test-cpp.yml

name: C++ Code Checks

on:
  push:
    branches: [ "master" ]
  pull_request:
  workflow_dispatch:

jobs:
  Code-Coverage:
    name: Code Coverage
    runs-on: ubuntu-22.04
    # Suddenly, the upload to codecov does not work anymore and times out after 6 hours -.-.
    # It's not like I used it much anyway, except to have a badge.
    if: false
    steps:
    - uses: actions/checkout@v4
      with:
        submodules: recursive

    - name: Install Dependencies
      run: |
        sudo apt-get -y install bzip2 cppcheck clang clang-tidy g++ lcov ninja-build wget gzip tabix pigz gztool libarchive-dev zlib1g-dev isal nasm
        python3 -m pip install --upgrade pip
        python3 -m pip install --upgrade-strategy eager --upgrade indexed_gzip pgzip

    - name: System Information
      run: |
        nproc
        cmake --version
        g++ --version
        clang++ --version
        cppcheck --version

    - name: Code Coverage
      run: |
        mkdir -p build-codeov && cd -- "$_"
        # It should be compiled with the same g++ version as anylzed with gcov!
        # If g++ --version and gcov --version print different versions, there might be problems when creating
        # the coverage report, e.g., I had: "version 'A85*', prefer 'B12*'".
        # It is possible to specify a different gcov version to lcov using, e.g., lcov --gcov-tool gcov-8.
        # For me it compiled with g++-8 but used gcov-11 by default!
        CXX=g++ CC=gcc cmake -G Ninja -DCMAKE_BUILD_TYPE=Debug -DCODE_COVERAGE=ON -DCMAKE_CXX_FLAGS="-DSHORT_TESTS" ..
        cmake --build . -- check
        lcov --capture --directory . --base-directory "$( cd .. && pwd  )" --no-external --output-file coverage.info
        lcov --list coverage.info
        bash <( wget -O- -q https://codecov.io/bash ) -f coverage.info

    - name: Run cppcheck
      # Crashes on templated variable REVERSED_BITS_LUT<T>[value] (internalAstError)
      if: false
      run: |
        set -o pipefail
        cppcheck -j $( nproc ) --enable=all --std=c++17 --suppress=unusedFunction --suppress=useStlAlgorithm \
            -I src/core \
            -I src/indexed_bzip2 \
            -I src/rapidgzip \
            -I src/rapidgzip/huffman \
            src/benchmarks \
            src/core \
            src/indexed_bzip2 \
            src/rapidgzip \
            src/tests \
            src/tools  2>&1 | tee cppcheck.log
        if grep -E -i 'error: .* \[[^]]*\]$' cppcheck.log; then
            echo -e '\e[31mThere were errors while running cppcheck!\e[0m'
            exit 1
        fi

  Clang-Tidy:
    name: Clang-Tidy
    runs-on: ubuntu-22.04
    steps:
    - uses: actions/checkout@v4
      with:
        submodules: recursive

    - name: Install Dependencies
      run: |
        sudo apt-get -y install clang clang-tidy ninja-build libarchive-dev zlib1g-dev nasm

    - name: Run clang-tidy
      run: |
        mkdir -p build-compile-commands && cd -- "$_"
        CC=clang CXX=clang++ cmake -G Ninja -DCMAKE_EXPORT_COMPILE_COMMANDS=ON -DUSE_SYSTEM_ZLIB=ON -DRUN_CLANG_TIDY=ON ..
        cmake --build .

  Check:
    name: Check without Sanitizer
    # And especially without -DSHORT_TESTS, which makes it non redundant to the sanitizer checks!
    runs-on: ubuntu-22.04
    strategy:
      matrix:
        use_system_zlib: [ON, OFF]

    steps:
    - uses: actions/checkout@v4
      with:
        submodules: recursive

    - name: Install Dependencies
      run: |
        sudo apt-get -y install g++ ninja-build gzip tabix pigz gztool libarchive-dev zlib1g-dev isal nasm
        python3 -m pip install --upgrade pip
        python3 -m pip install --upgrade-strategy eager --upgrade indexed_gzip pgzip

    - name: Run Tests With Sanitizers
      env:
        USE_SYSTEM_ZLIB: ${{ matrix.use_system_zlib }}
      run: |
        mkdir -p "build" && cd -- "$_"
        CXX=g++ CC=gcc cmake -G Ninja -DCMAKE_BUILD_TYPE=Debug -DWITH_ISAL=ON -DUSE_SYSTEM_ZLIB=$USE_SYSTEM_ZLIB ..
        cmake --build . -- check

