Add standalone IntaRNA 4.0 implementation

IntaRNAnew/.gitignore

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+IntaRNAnew
+IntaRNAnewBenchmark
+IntaRNAnewPvalue
+IntaRNAnewSvg
+IntaRNAnewTspot
+*.a
+*.d
+*.o
+*.dot
+/Testing/
+/cmake-build-*/
+/build/

IntaRNAnew/CMakeLists.txt

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+cmake_minimum_required(VERSION 3.25)
+
+project(IntaRNAnew VERSION 4.0.0 LANGUAGES CXX)
+
+set(CMAKE_CXX_EXTENSIONS OFF)
+
+include(CTest)
+include(GNUInstallDirs)
+include(CMakePackageConfigHelpers)
+find_package(Threads REQUIRED)
+
+option(INTARNANEW_ENABLE_SANITIZERS
+    "Enable address and undefined-behaviour sanitizers" OFF)
+option(INTARNANEW_BUILD_BENCHMARKS
+    "Build the POSIX benchmark when BUILD_TESTING is disabled" OFF)
+set(INTARNA_LEGACY_BIN "$ENV{INTARNA_LEGACY_BIN}" CACHE FILEPATH
+    "Optional IntaRNA Legacy executable for the 17-case black-box parity test")
+
+set(_intarnanew_local_parameter_dir
+    "${CMAKE_CURRENT_SOURCE_DIR}/../.conda-env/share/ViennaRNA")
+if(NOT EXISTS "${_intarnanew_local_parameter_dir}")
+    set(_intarnanew_local_parameter_dir "")
+endif()
+set(INTARNANEW_TEST_PARAMETER_DIR "${_intarnanew_local_parameter_dir}" CACHE PATH
+    "Directory containing public ViennaRNA .par files for thermodynamic tests")
+unset(_intarnanew_local_parameter_dir)
+
+function(intarnanew_enable_warnings target)
+    if(MSVC)
+        target_compile_options(${target} PRIVATE /W4 /permissive-)
+    elseif(CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang|AppleClang")
+        target_compile_options(${target} PRIVATE
+            -Wall -Wextra -Wpedantic -Wconversion -Wshadow)
+    endif()
+endfunction()
+
+function(intarnanew_enable_sanitizers target)
+    if(NOT INTARNANEW_ENABLE_SANITIZERS)
+        return()
+    endif()
+    if(CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang|AppleClang")
+        target_compile_options(${target} PRIVATE
+            -fsanitize=address,undefined -fno-omit-frame-pointer)
+        target_link_options(${target} PRIVATE -fsanitize=address,undefined)
+    else()
+        message(FATAL_ERROR
+            "INTARNANEW_ENABLE_SANITIZERS requires GCC, Clang, or AppleClang")
+    endif()
+endfunction()
+
+function(intarnanew_set_parameter_test_environment test_name)
+    if(INTARNANEW_TEST_PARAMETER_DIR)
+        set_tests_properties(${test_name} PROPERTIES ENVIRONMENT
+            "INTARNANEW_PARAMETER_DIR=${INTARNANEW_TEST_PARAMETER_DIR}")
+    endif()
+endfunction()
+
+add_library(intarnanew STATIC
+    src/accessibility.cpp
+    src/cli.cpp
+    src/compression.cpp
+    src/energy.cpp
+    src/folding.cpp
+    src/folding_parameters.cpp
+    src/helix_blocks.cpp
+    src/output.cpp
+    src/output_plan.cpp
+    src/predictor.cpp
+    src/runner.cpp
+    src/sequence.cpp
+    src/thermo_parameters.cpp
+)
+add_library(IntaRNAnew::core ALIAS intarnanew)
+set_target_properties(intarnanew PROPERTIES EXPORT_NAME core)
+target_include_directories(intarnanew PUBLIC
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+    $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
+target_compile_features(intarnanew PUBLIC cxx_std_23)
+target_link_libraries(intarnanew PUBLIC Threads::Threads)
+intarnanew_enable_warnings(intarnanew)
+intarnanew_enable_sanitizers(intarnanew)
