Modernize IntaRNA with focused C++23 facilities

.github/workflows/build.yml

@@ -2,53 +2,122 @@ name: C/C++ CI
 
 on:
   push:
-    branches: [ master ]
+    branches: [master, refactoring, 'refactor-to-c\+\+23']
   pull_request:
-    branches: [ master ]
-
+    branches: [master, refactoring, 'refactor-to-c\+\+23']
 
 defaults:
   run:
     shell: bash -el {0}
 
-
 jobs:
   build:
-
-    runs-on: ubuntu-latest
+    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: Check out sources from github
-      uses: actions/checkout@v2
-
-    - name: Setup conda environment
-      uses: conda-incubator/setup-miniconda@v2
-      with:
-        miniconda-version: "latest"
-        environment-file: conda-build-env.yml
-        activate-environment: conda-build-env
-
-    - name: Build and test IntaRNA
-      run: |
-        ##### start IntaRNA build #####
-        pwd
-        # generate autotools's files 
-        bash autotools-init.sh 
-        # run configure (without boost checks)
-        ENVPREFIX=`conda info --base`/envs/conda-build-env
-        export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ENVPREFIX/lib
-        ./configure \
-           --prefix=$HOME/IntaRNA \
-           --with-vrna=$ENVPREFIX \
-           --with-boost=$ENVPREFIX \
-           --with-boost-libdir=$ENVPREFIX/lib \
-           --with-zlib=$ENVPREFIX
-        # compile documentation
-        # - make doxygen-doc
-        # compile, test and install IntaRNA
-        make -j 2 && make install
-        make tests -j 2
-        ##### check IntaRNA build #####
-        # run installed IntaRNA with help output
-        $HOME/IntaRNA/bin/IntaRNA -h
+      - name: Compile and link an installed pkg-config consumer
+        run: |
+          consumer="$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"

ChangeLog

@@ -12,6 +12,10 @@
 
 # IntaRNA
 
+- C++23 required; build and installation checks with GCC 14 and Apple Clang
+- reduce temporary allocations and fix cleanup on error paths
+- avoid repeated partition-map lookups in exact ensemble prediction
+- add exhaustive interaction and seed oracles for short-sequence tests
 - BUGFIX : heuristic cell initialization and noLP ensemble recurrences
 - BUGFIX : ensemble filtering and seed-extension partition reset
 - BUGFIX : target accessibility limits and seed-free outMinPu filtering
@@ -30,6 +34,26 @@
 ################################################################################  
 ################################################################################
 
+260919 Alexander Mitrofanov
+ * configure.ac / m4 / .github/workflows/build.yml :
+   * C++23 requirement, library checks and GCC 14 / Apple Clang builds
+ * IntaRNA.pc.in :
+   * fix installed include and library flags
+ * IntaRNA/AccessibilityVrna / InteractionEnergyVrna :
+   * C++ string constraints, avoid sequence copies and ensure cleanup on errors
+ * bin/IntaRNA :
+   * automatic cleanup of accessibility, energy, output and predictor objects
+ * IntaRNA/OutputHandlerCsv / OutputHandlerEnsemble / OutputHandlerText :
+   * use stream views to avoid temporary string copies
+ * IntaRNA/PredictorMfeEns :
+   * updateZ() : single lookup for partition insertion and accumulation
+ * IntaRNA/RnaSequence :
+   * use string::contains() for alphabet and ambiguity checks
+ * tests :
+   + exhaustive interaction and seed oracles for short-sequence tests
+   + ViennaRNA constraint and repeated partition update tests
+   * update Catch to 2.13.10
+
 260919 Alexander Mitrofanov
  * IntaRNA/PredictorMfe2dHeuristic :
  * IntaRNA/PredictorMfe2dHeuristicSeed :

IntaRNA.pc.in

@@ -1,10 +1,10 @@
-prefix=@PREFIX_PATH@
-exec_prefix=${prefix}/bin
-libdir=${prefix}/lib
-includedir=${prefix}/include
-
-Name: IntaRNA
-Description: RNA-RNA interaction prediction C++ library
-Version: @VERSION@
-Libs: @LIBS@
-Cflags: 
+prefix=@prefix@
+exec_prefix=${prefix}
+libdir=${prefix}/lib
+includedir=${prefix}/include
+
+Name: IntaRNA
+Description: RNA-RNA interaction prediction C++ library
+Version: @VERSION@
+Libs: -L${libdir} -lIntaRNA @LIBS@
+Cflags: -I${includedir} @BOOST_CPPFLAGS@ @VRNA_CFLAGS@

README.md

@@ -180,7 +180,7 @@ you with an encapsulated IntaRNA installation.
 If you are going to compile IntaRNA from source, ensure you meet the following
 dependencies:
 