  Check-Without-Isal:
    name: Check without Sanitizer and without ISA-L

    # And especially without -DSHORT_TESTS, which makes it non redundant to the sanitizer checks!
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-22.04, macos-12, macos-13, windows-latest]

    env:
      MACOSX_DEPLOYMENT_TARGET: "10.15"

    steps:
    - name: System Information
      if: "! startsWith(matrix.os, 'windows')"
      run: |
        uname -a

    - name: Print Architecture
      if: "startsWith(matrix.os, 'macos')"
      run: |
        sysctl -n machdep.cpu.brand_string
        arch

    - uses: actions/checkout@v4
      with:
        submodules: recursive

    - uses: seanmiddleditch/gha-setup-ninja@master

    - name: Install System Dependencies
      if: "startsWith(matrix.os , 'macos')"
      run: |
        brew install ninja pigz zlib isa-l wget
        wget 'https://github.com/samtools/htslib/releases/download/1.20/htslib-1.20.tar.bz2'
        tar -xf htslib-1.20.tar.bz2
        cd htslib* && ./configure && make install

    - name: Install System Dependencies
      if: "startsWith(matrix.os , 'ubuntu')"
      run: |
        sudo apt-get -y install g++ ninja-build gzip tabix pigz gztool libarchive-dev zlib1g-dev isal

    - name: Fix pip
      if: "startsWith(matrix.os , 'macos')"
      run: |
        mkdir -p "$HOME/Library/Application Support/pip"
        cat <<EOF >> "$HOME/Library/Application Support/pip/pip.conf"
        [global]
        break-system-packages = true
        EOF

    - name: Install Python Dependencies
      run: |
        python3 -m pip install --upgrade pip
        python3 -m pip install --upgrade-strategy eager --upgrade indexed_gzip pgzip

    - name: Run Tests With Sanitizers
      if: "startsWith(matrix.os , 'ubuntu')"
      run: |
        mkdir -p "build" && cd -- "$_"
        cmake -G Ninja -DCMAKE_BUILD_TYPE=Debug -DWITH_ISAL=OFF -DUSE_SYSTEM_ZLIB=OFF ..
        cmake --build . -- check

    - name: Run Tests With Sanitizers
      if: "startsWith(matrix.os , 'macos')"
      run: |
        # For some reason MacOS ARM is much slower and runs into a timeout without -DSHORT_TESTS :/
        mkdir -p "build" && cd -- "$_"
        cmake -G Ninja -DCMAKE_BUILD_TYPE=Debug -DWITH_ISAL=OFF -DUSE_SYSTEM_ZLIB=OFF -DCMAKE_CXX_FLAGS="-DSHORT_TESTS" ..
        cmake --build . -- check

    - name: Run Tests With Sanitizers
      if: "startsWith(matrix.os , 'windows')"
      run: |
        mkdir -p "build" && cd -- "build"
        cmake -G Ninja -DCMAKE_BUILD_TYPE=Debug -DWITH_ISAL=OFF ..
        cmake --build . -- check

  Asan:
    name: ASan

    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-22.04, macos-13]

    steps:
    - uses: actions/checkout@v4
      with:
        submodules: recursive

    - name: Install System Dependencies
      if: "startsWith(matrix.os , 'macos')"
      run: |
        brew install ninja pigz zlib isa-l wget nasm
        wget 'https://github.com/samtools/htslib/releases/download/1.20/htslib-1.20.tar.bz2'
        tar -xf htslib-1.20.tar.bz2
        cd htslib* && ./configure && make install

    - name: Install System Dependencies
      if: "startsWith(matrix.os , 'ubuntu')"
      run: |
        sudo apt-get -y install clang g++ ninja-build gzip tabix pigz gztool libarchive-dev zlib1g-dev isal nasm

    - name: Install Python Dependencies
      run: |
        python3 -m pip install --upgrade pip
        python3 -m pip install --upgrade-strategy eager --upgrade indexed_gzip pgzip

    - name: Run Tests With Sanitizers
      if: "startsWith(matrix.os , 'macos')"
      run: |
        sanitizer=address
        mkdir -p "build-sanitized-$sanitizer" && cd -- "$_"
        cmake -G Ninja -DWITH_ISAL=OFF -DUSE_SYSTEM_ZLIB=OFF -DCMAKE_BUILD_TYPE=Debug \
            -DCMAKE_CXX_FLAGS="-fsanitize=$sanitizer -DSHORT_TESTS" ..
        cmake --build . -- check