+
+add_library(intarnanew_tools STATIC
+    src/tools/csv.cpp
+    src/tools/mutations.cpp
+    src/tools/pvalue.cpp
+    src/tools/statistics.cpp
+    src/tools/svg.cpp
+)
+add_library(IntaRNAnew::tools ALIAS intarnanew_tools)
+set_target_properties(intarnanew_tools PROPERTIES
+    EXPORT_NAME tools
+    OUTPUT_NAME intarnanew-tools
+)
+target_include_directories(intarnanew_tools PUBLIC
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+    $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
+target_compile_features(intarnanew_tools PUBLIC cxx_std_23)
+target_link_libraries(intarnanew_tools PUBLIC intarnanew Threads::Threads)
+intarnanew_enable_warnings(intarnanew_tools)
+intarnanew_enable_sanitizers(intarnanew_tools)
+
+add_executable(IntaRNAnew app/main.cpp)
+target_link_libraries(IntaRNAnew PRIVATE intarnanew)
+intarnanew_enable_warnings(IntaRNAnew)
+intarnanew_enable_sanitizers(IntaRNAnew)
+
+foreach(tool IN ITEMS csv stats svg mutate pvalue)
+    add_executable(intarnanew-${tool} tools/intarnanew-${tool}.cpp)
+    target_link_libraries(intarnanew-${tool} PRIVATE intarnanew_tools)
+    intarnanew_enable_warnings(intarnanew-${tool})
+    intarnanew_enable_sanitizers(intarnanew-${tool})
+endforeach()
+
+if(INTARNANEW_BUILD_BENCHMARKS AND NOT UNIX)
+    message(FATAL_ERROR "The black-box benchmark requires POSIX process APIs")
+endif()
+if(UNIX AND (INTARNANEW_BUILD_BENCHMARKS OR BUILD_TESTING))
+    add_executable(IntaRNAnewBenchmark benchmarks/compare.cpp)
+    target_compile_features(IntaRNAnewBenchmark PRIVATE cxx_std_23)
+    intarnanew_enable_warnings(IntaRNAnewBenchmark)
+    intarnanew_enable_sanitizers(IntaRNAnewBenchmark)
+endif()
+
+if(BUILD_TESTING)
+    add_executable(IntaRNAnewIntegrationTests tests/integration.cpp)
+    target_link_libraries(IntaRNAnewIntegrationTests PRIVATE intarnanew)
+    intarnanew_enable_warnings(IntaRNAnewIntegrationTests)
+    intarnanew_enable_sanitizers(IntaRNAnewIntegrationTests)
+    add_test(NAME real_interactions COMMAND IntaRNAnewIntegrationTests)
+    intarnanew_set_parameter_test_environment(real_interactions)
+
+    add_executable(IntaRNAnewCliIoOutputTests tests/cli_io_output.cpp)
+    target_link_libraries(IntaRNAnewCliIoOutputTests PRIVATE intarnanew)
+    intarnanew_enable_warnings(IntaRNAnewCliIoOutputTests)
+    intarnanew_enable_sanitizers(IntaRNAnewCliIoOutputTests)
+    add_test(NAME cli_io_output_regressions COMMAND IntaRNAnewCliIoOutputTests)
+
+    add_executable(IntaRNAnewConfigRegistryTests tests/config_registry.cpp)
+    target_link_libraries(IntaRNAnewConfigRegistryTests PRIVATE intarnanew)
+    intarnanew_enable_warnings(IntaRNAnewConfigRegistryTests)
+    intarnanew_enable_sanitizers(IntaRNAnewConfigRegistryTests)
+    add_test(NAME config_registry COMMAND IntaRNAnewConfigRegistryTests)
+    set_tests_properties(config_registry PROPERTIES ENVIRONMENT
+        "INTARNANEW_SOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR}")
+
+    add_executable(IntaRNAnewAccessibilityOracleTests tests/accessibility_oracle.cpp)
+    target_link_libraries(IntaRNAnewAccessibilityOracleTests PRIVATE intarnanew)
+    intarnanew_enable_warnings(IntaRNAnewAccessibilityOracleTests)
+    intarnanew_enable_sanitizers(IntaRNAnewAccessibilityOracleTests)
+    add_test(NAME accessibility_oracle COMMAND IntaRNAnewAccessibilityOracleTests)
