build.yml

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

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

jobs:
  build:

    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-20.04, macos-13]
        version:
        - 1.6.18
        - 2.0.2


    steps:
    - uses: actions/checkout@v4

    # 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 --recursive https://github.com/samtools/htslib.git
        cd htslib && git checkout 1.11 && autoheader && autoconf && ./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: 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.* /usr/local/lib
        sudo cp d4binding/include/d4.h /usr/local/include/
        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 -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 }}_executable
        path: bin/