    - name: Run Tests With Sanitizers
      if: "startsWith(matrix.os , 'ubuntu')"
      run: |
        sanitizer=address
        mkdir -p "build-sanitized-$sanitizer" && cd -- "$_"
        CXX=clang++ CC=clang cmake -G Ninja -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_FLAGS="-fsanitize=$sanitizer -DSHORT_TESTS" ..
        cmake --build . -- check
        cmake --build .
        bash ../src/tests/testRapidgzip.sh

  UBSan:
    name: UBSan

    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-22.04, macos-13]

    steps:
    - uses: actions/checkout@v4
      with:
        submodules: recursive

    - name: Install System Dependencies
      if: "startsWith(matrix.os , 'macos')"
      run: |
        brew install ninja pigz zlib isa-l wget nasm
        wget 'https://github.com/samtools/htslib/releases/download/1.20/htslib-1.20.tar.bz2'
        tar -xf htslib-1.20.tar.bz2
        cd htslib* && ./configure && make install

    - name: Install System Dependencies
      if: "startsWith(matrix.os , 'ubuntu')"
      run: |
        sudo apt-get -y install clang g++ ninja-build gzip tabix pigz gztool libarchive-dev zlib1g-dev isal nasm

    - name: Install Python Dependencies
      run: |
        python3 -m pip install --upgrade pip
        python3 -m pip install --upgrade-strategy eager --upgrade indexed_gzip pgzip

    - name: Run Tests With Sanitizers
      if: "startsWith(matrix.os , 'macos')"
      run: |
        sanitizer=undefined
        mkdir -p "build-sanitized-$sanitizer" && cd -- "$_"
        cmake -G Ninja -DWITH_ISAL=OFF -DUSE_SYSTEM_ZLIB=OFF -DCMAKE_BUILD_TYPE=Debug \
            -DCMAKE_CXX_FLAGS="-fsanitize=$sanitizer -DSHORT_TESTS" ..
        cmake --build . -- testParallelGzipReader
        src/tests/rapidgzip/testParallelGzipReader

    - name: Run Tests With Sanitizers
      if: "startsWith(matrix.os , 'ubuntu')"
      run: |
        sanitizer=undefined
        mkdir -p "build-sanitized-$sanitizer" && cd -- "$_"
        CXX=clang++ CC=clang cmake -G Ninja -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_FLAGS="-fsanitize=$sanitizer -DSHORT_TESTS" ..
        cmake --build . -- check

  Safe-Stack:
    name: Safe-Stack

    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-22.04, macos-13]

    steps:
    - uses: actions/checkout@v4
      with:
        submodules: recursive

    - name: Install System Dependencies
      if: "startsWith(matrix.os , 'macos')"
      run: |
        brew install ninja pigz zlib isa-l wget nasm gcc
        wget 'https://github.com/samtools/htslib/releases/download/1.20/htslib-1.20.tar.bz2'
        tar -xf htslib-1.20.tar.bz2
        cd htslib* && ./configure && make install

    - name: Install System Dependencies
      if: "startsWith(matrix.os , 'ubuntu')"
      run: |
        sudo apt-get -y install clang g++ ninja-build gzip tabix pigz gztool libarchive-dev zlib1g-dev isal nasm

    - name: Install Python Dependencies
      run: |
        python3 -m pip install --upgrade pip
        python3 -m pip install --upgrade-strategy eager --upgrade indexed_gzip pgzip

    - name: Run Tests With Sanitizers
      if: "startsWith(matrix.os , 'macos')"
      run: |
        sanitizer=address
        mkdir -p "build-sanitized-$sanitizer" && cd -- "$_"
        CXX=g++ CC=gcc cmake -G Ninja -DWITH_ISAL=OFF -DUSE_SYSTEM_ZLIB=OFF -DCMAKE_BUILD_TYPE=Debug \
            -DCMAKE_CXX_FLAGS="-fsanitize=$sanitizer -DSHORT_TESTS" ..
        cmake --build . -- testParallelGzipReader
        src/tests/rapidgzip/testParallelGzipReader

    - name: Run Tests With Sanitizers
      if: "startsWith(matrix.os , 'ubuntu')"
      run: |
        sanitizer=safe-stack
        mkdir -p "build-sanitized-$sanitizer" && cd -- "$_"
        CXX=clang++ CC=clang cmake -G Ninja -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_FLAGS="-fsanitize=$sanitizer -DSHORT_TESTS" ..
        cmake --build . -- check

