build.yml

# copied from Daniel Cook's Seq collection
name: Build

on:
  push:
    branches:
      - master
      - dev
  pull_request:
    branches:
      - master
      - dev

jobs:
  build:
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-22.04, macos-14]
        version:
          - 1.6.18
          - 2.0.2

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: true
          fetch-depth: 0

      # Caching
      - name: Cache choosenim
        id: cache-choosenim
        uses: actions/cache@v4
        with:
          path: ~/.choosenim
          key: ${{ runner.os }}-choosenim-stable

      - name: Cache nimble
        id: cache-nimble
        uses: actions/cache@v4
        with:
          path: ~/.nimble
          key: ${{ runner.os }}-nimble-stable

      - name: Cache htslib
        id: cache-htslib
        uses: actions/cache@v4
        with:
          path: $HOME/htslib
          key: ${{ runner.os }}-htslib-1.10

      # Install Dependencies
      - name: Install dependencies (Linux)
        if: runner.os == 'Linux'
        run: |
          sudo apt-get update
          sudo apt-get -qy install bwa make build-essential cmake libncurses-dev ncurses-dev libbz2-dev lzma-dev liblzma-dev \
               curl libssl-dev libtool autoconf automake libcurl4-openssl-dev zlib1g-dev

      # Setup htslib
      - name: Install htslib (linux)
        if: runner.os == 'Linux'
        run: |
          cd
          git clone -b 1.22.1 --recursive https://github.com/samtools/htslib.git
          cd htslib && autoheader && autoconf && autoreconf -i && ./configure --enable-libcurl
          sudo make -j 4 install
          sudo ldconfig
          #echo "::set-env name=LD_LIBRARY_PATH::${LD_LIBRARY_PATH}:${HOME}/htslib"
          #ls -lh $HOME/htslib/*.so

      - name: Install hstlib (macos)
        if: runner.os == 'macOS'
        run: |
          brew install htslib

      - name: Set DYLD_LIBRARY_PATH
        if: runner.os == 'macOS'
        run: |
          echo "DYLD_LIBRARY_PATH=$(brew --prefix htslib)/lib" >> $GITHUB_ENV
          echo "DYLD_INCLUDE_PATH=$(brew --prefix htslib)/include" >> $GITHUB_ENV
          echo "LIBRARY_PATH=$(brew --prefix htslib)/lib" >> $GITHUB_ENV
          echo "CPATH=$(brew --prefix htslib)/include" >> $GITHUB_ENV

      - name: Set DYLD_LIBRARY_PATH (Linux)
        if: runner.os == 'Linux'
        run: |
          echo "DYLD_LIBRARY_PATH=/usr/local/lib" >> $GITHUB_ENV
          echo "DYLD_INCLUDE_PATH=/usr/local/include" >> $GITHUB_ENV

      - name: Make libhts discoverable for tests
        run: |
          # Detect htslib location via Homebrew or fallback to $HOME/htslib
          HTS_LIB_DIR=""
          if command -v brew >/dev/null 2>&1; then
            BREW_PREFIX="$(brew --prefix htslib 2>/dev/null || true)"
            if [ -n "$BREW_PREFIX" ] && [ -d "$BREW_PREFIX/lib" ]; then
              HTS_LIB_DIR="$BREW_PREFIX/lib"
            fi
          fi
          if [ -z "$HTS_LIB_DIR" ] && [ -d "$HOME/htslib" ]; then
            HTS_LIB_DIR="$HOME/htslib"
          fi
          if [ -z "$HTS_LIB_DIR" ]; then
            echo "ERROR: libhts not found via Homebrew or at \$HOME/htslib" >&2
            exit 1
          fi
          echo "Using htslib dir: $HTS_LIB_DIR"
          if [ "${RUNNER_OS:-}" = "macOS" ]; then
            #echo "DYLD_LIBRARY_PATH=$HTS_LIB_DIR:${DYLD_LIBRARY_PATH:-}" >> "$GITHUB_ENV"
            echo "DYLD_LIBRARY_PATH=$HTS_LIB_DIR" >> "$GITHUB_ENV"
          else
            #echo "LD_LIBRARY_PATH=$HTS_LIB_DIR:${LD_LIBRARY_PATH:-}" >> "$GITHUB_ENV"
            echo "LD_LIBRARY_PATH=$HTS_LIB_DIR" >> "$GITHUB_ENV"
          fi

      - name: Install d4
        run: |
          #export HTSLIB=system
          git clone https://github.com/38/d4-format
          echo 'location' >> ~/.curlrc # https://github.com/38/d4-format/pull/77#issuecomment-2044438359
          cd d4-format
          cargo build --release --all-features --package=d4binding
          sudo cp target/release/libd4binding.* $DYLD_LIBRARY_PATH
          sudo cp d4binding/include/d4.h $DYLD_INCLUDE_PATH
          sudo ldconfig || true

      - uses: iffy/install-nim@v5
        with:
          version: ${{ matrix.version }}

      - name: Rust Toolchain
        uses: dtolnay/rust-toolchain@nightly
        with:
          toolchain: stable

      # Build and Test
      - name: Build test executable
        run: nimble build -Y mosdepth.nimble

      - name: "Copy binary"
        run: chmod +x mosdepth && mkdir bin && cp mosdepth bin/mosdepth_debug_${{ matrix.os }}

      - name: "Build and Copy release binary"
        run: nim c --mm:refc -d:danger -d:release -o:bin/mosdepth_${{ matrix.os }} mosdepth

      - name: Functional Tests
        env:
          TERM: "xterm"
        run: |
          bash ./functional-tests.sh

      - name: Unit Tests
        run: |
          nim c -r tests/all.nim

      - name: Upload Artifact
        if: success()
        uses: actions/upload-artifact@v4
        with:
          name: mosdepth_${{ matrix.os }}_nim${{ matrix.version }}_executable
          path: bin/