build.yml

name: C/C++ CI

on:
  push:
    branches: [master]
  pull_request:

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
            std_mdspan: 0
          - name: GCC 14 debug
            os: ubuntu-24.04
            compiler: gcc
            configure_debug: --enable-debug
            std_mdspan: 0
          - name: Apple Clang release
            os: macos-15
            compiler: apple-clang
            configure_debug: --disable-debug
            std_mdspan: 1

    steps:
      - name: Check out sources
        uses: actions/checkout@v7

      - 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
          automake --warnings=portability,error
          ./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
          grep -q '^#define INTARNA_USE_STD_MDSPAN ${{ matrix.std_mdspan }}$' src/config.h
          grep -q '^#define INTARNA_USE_STD_MDSPAN ${{ matrix.std_mdspan }}$' src/IntaRNA/intarna_config.h

      - name: Build, install, and run full test suite
        run: |
          make -j 2
          make install
          make tests -j 2
          python3 -m pip install -r python/requirements-output-tools.txt
          PATH="$RUNNER_TEMP/intarna-install/bin:$PATH" make -C python check-python-tools
          "$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="$RUNNER_TEMP/intarna-consumer.cpp"
          printf '#include <IntaRNA/RnaSequence.h>\n#include <IntaRNA/Matrix.h>\nint main() { IntaRNA::RnaSequence rna("test", "ACGU"); IntaRNA::Matrix<int> matrix(2, 3); matrix(1, 2) = 42; return rna.size() == 4 && matrix(1, 2) == 42 ? 0 : 1; }\n' > "$consumer"
          test -f "$RUNNER_TEMP/intarna-install/include/IntaRNA/mdspan/LICENSE"
          test -f "$RUNNER_TEMP/intarna-install/include/IntaRNA/experimental/LICENSE"
          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"
          "$RUNNER_TEMP/intarna-consumer"
          "$CXX" -std=c++23 ${CPPFLAGS:-} ${CXXFLAGS:-} doc/seeded-probabilities-example.cpp \
            ${LDFLAGS:-} $(pkg-config --cflags --libs IntaRNA) \
            -o "$RUNNER_TEMP/intarna-probabilities-consumer"
          "$RUNNER_TEMP/intarna-probabilities-consumer" > "$RUNNER_TEMP/intarna-pair-probabilities.csv"
          grep -q '^bpProb;' "$RUNNER_TEMP/intarna-pair-probabilities.csv"