  TSan:
    name: TSan
    runs-on: ubuntu-22.04
    steps:
    - uses: actions/checkout@v4
      with:
        submodules: recursive

    - name: Install Dependencies
      run: |
        sudo apt-get -y install clang g++ ninja-build gzip tabix pigz gztool libarchive-dev zlib1g-dev isal nasm
        python3 -m pip install --upgrade pip
        python3 -m pip install --upgrade-strategy eager --upgrade indexed_gzip pgzip

    - name: Run Tests With Thread Sanitizer
      run: |
        sanitized=thread
        mkdir -p "build-sanitized-$sanitized" && cd -- "$_"
        #
        # TSAN in clang 10 and 11 shows false positives in condition variables:
        # https://github.com/google/sanitizers/issues/1259
        # Similar false positives appear with GCC 10.
        # NO warnings appear with: GCC 8, 9 and clang 12,
        # so I'm pretty sure that these are the referenced false positives.
        clangMajorVersion=$( clang++ --version | sed -n -E 's|.* ([0-9]+)[.][0-9]+[.][0-9]+.*|\1|p' | head -1 )
        if [[ ( "$sanitized" == thread ) && ( "$clangMajorVersion" -le 11 ) ]]; then
            g++ --version
            gccMajorVersion=$( g++ --version | sed -n -E 's|.* ([0-9]+)[.][0-9]+[.][0-9]+.*|\1|p' | head -1 )
            if [[ "$gccMajorVersion" -ge 10 ]]; then
                echo "Could not find a compiler version without known false positives. Skipping TSAN."
                continue
            fi
            CXX=g++
            CC=gcc
        else
            CXX=clang++
            CC=clang
        fi
        export CC CXX
        #
        cmake -G Ninja -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_FLAGS="-fsanitize=$sanitized -DSHORT_TESTS" ..
        cmake --build . -- check

  Code-Checks:
    name: Check with Infer
    runs-on: ubuntu-22.04
    steps:
    - uses: actions/checkout@v4
      with:
        submodules: recursive

    - name: Install Dependencies
      run: |
        sudo apt-get -y install ninja-build wget nasm
        # Install infer
        VERSION=1.1.0
        wget -q -O- "https://github.com/facebook/infer/releases/download/v$VERSION/infer-linux64-v$VERSION.tar.xz" | tar -xJ
        echo "$PWD/infer-linux64-v$VERSION/bin" >> $GITHUB_PATH

    - name: Run infer
      run: |
        mkdir -p build-compile-commands && cd -- "$_"
        CC=clang CXX=clang++ cmake .. -DCMAKE_EXPORT_COMPILE_COMMANDS=ON
        infer run --report-blacklist-path-regex '.*testParallelBitStringFinder.cpp' --compilation-database compile_commands.json

  Ibzip2-Tests:
    name: Ibzip2 Tests

    # And especially without -DSHORT_TESTS, which makes it non redundant to the sanitizer checks!
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-22.04, macos-13, macos-14, windows-latest]

    steps:
    - uses: actions/checkout@v4
      with:
        submodules: recursive

    - uses: seanmiddleditch/gha-setup-ninja@master

    - name: Install System Dependencies
      if: "startsWith(matrix.os , 'macos')"
      run: |
        brew install ninja

    - name: Install System Dependencies
      if: "startsWith(matrix.os , 'ubuntu')"
      run: |
        sudo apt-get -y install g++ ninja-build

    - name: Fix pip
      if: "startsWith(matrix.os , 'macos')"
      run: |
        mkdir -p "$HOME/Library/Application Support/pip"
        cat <<EOF >> "$HOME/Library/Application Support/pip/pip.conf"
        [global]
        break-system-packages = true
        EOF

    - name: Install Python Dependencies
      run: |
        python3 -m pip install --upgrade pip
        python3 -m pip install build

    - name: Install indexed_bzip2
      working-directory: python/indexed_bzip2
      shell: bash
      run: |
        python3 -m build
        python3 -m pip install dist/*.tar.gz

    - name: Run Standard Tests
      shell: bash
      # At this step, indexed_bzip2 should be installed.
      run: |
        mkdir -p build-ibzip2 && cd -- "$_"
        cmake -G Ninja -DCMAKE_BUILD_TYPE=Debug -DWITH_ISAL=OFF ..
        cmake --build . -- ibzip2
        set -o pipefail
        bash ../src/tests/testIbzip2.sh | tee run-standard-tests.log
        if grep -i 'failed' run-standard-tests.log; then
            echo -e '\e[31mThere were errors while running the tests!\e[0m'
            exit 1
        fi