From 0edac0d32bb46271e865db0524c4b1b09cf486eb Mon Sep 17 00:00:00 2001
From: Lucas Czech <luc.czech@gmail.com>
Date: Tue, 12 Nov 2024 17:20:30 +0100
Subject: [PATCH] Various CI compiler fixes

---
 lib/genesis/taxonomy/functions/kmer.cpp |  6 +++++-
 lib/genesis/utils/core/std.hpp          | 11 +++++++++--
 lib/genesis/utils/io/parser.cpp         |  3 +++
 lib/genesis/utils/math/bit.hpp          | 14 ++++++++++++--
 4 files changed, 29 insertions(+), 5 deletions(-)

diff --git a/lib/genesis/taxonomy/functions/kmer.cpp b/lib/genesis/taxonomy/functions/kmer.cpp
index d2e5d62c..c4ddf2cc 100644
--- a/lib/genesis/taxonomy/functions/kmer.cpp
+++ b/lib/genesis/taxonomy/functions/kmer.cpp
@@ -125,7 +125,7 @@ void assign_children_to_group_(
 ) {
     // Get the data and assert that we are in the right type of taxon
     auto& data = taxon.data<KmerTaxonData>();
-    assert( data.group_status = KmerTaxonData::GroupStatus::kAssigned );
+    assert( data.group_status == KmerTaxonData::GroupStatus::kAssigned );
     assert( data.group_index != std::numeric_limits<size_t>::max() );
 
     // In some previous iteration of the procedur, we already decided that this taxon here is
@@ -299,6 +299,10 @@ size_t group_with_target_number_of_groups( TaxonGroupingSearchParams const& para
     // in which case we cannot get any closer to our target number of groups.
     while( true ) {
 
+        // The current limit always is in between the low and high
+        assert( limit_l <= limit_c );
+        assert( limit_c <= limit_h );
+
         // Construct groups with the current limits.
         // Depending on whether the given params want us to modify the number of sequences,
         // or their total combined length per group, we set the internal "limit" here, which can
diff --git a/lib/genesis/utils/core/std.hpp b/lib/genesis/utils/core/std.hpp
index 11eb3aad..99beaf8f 100644
--- a/lib/genesis/utils/core/std.hpp
+++ b/lib/genesis/utils/core/std.hpp
@@ -227,6 +227,11 @@ struct genesis_invoke_result
 //     container traits
 // -------------------------------------------------------------------------
 
+// Implement void_t for C++11.
+// We are not using the C++17 version here, for simplicity.
+template <typename...>
+using void_t = void;
+
 template <typename T, typename = void>
 struct is_container : std::false_type {};
 
@@ -236,7 +241,7 @@ struct is_container : std::false_type {};
  */
 template <typename T>
 struct is_container<
-    T, std::void_t<
+    T, void_t<
         typename T::value_type,
         decltype(std::declval<T>().begin()),
         decltype(std::declval<T>().end())
@@ -252,7 +257,9 @@ template <typename T, typename = void>
 struct has_reserve : std::false_type {};
 
 template <typename T>
-struct has_reserve<T, std::void_t<decltype(std::declval<T&>().reserve(std::declval<size_t>()))>> : std::true_type {};
+struct has_reserve<
+    T, void_t<decltype(std::declval<T&>().reserve(std::declval<size_t>()))>
+> : std::true_type {};
 
 // Convenience variable template for has_reserve trait
 template <typename T>
diff --git a/lib/genesis/utils/io/parser.cpp b/lib/genesis/utils/io/parser.cpp
index 7f67335b..27a9bed4 100644
--- a/lib/genesis/utils/io/parser.cpp
+++ b/lib/genesis/utils/io/parser.cpp
@@ -266,6 +266,9 @@ size_t parse_unsigned_integer_from_chars_( utils::InputStream& source )
     using namespace utils;
     T x = 0;
 
+    // If we want to use __builtin_mul_overflow here, we should check its existence first,
+    // using __has_builtin first. See genesis/utils/math/bit.hpp for examples.
+
     // Hardcoded base 10. See below for other version that allows to select base.
     auto raise_and_add_ = []( T& val, unsigned char c ) {
         return !(
diff --git a/lib/genesis/utils/math/bit.hpp b/lib/genesis/utils/math/bit.hpp
index b585b168..b6c6a8ce 100644
--- a/lib/genesis/utils/math/bit.hpp
+++ b/lib/genesis/utils/math/bit.hpp
@@ -57,12 +57,20 @@ namespace utils {
 //     Pop Count
 // ================================================================================================
 
+// Following the preprocessor documentation for __has_builtin
+// https://gcc.gnu.org/onlinedocs/cpp/_005f_005fhas_005fbuiltin.html
+#ifdef __has_builtin
+#  if __has_builtin(__builtin_popcount) && __has_builtin(__builtin_popcountl) && __has_builtin(__builtin_popcountll)
+#    define GENESIS_HAS_BUILTIN_POPCOUNT
+#  endif
+#endif
+
 /**
  * @brief Compute the pop count (Hamming weight) of an unsigned int.
  */
 template <typename T>
 inline
-#if defined(__cpp_lib_bitops) || (defined(__has_builtin) && __has_builtin(__builtin_popcountll))
+#if defined(__cpp_lib_bitops) || defined(GENESIS_HAS_BUILTIN_POPCOUNT)
 constexpr
 #endif
 typename std::enable_if<std::is_unsigned<T>::value, uint64_t>::type
@@ -75,7 +83,7 @@ pop_count( T n )
         // https://en.cppreference.com/w/cpp/numeric/popcount
         return std::popcount(n);
 
-    #elif defined(__has_builtin) && __has_builtin(__builtin_popcountll)
+    #elif defined(GENESIS_HAS_BUILTIN_POPCOUNT)
 
         // Otherwise, use GCC/Clang intrinsic if available.
         if (sizeof(T) <= sizeof(unsigned int)) {
@@ -112,6 +120,8 @@ pop_count( T n )
     #endif
 }
 
+#undef GENESIS_HAS_BUILTIN_POPCOUNT
+
 // ================================================================================================
 //     Bit Extract
 // ================================================================================================