+
+    add_executable(IntaRNAnewFoldingOracleTests tests/folding_oracle.cpp)
+    target_link_libraries(IntaRNAnewFoldingOracleTests PRIVATE intarnanew)
+    intarnanew_enable_warnings(IntaRNAnewFoldingOracleTests)
+    intarnanew_enable_sanitizers(IntaRNAnewFoldingOracleTests)
+    add_test(NAME folding_oracle COMMAND IntaRNAnewFoldingOracleTests)
+    intarnanew_set_parameter_test_environment(folding_oracle)
+
+    add_executable(IntaRNAnewPredictorOracleTests tests/predictor_oracle.cpp)
+    target_link_libraries(IntaRNAnewPredictorOracleTests PRIVATE intarnanew)
+    intarnanew_enable_warnings(IntaRNAnewPredictorOracleTests)
+    intarnanew_enable_sanitizers(IntaRNAnewPredictorOracleTests)
+    add_test(NAME predictor_oracle COMMAND IntaRNAnewPredictorOracleTests)
+
+    add_executable(IntaRNAnewExecutionRegionsTests tests/execution_regions.cpp)
+    target_link_libraries(IntaRNAnewExecutionRegionsTests PRIVATE intarnanew)
+    intarnanew_enable_warnings(IntaRNAnewExecutionRegionsTests)
+    intarnanew_enable_sanitizers(IntaRNAnewExecutionRegionsTests)
+    add_test(NAME region_window_execution COMMAND IntaRNAnewExecutionRegionsTests)
+
+    add_executable(IntaRNAnewModelSemanticsTests tests/model_semantics.cpp)
+    target_link_libraries(IntaRNAnewModelSemanticsTests PRIVATE intarnanew)
+    intarnanew_enable_warnings(IntaRNAnewModelSemanticsTests)
+    intarnanew_enable_sanitizers(IntaRNAnewModelSemanticsTests)
+    add_test(NAME interaction_model_semantics COMMAND IntaRNAnewModelSemanticsTests)
+
+    add_executable(IntaRNAnewCompressionIoTests tests/compression_io.cpp)
+    target_link_libraries(IntaRNAnewCompressionIoTests PRIVATE intarnanew)
+    intarnanew_enable_warnings(IntaRNAnewCompressionIoTests)
+    intarnanew_enable_sanitizers(IntaRNAnewCompressionIoTests)
+    add_test(NAME compression_and_gzip_io COMMAND IntaRNAnewCompressionIoTests)
+
+    add_executable(IntaRNAnewOutputExecutionTests tests/output_execution.cpp)
+    target_link_libraries(IntaRNAnewOutputExecutionTests PRIVATE intarnanew)
+    intarnanew_enable_warnings(IntaRNAnewOutputExecutionTests)
+    intarnanew_enable_sanitizers(IntaRNAnewOutputExecutionTests)
+    add_test(NAME output_planning_and_parallel_execution
+        COMMAND IntaRNAnewOutputExecutionTests)
+
+    add_executable(IntaRNAnewRunnerContractTests tests/runner_contracts.cpp)
+    target_link_libraries(IntaRNAnewRunnerContractTests PRIVATE intarnanew)
+    intarnanew_enable_warnings(IntaRNAnewRunnerContractTests)
+    intarnanew_enable_sanitizers(IntaRNAnewRunnerContractTests)
+    add_test(NAME in_process_pair_runner COMMAND IntaRNAnewRunnerContractTests)
+
+    add_executable(IntaRNAnewToolsContractTests tests/tools_contracts.cpp)
+    target_link_libraries(IntaRNAnewToolsContractTests PRIVATE intarnanew_tools)
+    intarnanew_enable_warnings(IntaRNAnewToolsContractTests)
+    intarnanew_enable_sanitizers(IntaRNAnewToolsContractTests)
+    add_test(NAME native_tools_contracts COMMAND IntaRNAnewToolsContractTests)
+
+    if(UNIX)
+        add_executable(IntaRNAnewPvalueExecutableTests tests/pvalue_executable.cpp)
+        target_compile_features(IntaRNAnewPvalueExecutableTests PRIVATE cxx_std_23)
+        intarnanew_enable_warnings(IntaRNAnewPvalueExecutableTests)
