ci.yaml

# ==================================================================================================
#     Header
# ==================================================================================================

name: CI
on: [push, pull_request]

# on:
#   pull_request:
#   push:
#     branches:
#       - master
#       - misc

# ==================================================================================================
#     Jobs
# ==================================================================================================

jobs:
  ci:
    runs-on: ${{ matrix.os }}

    # We have issues with MacOS... because of reasons...
    # So we have tests that are currently failing, but still want to keep them around,
    # as some of them seem to be issues with Clang itself, and not with our code,
    # and are hence expected to be solved with some update on their end at a later point.
    # We try to use this here to have the whole workflow succeed even with these jobs failing,
    # see https://github.com/actions/toolkit/issues/399
    # --> We have deactivated the failing macos jobs for now, so let's deactivate this switch here,
    # so that for now, we fail the workflow when a single job fails. That makes it easier to see
    # problems down the line.
    # continue-on-error: true

    # ==========================================================================
    #     Matrix
    # ==========================================================================

    strategy:
      fail-fast: false

      # -------------------------------------------------------
      #     matrix
      # -------------------------------------------------------

      matrix:
        os:
          # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#choosing-github-hosted-runners
          - ubuntu-20.04
          - ubuntu-22.04
          - macos-11
          - macos-12

        compiler:
          # - gcc-5
          # - gcc-6
          - gcc-7
          - gcc-8
          - gcc-9
          - gcc-10
          - gcc-11
          - gcc-12
          - gcc-13
          - llvm-5
          - llvm-6
          - llvm-7
          - llvm-8
          - llvm-9
          - llvm-10
          - llvm-11
          - llvm-12
          - llvm-13

        build_type:
          - DEBUG
          # - RELEASE

        htslib:
          - ON
          # - OFF

        # -------------------------------------------------------
        #     exclude
        # -------------------------------------------------------

        exclude:
          # Newer GCC versions are not available on all Ubuntu
          - os: ubuntu-20.04
            compiler: gcc-12
          - os: ubuntu-20.04
            compiler: gcc-13
          - os: ubuntu-20.04
            compiler: llvm-13

          # Older GCC versions are not supported by Ubuntu any more
          - os: ubuntu-22.04
            compiler: gcc-7
          - os: ubuntu-22.04
            compiler: gcc-8

          # llvm-9 causes weird segfauls on Ubuntu, which do not seem to be our fault.
          # Need to investiage further at some point. We used setup-cpp locally to install
          # the very same version of llvm-9, and got tons of segfauls for all kind of functions...
          - os: ubuntu-20.04
            compiler: llvm-9
          - os: ubuntu-22.04
            compiler: llvm-9

          # We also currently exclude clang from macos, as it fails with different types of
          # linker errors. As this is merely a problem in the setup, we defer solving this for now.
          # Wildcards do not work here, so we have to list them all... :-(
          - os: macos-11
            compiler: llvm-5
          - os: macos-11
            compiler: llvm-6
          - os: macos-11
            compiler: llvm-7
          - os: macos-11
            compiler: llvm-8
          - os: macos-11
            compiler: llvm-9
          - os: macos-11
            compiler: llvm-10
          - os: macos-11
            compiler: llvm-11
          - os: macos-11
            compiler: llvm-12
          - os: macos-11
            compiler: llvm-13
          - os: macos-12
            compiler: llvm-5
          - os: macos-12
            compiler: llvm-6
          - os: macos-12
            compiler: llvm-7
          - os: macos-12
            compiler: llvm-8
          - os: macos-12
            compiler: llvm-9
          - os: macos-12
            compiler: llvm-10
          - os: macos-12
            compiler: llvm-11
          - os: macos-12
            compiler: llvm-12
          - os: macos-12
            compiler: llvm-13

        # -------------------------------------------------------
        #     include
        # -------------------------------------------------------

        include:
          # Test the release version with both compilers and OSs
          - os: ubuntu-latest
            compiler: gcc
            build_type: RELEASE
          - os: ubuntu-latest
            compiler: llvm
            build_type: RELEASE
          - os: macos-latest
            compiler: gcc
            build_type: RELEASE
          - os: macos-latest
            compiler: llvm
            build_type: RELEASE

          # Test without htslib with both compilers and OSs
          - os: ubuntu-latest
            compiler: gcc
            htslib: OFF
          - os: ubuntu-latest
            compiler: llvm
            htslib: OFF
          - os: macos-latest
            compiler: gcc
            htslib: OFF
          - os: macos-latest
            compiler: llvm
            htslib: OFF

          # We test AppleClang as well, as a special case.
          # - os: macos-10.15
          #   compiler: apple
          - os: macos-11
            compiler: apple
          - os: macos-12
            compiler: apple

    # ==========================================================================
    #     Steps
    # ==========================================================================

    steps:
      - name: Checkout
        uses: actions/checkout@v3.1.0

      # -------------------------------------------------------
      #     Setup
      # -------------------------------------------------------

      - name: Setup C++
        # Reference: https://github.com/marketplace/actions/setup-cpp-c-c
        uses: aminya/setup-cpp@v0.22.0
        if: matrix.compiler != 'apple'
        with:
          compiler: ${{ matrix.compiler }}
          cmake: true

      - name: Setup C++ - AppleClang
        if: matrix.compiler == 'apple'
        run: |
          brew install cmake

      # -------------------------------------------------------
      #     Dependencies
      # -------------------------------------------------------

