[CI] Pin setuptools to <74 because of removed MSVCCompiler class #572
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| 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 |