-- compiler supporting C++11 standard and OpenMP
+- compiler supporting C++23 and OpenMP (GCC 14 or Apple Clang)
 - [boost C++ library](http://www.boost.org/) version >= 1.50.0
   (ensure the following libraries are installed for development (not just runtime libraries!); or install all e.g. in Ubuntu via package `libboost-all-dev`)
     - libboost_regex
@@ -312,57 +312,34 @@ directory to your [`Path` System variable](http://www.computerhope.com/issues/ch
 <br /><br />
 <a name="instosx" />
 
-## OS X installation with homebrew (thanks to Lars Barquist)
+## macOS installation with Homebrew
 
-If you do not want to or can use the pre-compiled binaries for OS X available from
-[bioconda](https://anaconda.org/bioconda/intarna), you can compile `IntaRNA`
-locally.
+The [Bioconda package](https://anaconda.org/bioconda/intarna) is the simplest
+installation route. To build locally with the system Apple Clang compiler,
+install the dependencies and the OpenMP runtime:
 
-The following wraps up how to build `IntaRNA-2.0.2` under OS X (Sierra 10.12.4) using homebrew.
-
-First, install homebrew! :)
-
-```[bash]
-brew install gcc --without-multilib
-```
-
-`--without-multilib` is necessary for OpenMP multithreading support -- note
-OS X default `gcc`/`clang` doesn't support OpenMP, so we need to install standard
-`gcc`/`g++`
-
-```[bash]
-brew install boost --cc=gcc-6
-```
-
-`--cc=gcc-6` is necessary to build `boost` with standard `gcc`, rather than the
-default bottle which appears to have been built with the system `clang`.
-Brew installs `gcc`/`g++` as `/usr/local/bin/gcc-VERSION` by default to avoid
-clashing with the system's `gcc`/`clang`. `6` is the current version as of
-writing, but may change.
-
-```[bash]
-brew install viennarna
-brew install doxygen
-```
-
-Download and extract the IntaRNA source code package (e.g. `intaRNA-2.0.2.tar.gz`) from the [release page](https://github.com/BackofenLab/IntaRNA/releases/latest).
-
-```[bash]
-./configure CC=gcc-6 CXX=g++-6
+```bash
+brew install autoconf automake boost libtool libomp pkg-config viennarna
 ```
 
-This sets up makefiles to use standard `gcc`/`g++` from brew, which will
-need an update to the appropriate compiler version if not still `6`.
-You might also want to
-set `--prefix=INSTALLPATH` if you dont want to install IntaRNA globally.
+Apple Clang needs the Homebrew `libomp` headers, library and preprocessing flag.
+The following keeps the normal optimized, multithreaded build:
 
-
-```[bash]
-make
-make tests
+```bash
+LIBOMP_PREFIX="$(brew --prefix libomp)"
+CPPFLAGS="-I${LIBOMP_PREFIX}/include" \
+CXXFLAGS="-Xpreprocessor -fopenmp" \
+LDFLAGS="-L${LIBOMP_PREFIX}/lib -Wl,-rpath,${LIBOMP_PREFIX}/lib" \
+LIBS="-lomp" \
+./configure CC=clang CXX=clang++
+make -j2
+make tests -j2
 make install
 ```
 
+Use `--prefix=INSTALLPATH` with `./configure` when a system-wide installation
+is not desired.
+
 
 [![up](doc/figures/icon-up.28.png) back to overview](#overview)
 
@@ -2209,6 +2186,11 @@ processed using doxygen to generate html/pdf versions.
 When IntaRNA is build while `pkg-config` is present, according pkg-config
 information is generated and installed too.
 
+IntaRNA's public headers require C++23. External consumers must therefore
+select `-std=c++23` (or a newer standard) in their own build; the installed
+pkg-config metadata supplies IntaRNA and dependency flags but deliberately
+does not override the consuming project's language mode.
+
 ## Mandatory `Easylogging++` initalization !
 
 Since IntaRNA makes heavy use of the `Easylogging++` library, you have to add (and adapt)
@@ -2255,5 +2237,3 @@ flags are used within the IntaRNA configuration:
 [![up](doc/figures/icon-up.38.png)](https://www.freepik.com/free-vector/colored-arrows_794372.htm)
 Designed by Freepik
 
-
-

conda-build-env.yml

@@ -1,4 +1,3 @@
-
 name: intarna-build-env
 
 channels:
@@ -7,10 +6,10 @@ channels:
   - defaults
 
 dependencies:
-  - gcc_linux-64 
-  - gxx_linux-64 
+  - autoconf
+  - automake
+  - libtool
   - pkgconfig
   - zlib
-  - boost-cpp 
+  - boost-cpp
   - viennarna>=2.4.14
-