+        intarnanew_enable_sanitizers(IntaRNAnewPvalueExecutableTests)
+        add_test(NAME pvalue_executable_contracts
+            COMMAND IntaRNAnewPvalueExecutableTests
+                "$<TARGET_FILE:intarnanew-pvalue>")
+        set_tests_properties(pvalue_executable_contracts PROPERTIES TIMEOUT 120)
+
+        set(_intarnanew_legacy_test_arguments)
+        if(INTARNA_LEGACY_BIN)
+            list(APPEND _intarnanew_legacy_test_arguments
+                --legacy "${INTARNA_LEGACY_BIN}")
+        endif()
+        add_test(NAME legacy_blackbox_17
+            COMMAND IntaRNAnewBenchmark
+                --new "$<TARGET_FILE:IntaRNAnew>"
+                --cases "${CMAKE_CURRENT_SOURCE_DIR}/tests/fixtures/parameters"
+                --verify-only --expect-cases 17 --skip-without-legacy
+                ${_intarnanew_legacy_test_arguments})
+        set_tests_properties(legacy_blackbox_17 PROPERTIES
+            SKIP_REGULAR_EXPRESSION "^SKIP:")
+        unset(_intarnanew_legacy_test_arguments)
+    endif()
+endif()
+
+install(TARGETS intarnanew intarnanew_tools
+    EXPORT IntaRNAnewTargets
+    ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+    RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
+    INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+)
+install(TARGETS IntaRNAnew
+    intarnanew-csv intarnanew-stats intarnanew-svg intarnanew-mutate
+    intarnanew-pvalue
+    RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
+)
+install(DIRECTORY include/intarnanew
+    DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+    FILES_MATCHING PATTERN "*.hpp"
+)
+install(FILES README.md MATHEMATICAL_AUDIT.md LICENSE
+    DESTINATION ${CMAKE_INSTALL_DOCDIR}
+)
+install(FILES tools/README.md
+    DESTINATION ${CMAKE_INSTALL_DOCDIR}/tools
+)
+
+set(intarnanew_package_dir
+    "${CMAKE_INSTALL_LIBDIR}/cmake/IntaRNAnew")
+configure_package_config_file(
+    IntaRNAnewConfig.cmake.in
+    "${CMAKE_CURRENT_BINARY_DIR}/IntaRNAnewConfig.cmake"
+    INSTALL_DESTINATION "${intarnanew_package_dir}"
+)
+write_basic_package_version_file(
+    "${CMAKE_CURRENT_BINARY_DIR}/IntaRNAnewConfigVersion.cmake"
+    VERSION ${PROJECT_VERSION}
+    COMPATIBILITY SameMajorVersion
+)
+install(EXPORT IntaRNAnewTargets
+    FILE IntaRNAnewTargets.cmake
+    NAMESPACE IntaRNAnew::
+    DESTINATION "${intarnanew_package_dir}"
+)
+install(FILES
+    "${CMAKE_CURRENT_BINARY_DIR}/IntaRNAnewConfig.cmake"
+    "${CMAKE_CURRENT_BINARY_DIR}/IntaRNAnewConfigVersion.cmake"
+    DESTINATION "${intarnanew_package_dir}"
+)

IntaRNAnew/IntaRNAnewConfig.cmake.in

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+@PACKAGE_INIT@
+
+include(CMakeFindDependencyMacro)
+find_dependency(Threads)
+
+include("${CMAKE_CURRENT_LIST_DIR}/IntaRNAnewTargets.cmake")
+check_required_components(IntaRNAnew)

IntaRNAnew/LICENSE

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+SPDX-License-Identifier: GPL-3.0-or-later
+
+Copyright (C) 2026 IntaRNAnew contributors
+
+This program is free software: you can redistribute it and/or modify it under
+the terms of the GNU General Public License as published by the Free Software
+Foundation, either version 3 of the License, or (at your option) any later
+version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See <https://www.gnu.org/licenses/>.