - name: Configure bcftools
      if: ${{ matrix.use-configure == 'use-configure' }}
      run: |
        autoreconf -i

        with_htslib="--with-htslib=$htsdir"
        ldflags="${ldflags:+$ldflags }-Wl,-rpath=${htsdir}/lib"

        printf "\nRunning ./configure ${with_htslib} ${configure_opts}${cc:+ CC='$cc'}${cflags:+ CFLAGS='$cflags'}${ldflags:+ LDFLAGS='$ldflags'} ...\n\n"

        { ./configure $with_htslib ${configure_opts} ${cc:+CC="$cc"} ${cflags:+CFLAGS="$cflags"} ${ldflags:+LDFLAGS="$ldflags"} &&
          { grep -qE 'CFLAGS *=.*-Werror' config.mk ||
            { printf "\nStopping as -Werror was not set.\n" 1>&2 ; false ; } ;
          } ;
        } || { printf "\n### config.log content follows...\n\n" 1>&2 ; cat config.log ; false ; }

    - name: Compile bcftools
      run: |
        if [ '${{ matrix.use-configure }}' = 'use-configure' ] ; then
          make -j5
        else
          make -j5 ${cc:+CC="$cc"} ${cflags:+CFLAGS="$cflags -Werror"}
        fi

    - name: Check
      run: |
        if [ '${{ matrix.use-configure }}' = 'use-configure' ] ; then
          make check BGZIP=$htsdir/bin/bgzip TABIX=$htsdir/bin/tabix
        else
          make check ${cc:+CC="$cc"} ${cflags:+CFLAGS="$cflags -Werror"}
        fi