      - name: Install Dependencies - Ubuntu
        if: runner.os == 'linux'
        # 1: htslib dependencies, see https://github.com/samtools/htslib/blob/develop/INSTALL
        # 2: clang on ubuntu 22 is not properly set up, we need libtinfo5,
        #    see https://github.com/aminya/setup-cpp/issues/149
        # 3: Install gdb for debugging output.
        run: |
          sudo apt-get install autoconf automake zlib1g-dev libbz2-dev liblzma-dev
          sudo apt-get install libtinfo5 gdb
        # sudo apt-get remove autoconf
        # sudo apt-get install autoconf2.64 liblzma-dev libbz2-dev

      - name: Install Dependencies - MacOS
        if: runner.os == 'macos'
        # The commands below were try and error with the CI...
        #  - install simple dependencies of htslib, and for (trying to get) OpenMP
        #  - switch xcode mode, see https://stackoverflow.com/a/67654877
        #  - output xcode info for debugging, see https://stackoverflow.com/a/73765819
        #  - we also tried xocde-select from https://mac.r-project.org/openmp/ and
        #    https://open-box.readthedocs.io/en/latest/installation/openmp_macos.html
        #    but that did not work
        #  - previously, we used an htslib version that required autoconf 2.69.
        #    we switched now, but keep this here for reference if needed later
        run: |
          brew install autoconf automake libdeflate libomp gdb

          if [[ "${{ matrix.compiler }}" == gcc* ]]; then
            echo "Patching xcode gcc issues"
            sudo xcode-select --switch /Library/Developer/CommandLineTools
          fi
        # xcode-select -p
        # xcode-select -p
        # pkgutil --pkg-info=com.apple.pkg.CLTools_Executables
        # /usr/bin/xcodebuild -version
        # xcode-select --install
        # brew uninstall --ignore-dependencies autoconf
        # brew install autoconf@2.69
        # echo 'export PATH="/usr/local/opt/autoconf@2.69/bin:$PATH"' >> /Users/runner/.bash_profile

      # -------------------------------------------------------
      #     Configure
      # -------------------------------------------------------

      - name: Configure
        run: |
          export GENESIS_DEBUG=ON
          export GENESIS_USE_HTSLIB=ON
          export GENESIS_USE_OPENMP=ON

          # Take matrix includes into account
          if [[ "${{ matrix.build_type }}" == "RELEASE" ]]; then export GENESIS_DEBUG=OFF; fi
          if [[ "${{ matrix.htslib }}" == "OFF" ]]; then export GENESIS_USE_HTSLIB=OFF; fi

          # Deactivate OpenMP on MacOS for now. Causes way too much trouble.
          if [[ "${RUNNER_OS}" == "macOS" ]]; then export GENESIS_USE_OPENMP=OFF; fi

          # Need to set the xcode patch here as well, as job steps don't keep status.
          if [[ "${RUNNER_OS}" == "macOS" ]] && [[ "${{ matrix.compiler }}" == gcc* ]]; then
            echo "Patching xcode gcc issues"
            sudo xcode-select --switch /Library/Developer/CommandLineTools
          fi

          cmake -S . -B ./build -DGENESIS_USE_HTSLIB=${GENESIS_USE_HTSLIB} -DGENESIS_USE_OPENMP=${GENESIS_USE_OPENMP}

      # - name: MacOS CMake debug
      #   if: always() && runner.os == 'macos'
      #   run: |
      #     CMAKE_OUT="/Users/runner/work/genesis/genesis/build/CMakeFiles/CMakeOutput.log"
      #     CMAKE_ERR="/Users/runner/work/genesis/genesis/build/CMakeFiles/CMakeError.log"
      #     if [[ -f ${CMAKE_OUT} ]]; then
      #       cat ${CMAKE_OUT}
      #     fi
      #     if [[ -f ${CMAKE_ERR} ]]; then
      #       cat ${CMAKE_ERR}
      #     fi

      # -------------------------------------------------------
      #     Build & Test
      # -------------------------------------------------------

      - name: Build
        # Below we use a workaround for LLVM as configured by setup-cpp, which clashes with htslib:
        # https://github.com/samtools/htslib/issues/1527 and
        # https://github.com/aminya/setup-cpp/issues/145
        run: |
          if [[ ! -z "${LLVM_PATH}" ]]; then
            export LDFLAGS=`echo ${LDFLAGS} | sed 's/"//g'`
            export CPPFLAGS=`echo ${CPPFLAGS} | sed 's/"//g'`
          fi

          # Need to set the xcode patch here as well, as job steps don't keep status.
          if [[ "${RUNNER_OS}" == "macOS" ]] && [[ "${{ matrix.compiler }}" == gcc* ]]; then
            echo "Patching xcode gcc issues"
            sudo xcode-select --switch /Library/Developer/CommandLineTools
          fi

          cmake --build ./build -- -j 2

      - name: Tests
        id: test
        if: >
          success() &&
          runner.os != 'windows' &&
          matrix.build_type != 'RELEASE'
        run: |
          ./bin/test/genesis_tests

      - name: Test - gdb
        # If the regular test run failed, we repeat with gdb, to print the stack.
        # We are not using the `./test/run.sh gdb` here, to make it easier for MacOS.
        # gdb on Mac needs to be code signed for executing without admin rights...
        # See https://sourceware.org/gdb/wiki/PermissionsDarwin, which seems super compilcated.
        # So we just run it via sudo instead ;-)
        if: ${{ failure() && steps.test.conclusion == 'failure' }}
        run: |
          GDBEXE="gdb"
          # if [[ ${{ matrix.os }} == macos* ]] ; then
          #   GDBEXE="sudo gdb"
          # fi
          ${GDBEXE} -ex "set confirm off" -iex "set pagination off" -ex "run" -ex "thread apply all bt" -ex "quit" --args ./bin/test/genesis_tests