[MISC] Add workaround for bogus gcc 12.1 warnings

include/seqan3/core/platform.hpp

@@ -323,6 +323,17 @@
 #   endif
 #endif
 
+/*!\brief Workaround bogus memcpy errors in GCC 12.1. (Wrestrict and Wstringop-overflow)
+ * \see https://gcc.gnu.org/bugzilla/show_bug.cgi?id=105545
+ */
+#ifndef SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY
+#   if defined(__GNUC__) && (__GNUC__ == 12 && __GNUC_MINOR__ < 2)
+#       define SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY 1
+#   else
+#       define SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY 0
+#   endif
+#endif
+
 /*!\brief gcc only: Constrain friend declarations to limit access to internals.
  *
  * \details

include/seqan3/utility/container/small_vector.hpp

@@ -756,7 +756,14 @@ class small_vector
         for (size_type i = sz + length - 1; i > pos_as_num + length - 1; --i)
             data_[i] = data_[i - length];
 
+#if SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wstringop-overflow"
+#endif // SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY
         std::ranges::copy(begin_it, end_it, &data_[pos_as_num]);
+#if SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY
+#pragma GCC diagnostic pop
+#endif // SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY
         sz += length;
         return begin() + pos_as_num;
     }

test/unit/alphabet/container/container_concept_test.cpp

@@ -67,13 +67,20 @@ TEST(container, sequence_container_former_travis_bug)
     s.insert(0, 1, 'E');
     EXPECT_EQ("Exmplr", s);
 
+#if SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wrestrict"
+#endif // SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY
     // insert(size_type index, const char* s)
     s.insert(2, "e");
     EXPECT_EQ("Exemplr", s);
 
     // insert(size_type index, string const& str)
     s.insert(6, "a"s);
     EXPECT_EQ("Exemplar", s);
+#if SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY
+#pragma GCC diagnostic pop
+#endif // SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY
 
     // insert(size_type index, string const& str, size_type index_str, size_type count)
     s.insert(8, " is an example string."s, 0, 14);
@@ -96,9 +103,16 @@ TEST(container, sequence_container_former_travis_bug)
         EXPECT_EQ("Exemplar is an:== example string", s);
     }
 
+#if SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wrestrict"
+#endif // SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY
     // insert(const_iterator pos, std::initializer_list<char>)
     s.insert(s.begin() + s.find_first_of('g') + 1, { '.' });
     EXPECT_EQ("Exemplar is an:== example string.", s);
+#if SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY
+#pragma GCC diagnostic pop
+#endif // SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY
 #else // ^^^ workaround / no workaround vvv
     // insert(const_iterator pos, char ch)
     s.insert(s.cbegin() + s.find_first_of('n') + 1, ':');
@@ -117,8 +131,15 @@ TEST(container, sequence_container_former_travis_bug)
     }
 
     // insert(const_iterator pos, std::initializer_list<char>)
+#if SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wrestrict"
+#endif // SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY
     s.insert(s.cbegin() + s.find_first_of('g') + 1, { '.' });
     EXPECT_EQ("Exemplar is an:== example string.", s);
+#if SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY
+#pragma GCC diagnostic pop
+#endif // SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY
 #endif // SEQAN3_WORKAROUND_GCC_NO_CXX11_ABI
 }
 

test/unit/search/helper_search_scheme.hpp

@@ -43,11 +43,12 @@ inline void get_ordered_search(auto const & search, auto const & blocks_length,
 }
 
 // Helper function for search_error_distribution(res, search).
-inline void search_error_distribution(std::vector<std::vector<uint8_t> > & res, auto l, auto u, uint8_t const e)
+template <typename t>
+void search_error_distribution(std::vector<std::vector<t>> & res, auto l, auto u, uint8_t const e)
 {
     if (l.size() == 0)
     {
-        res.emplace_back(std::forward<std::vector<uint8_t>>(std::vector<uint8_t>{}));
+        res.emplace_back(std::forward<std::vector<t>>(std::vector<t>{}));
         return;
     }
 
@@ -58,7 +59,7 @@ inline void search_error_distribution(std::vector<std::vector<uint8_t> > & res,
 
     for (uint8_t i = std::max(e, l0); i <= u0; ++i)
     {
-        std::vector<std::vector<uint8_t> > res_recursive;
+        std::vector<std::vector<t>> res_recursive;
         search_error_distribution(res_recursive, l, u, i);
         for (auto & res_elem : res_recursive)
         {
@@ -70,21 +71,23 @@ inline void search_error_distribution(std::vector<std::vector<uint8_t> > & res,
 
 // Compute all possible error distributions given a search.
 // The result is in the same order as the search (i.e. search.pi).
-inline void search_error_distribution(std::vector<std::vector<uint8_t> > & res, auto const & search)
+template <typename t>
+void search_error_distribution(std::vector<std::vector<t>> & res, auto const & search)
 {
     res.clear();
-    std::vector<uint8_t> l(search.l.begin(), search.l.end());
-    std::vector<uint8_t> u(search.u.begin(), search.u.end());
+    std::vector<t> l(search.l.begin(), search.l.end());
+    std::vector<t> u(search.u.begin(), search.u.end());
     search_error_distribution(res, l, u, 0u);
 }
 
 // Compute all possible error distributions for each search given a search scheme.
-inline void search_scheme_error_distribution(std::vector<std::vector<uint8_t> > & res, auto const & search_scheme)
+template <typename t>
+void search_scheme_error_distribution(std::vector<std::vector<t>> & res, auto const & search_scheme)
 {
     res.clear();
     for (auto && search : search_scheme)
     {
-        std::vector<std::vector<uint8_t> > res_search;
+        std::vector<std::vector<t>> res_search;
         search_error_distribution(res_search, search);
         for (auto & single_error_distribution : res_search)
             order_search_vector(single_error_distribution, search);

test/unit/search/search_scheme_test.cpp

@@ -14,6 +14,12 @@
 
 #include <gtest/gtest.h>
 
+#if SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY
+using integral_t = uint16_t;
+#else
+using integral_t = uint8_t;
+#endif // SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY
+
 template <uint8_t min_error, uint8_t max_error, bool precomputed_scheme>
 void error_distributions(auto & expected, auto & actual)
 {
@@ -39,7 +45,7 @@ void error_distributions(auto & expected, auto & actual)
 
 TEST(search_scheme_test, error_distribution_coverage_optimum_search_schemes)
 {
-    std::vector<std::vector<uint8_t> > expected, actual;
+    std::vector<std::vector<integral_t>> expected, actual;
 
     error_distributions<0, 0, true>(expected, actual);
     EXPECT_EQ(actual, expected);
@@ -74,7 +80,7 @@ TEST(search_scheme_test, error_distribution_coverage_optimum_search_schemes)
 
 TEST(search_scheme_test, error_distribution_coverage_computed_search_schemes)
 {
-    std::vector<std::vector<uint8_t> > expected, actual;
+    std::vector<std::vector<integral_t>> expected, actual;
 
     error_distributions<0, 0, false>(expected, actual);
     EXPECT_EQ(actual, expected);
@@ -117,7 +123,7 @@ TEST(search_scheme_test, error_distribution_coverage_computed_search_schemes)
 template <uint8_t min_error, uint8_t max_error, bool precomputed_scheme>
 bool check_disjoint_search_scheme()
 {
-    std::vector<std::vector<uint8_t> > error_distributions;
+    std::vector<std::vector<integral_t> > error_distributions;
 
     auto const & oss{seqan3::detail::optimum_search_scheme<min_error, max_error>};
     seqan3::search_scheme_error_distribution(error_distributions, oss);