dbuild-linux.yml

name: linux ldc build
on: [push, pull_request]

jobs:
  linux-build:
    name: linux Dub build
    strategy:
      matrix:
        os: [ubuntu-latest]
        dc: [ldc-latest]

    runs-on: ${{ matrix.os }}
    steps:
      - uses: actions/checkout@v2
        with:
          submodules: recursive

      - name: Install D compiler
        uses: dlang-community/setup-dlang@v1
        with:
          compiler: ${{ matrix.dc }}

      - name: Install htslib deps
        run: |
            sudo apt-get update && sudo apt-get install -y build-essential autoconf zlib1g-dev libbz2-dev liblzma-dev libcurl4-openssl-dev libssl-dev python cython
      - name: Get dhtslib commit
        id: get-dhtslib-commit
        run: echo "::set-output name=sha_short::$(git rev-parse --short :dhtslib)"

      - name: Cache dhtslib
        id: cache-dhtslib
        uses: actions/cache@v2
        with:
          path: dhtslib
          key: ${{ runner.os}}-dhtslib-${{ steps.get-dhtslib-commit.outputs.sha_short }}

      - name: Build htslib
        if: steps.cache-dhtslib.outputs.cache-hit != 'true'
        run: |
            cd dhtslib/htslib
            autoreconf -i
            ./configure
            make
      - name: Install htslib
        run: |
            cd dhtslib/htslib
            sudo make install
            sudo ldconfig
      - name: Setup additional test files
        run: |
            cd dhtslib/htslib
            cd test
            cd tabix
            bgzip -c gff_file.gff > gff_file.gff.gz
            tabix gff_file.gff.gz
            bgzip -c bed_file.bed > bed_file.bed.gz
            tabix bed_file.bed.gz
            bgzip -c vcf_file.vcf > vcf_file.vcf.gz
            tabix vcf_file.vcf.gz
            
      - name: Run build
        run: dub build
        env:
          LIBRARY_PATH: /usr/local/lib

      - name: Run unittests
        run: dub test
        env:
          LIBRARY_PATH: /usr/local/lib

      - name: Run integration tests
        run: |
            cd tests
            dub test
        env:
          LIBRARY_PATH: /usr/local/lib
      
      - name: generate coverage
        run: dub -q test -b=unittest-cov
        env:
          LIBRARY_PATH: /usr/local/lib

      - name: Upload coverage
        run: bash <(curl -s https://codecov.io/bash)