Fix some compatibility issues with C++17 and later

CMakeLists.txt

@@ -284,7 +284,7 @@ else ()
     ENDIF()
 endif ()
 
-set (CMAKE_CXX_FLAGS         "${CMAKE_CXX_FLAGS} -mbmi2 ${WARN_FLAGS}")
+set (CMAKE_CXX_FLAGS         "${CMAKE_CXX_FLAGS} ${WARN_FLAGS}")
 set (CMAKE_CXX_FLAGS_DEBUG   "${CMAKE_CXX_FLAGS_DEBUG} -O2 -DDEBUG -g -ggdb3 -D_GLIBCXX_DEBUG -D_GLIBCXX_DEBUG_PEDANTIC")
 set (CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3 -DNDEBUG")
 

lib/genesis/placement/simulator/distributions.cpp

@@ -1,6 +1,6 @@
 /*
     Genesis - A toolkit for working with phylogenetic data.
-    Copyright (C) 2014-2019 Lucas Czech and HITS gGmbH
+    Copyright (C) 2014-2024 Lucas Czech
 
     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
@@ -38,6 +38,7 @@
 #include <algorithm>
 #include <cassert>
 #include <numeric>
+#include <random>
 #include <stdexcept>
 
 namespace genesis {
@@ -127,13 +128,19 @@ std::vector<size_t> SimulatorExtraPlacementDistribution::generate( PlacementTree
         return result;
     }
 
+    // Set up a random engine. Proably should use the global seed, but well, good enough for now.
+    std::random_device rd;
+    std::default_random_engine rng(rd());
+
     // We make sure that an edge gets at most one placement per pquery by maintaining a list of
     // possible candidate edges that do not have a placement (for this pquery) yet.
     // For this, get a list of all possible candidates of neighbouring edges of the given edge.
     // We shuffle them so that we take different edges for every pquery.
     auto edge_prox = edge_proximities_[ edge.index() ];
     for( auto& candidates : edge_prox.candidates_per_level ) {
-        std::random_shuffle( candidates.begin() , candidates.end() );
+        // Update for C++17 and later:
+        // std::random_shuffle( candidates.begin() , candidates.end() );
+        std::shuffle( candidates.begin(), candidates.end(), rng );
     }
 
     // We can only place as many placements as there are neighbouring edges.

lib/genesis/utils/containers/optional.hpp

@@ -3,7 +3,7 @@
 
 /*
     Genesis - A toolkit for working with phylogenetic data.
-    Copyright (C) 2014-2022 Lucas Czech
+    Copyright (C) 2014-2024 Lucas Czech
 
     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
@@ -89,10 +89,13 @@
 #    define GENESIS_OPTIONAL_HAVE_STD_OPTIONAL  0
 #endif
 
-// Use C++17 std::optional if available and requested:
-// Currently, we default to using std::optional if it is available.
-// Might make this configurable in the future.
-#define GENESIS_OPTIONAL_USES_STD_OPTIONAL GENESIS_OPTIONAL_HAVE_STD_OPTIONAL
+// We offer a switch to use C++17 std::optional if available and requested.
+// However, this currently is not working under MacOS with GCC,
+// where somehow our test case Containers.OptionalObservers triggers an assertion
+// of std::optional to fail... So we just keep using our implementation for now,
+// and decativate to offer using std::optional.
+// #define GENESIS_OPTIONAL_USES_STD_OPTIONAL GENESIS_OPTIONAL_HAVE_STD_OPTIONAL
+#define GENESIS_OPTIONAL_USES_STD_OPTIONAL 0
 
 // =================================================================================================
 //     Using std::optional

lib/genesis/utils/formats/json/iterator.hpp

@@ -3,7 +3,7 @@
 
 /*
     Genesis - A toolkit for working with phylogenetic data.
-    Copyright (C) 2014-2017 Lucas Czech
+    Copyright (C) 2014-2024 Lucas Czech
 
