Migrate IntaRNA to strict C++23 #80
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| name: C/C++ CI | |
| on: | |
| push: | |
| branches: [master, refactoring] | |
| pull_request: | |
| branches: [master, refactoring] | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| jobs: | |
| build: | |
| name: Build and test (${{ matrix.name }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - name: GCC 14 release | |
| os: ubuntu-24.04 | |
| compiler: gcc | |
| configure_debug: --disable-debug | |
| - name: GCC 14 debug | |
| os: ubuntu-24.04 | |
| compiler: gcc | |
| configure_debug: --enable-debug | |
| - name: Apple Clang release | |
| os: macos-15 | |
| compiler: apple-clang | |
| configure_debug: --disable-debug | |
| steps: | |
| - name: Check out sources | |
| uses: actions/checkout@v4 | |
| - name: Set up conda environment | |
| uses: conda-incubator/setup-miniconda@v4 | |
| with: | |
| miniconda-version: latest | |
| environment-file: conda-build-env.yml | |
| activate-environment: intarna-build-env | |
| - name: Install and select GCC 14 | |
| if: matrix.compiler == 'gcc' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install --yes gcc-14 g++-14 | |
| echo "CC=gcc-14" >> "$GITHUB_ENV" | |
| echo "CXX=g++-14" >> "$GITHUB_ENV" | |
| echo "LDFLAGS=-L${CONDA_PREFIX}/lib -Wl,-rpath,${CONDA_PREFIX}/lib" >> "$GITHUB_ENV" | |
| - name: Verify GCC 14 | |
| if: matrix.compiler == 'gcc' | |
| run: | | |
| "$CC" --version | |
| "$CXX" --version | |
| test "$("$CC" -dumpfullversion | cut -d. -f1)" = 14 | |
| test "$("$CXX" -dumpfullversion | cut -d. -f1)" = 14 | |
| - name: Set up Apple Clang with OpenMP | |
| if: matrix.compiler == 'apple-clang' | |
| run: | | |
| brew install libomp | |
| libomp_prefix="$(brew --prefix libomp)" | |
| echo "CC=/usr/bin/clang" >> "$GITHUB_ENV" | |
| echo "CXX=/usr/bin/clang++" >> "$GITHUB_ENV" | |
| echo "CPPFLAGS=-I${libomp_prefix}/include" >> "$GITHUB_ENV" | |
| echo "CXXFLAGS=-Xpreprocessor -fopenmp" >> "$GITHUB_ENV" | |
| echo "LDFLAGS=-L${libomp_prefix}/lib -Wl,-rpath,${libomp_prefix}/lib -L${CONDA_PREFIX}/lib -Wl,-rpath,${CONDA_PREFIX}/lib" >> "$GITHUB_ENV" | |
| echo "LIBS=-lomp" >> "$GITHUB_ENV" | |
| vrna_libs="$(pkg-config --libs RNAlib2)" | |
| vrna_libs="${vrna_libs//-Wl,-fno-lto/}" | |
| echo "VRNA_LIBS=${vrna_libs}" >> "$GITHUB_ENV" | |
| - name: Verify Apple Clang | |
| if: matrix.compiler == 'apple-clang' | |
| run: | | |
| "$CC" --version | |
| "$CXX" --version | |
| "$CXX" --version | grep -q "Apple clang" | |
| - name: Bootstrap and configure | |
| run: | | |
| bash autotools-init.sh | |
| ./configure \ | |
| --prefix="$RUNNER_TEMP/intarna-install" \ | |
| --with-vrna="$CONDA_PREFIX" \ | |
| --with-boost="$CONDA_PREFIX" \ | |
| --with-boost-libdir="$CONDA_PREFIX/lib" \ | |
| --with-zlib="$CONDA_PREFIX" \ | |
| ${{ matrix.configure_debug }} | |
| grep -Eq '^CXX = .* -std=c\+\+23([[:space:]]|$)' Makefile | |
| grep -q '^#define INTARNA_MULITHREADING 1' src/config.h | |
| - name: Build, install, and run full test suite | |
| run: | | |
| make -j 2 | |
| make install | |
| make tests -j 2 | |
| "$RUNNER_TEMP/intarna-install/bin/IntaRNA" -h | |
| - name: Compile every installed public header independently | |
| run: | | |
| header_probe="$RUNNER_TEMP/intarna-header-probe.cpp" | |
| for header in "$RUNNER_TEMP/intarna-install/include/IntaRNA/"*.h; do | |
| printf '#include <IntaRNA/%s>\nint main() { return 0; }\n' "$(basename "$header")" > "$header_probe" | |
| "$CXX" -std=c++23 ${CPPFLAGS:-} ${CXXFLAGS:-} \ | |
| -I"$RUNNER_TEMP/intarna-install/include" \ | |
| -I"$CONDA_PREFIX/include" \ | |
| -fsyntax-only "$header_probe" | |
| done | |
| - name: Compile and link an installed pkg-config consumer | |
| run: | | |
| consumer="$RUNNER_TEMP/intarna-consumer.cpp" | |
| printf '#include <IntaRNA/RnaSequence.h>\nint main() { IntaRNA::RnaSequence rna("test", "ACGU"); return rna.size() == 4 ? 0 : 1; }\n' > "$consumer" | |
| export PKG_CONFIG_PATH="$RUNNER_TEMP/intarna-install/lib/pkgconfig" | |
| "$CXX" -std=c++23 ${CPPFLAGS:-} ${CXXFLAGS:-} "$consumer" \ | |
| ${LDFLAGS:-} $(pkg-config --cflags --libs IntaRNA) \ | |
| -o "$RUNNER_TEMP/intarna-consumer" | |
| "$RUNNER_TEMP/intarna-consumer" |