     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
@@ -99,7 +99,7 @@ namespace utils {
  * @link supplement_acknowledgements_code_reuse_json_document Acknowledgements@endlink.
  */
 template<typename U>
-class JsonIterator : public std::iterator<std::random_access_iterator_tag, U>
+class JsonIterator // : public std::iterator<std::random_access_iterator_tag, U>
 {
     // -------------------------------------------------------------------------
     //     Friends and Asserts

lib/genesis/utils/io/parser.cpp

@@ -40,10 +40,15 @@
 #include <stdexcept>
 
 // For C++17, we have a little speedup in the integer parsing part.
+// Not avaiable on GCC < 8 though, so we need an additional check here...
 #if ((defined(_MSVC_LANG) && _MSVC_LANG >= 201703L) || __cplusplus >= 201703L)
+#if defined( __has_include ) && __has_include(<charconv>)
+    #define GENESIS_COMPILER_HAS_CHARCONV
+#endif
+#endif
 
+#ifdef GENESIS_COMPILER_HAS_CHARCONV
     #include <charconv>
-
 #endif
 
 namespace genesis {
@@ -323,8 +328,8 @@ size_t parse_unsigned_integer_from_chars_( utils::InputStream& source )
 //     parse_unsigned_integer_std_from_chars_
 // -------------------------------------------------------------------------
 
-// Only use C++17 code if we are compiled with that version.
-#if ((defined(_MSVC_LANG) && _MSVC_LANG >= 201703L) || __cplusplus >= 201703L)
+// Only use C++17 code if we are compiled with that version and charconv support.
+#ifdef GENESIS_COMPILER_HAS_CHARCONV
 
 /**
  * @brief Another speedup technique using std::from_chars(),
@@ -389,7 +394,7 @@ size_t parse_unsigned_integer_std_from_chars_( utils::InputStream& source )
     return x;
 }
 
-#endif // ((defined(_MSVC_LANG) && _MSVC_LANG >= 201703L) || __cplusplus >= 201703L)
+#endif // GENESIS_COMPILER_HAS_CHARCONV
 
 // -------------------------------------------------------------------------
 //     parse_unsigned_integer_naive_
@@ -458,7 +463,7 @@ size_t parse_unsigned_integer_size_t( utils::InputStream& source )
         // If we have GCC or Clang, use our own handcrafted fast-as-hell implementation.
         return parse_unsigned_integer_gcc_intrinsic_( source );
 
-    // #elif ((defined(_MSVC_LANG) && _MSVC_LANG >= 201703L) || __cplusplus >= 201703L)
+    // #elif GENESIS_COMPILER_HAS_CHARCONV
     //
     //     // Otherwise, if this is C++17, at least use its own fast version,
     //     // that can use some compiler intrinsics itself.

lib/genesis/utils/threading/thread_pool.hpp

@@ -452,9 +452,11 @@ class ThreadPool
      */
     template<class F, class... Args>
     auto enqueue_and_retrieve( F&& f, Args&&... args )
-    -> ProactiveFuture<typename std::result_of<F(Args...)>::type>
+    -> ProactiveFuture<typename std::invoke_result<F, Args...>::type>
     {
-        using result_type = typename std::result_of<F(Args...)>::type;
+        // Updated for C++17 and later:
+        // using result_type = typename std::result_of<F(Args...)>::type;
+        using result_type = typename std::invoke_result<F, Args...>::type;
 
         // Make sure that we do not enqueue more tasks than the max size.
         run_tasks_until_below_max_queue_size_();

tools/cmake/DetectCppVersion.cmake

@@ -41,10 +41,13 @@ set(CPP_VERSIONS_AND_FLAGS
 
 # Function to detect the highest available C++ standard
 function(detect_highest_cpp_version HIGHEST_SUPPORTED_CXX_VERSION)
-    # Create a minimal C++ source code snippet for testing
+    # Create a minimal C++ source code snippet for testing.
+    # We also include the chrono header here as a super ugly ad-hoc patch for a clang bug,
+    # which occurs with that header and clang 10 to 14, see
+    # https://stackoverflow.com/a/63985023/4184258
     file(
         WRITE "${CMAKE_BINARY_DIR}/test_cpp_version.cpp"
-        "#include <iostream>\nint main() { std::cout << \"C++ version check\" << std::endl; return 0; }\n"
+        "#include <iostream>\n#include <chrono>\nint main() { std::cout << \"C++ version check\" << std::endl; return 0; }\n"
     )
 
     # Iterate over the list of C++ versions and their corresponding and check if it is supported