Merge pull request #3212 from eseiler/infra/snippet

[FIX] libc++: snippet tests

.github/workflows/ci_misc.yml

@@ -31,6 +31,13 @@ jobs:
       fail-fast: false
       matrix:
         include:
+          - name: "Snippet clang17 libc++"
+            compiler: "clang-17"
+            build: snippet
+            build_type: Release
+            test_threads: 1 # snippets create and delete files and some separate tests create/delete the same files
+            cxx_flags: "-stdlib=libc++"
+
           - name: "Snippet gcc11"
             compiler: "gcc-11"
             build: snippet

doc/cookbook/simd_dna4.cpp

@@ -5,5 +5,5 @@
 
 int main()
 {
-    [[maybe_unused]] simd_dna4 letter{};
+    simd_dna4 letter{};
 }

doc/tutorial/04_alphabet/alphabet_main.cpp

@@ -115,23 +115,6 @@ int main()
     std::set<seqan3::dna4> pyrimidines{'C'_dna4, 'T'_dna4};
     //! [containers]
 
-    // Prevent -Wunused-variable warnings.
-    (void)rank_a;
-    (void)rank_g;
-    (void)char_a;
-    (void)char_g;
-    (void)size1;
-    (void)size2;
-    (void)dna_sequence;
-    (void)alignment_column;
-    (void)pyrimidines;
-    (void)eq;
-    (void)neq;
-    (void)geq;
-    (void)gt;
-    (void)seq;
-    (void)st;
-
     //! [closing]
     return 0;
 }

doc/tutorial/06_minimisers/minimisers_snippets.cpp

@@ -24,7 +24,7 @@ int main()
         uint64_t const seed = 0x8F3F73B5CF1C9ADE;
         auto minimisers = text | seqan3::views::kmer_hash(seqan3::ungapped{4})
                         | std::views::transform(
-                              [seed](uint64_t i)
+                              [](uint64_t i)
                               {
                                   return i ^ seed;
                               })

doc/tutorial/08_pairwise_alignment/configurations.cpp

@@ -41,7 +41,6 @@ int main()
                                                        seqan3::align_cfg::free_end_gaps_sequence1_trailing{false},
                                                        seqan3::align_cfg::free_end_gaps_sequence2_trailing{true}};
         //! [method_global_free_end_gaps]
-        (void)config;
     }
 
     {
@@ -57,8 +56,6 @@ int main()
         aa_scheme.set_similarity_matrix(seqan3::aminoacid_similarity_matrix::blosum30);
         auto sc_aa = aa_scheme.score('M'_aa27, 'K'_aa27); // sc_aa == 2.
         //! [scoring_scheme]
-        (void)sc_nc;
-        (void)sc_aa;
     }
 
     {
@@ -71,8 +68,6 @@ int main()
         int open_score = affine_scheme.open_score;           // == -10
         int extension_score = affine_scheme.extension_score; // == -1
         //! [gap_cost_affine]
-        (void)open_score;
-        (void)extension_score;
     }
 
     {
@@ -81,7 +76,6 @@ int main()
         // Configure the alignment to only compute the score.
         auto cfg = seqan3::align_cfg::output_score{};
         //! [output]
-        (void)cfg;
     }
 
     {
@@ -91,7 +85,6 @@ int main()
         auto cfg = seqan3::align_cfg::band_fixed_size{seqan3::align_cfg::lower_diagonal{-4},
                                                       seqan3::align_cfg::upper_diagonal{4}};
         //! [band]
-        (void)cfg;
     }
 
     {
@@ -100,6 +93,5 @@ int main()
         // Configure an edit distance alignment.
         auto cfg = seqan3::align_cfg::method_global{} | seqan3::align_cfg::edit_scheme;
         //! [edit]
-        (void)cfg;
     }
 }

doc/tutorial/11_read_mapper/read_mapper_step2.cpp

@@ -46,19 +46,21 @@ void map_reads(std::filesystem::path const & query_path,
 
     seqan3::sequence_file_input query_file_in{query_path};
 
+    (void)sam_path; // Silence warning about unused parameter. We are not yet using `sam_path`.
+
     seqan3::configuration const search_config =
         seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{errors}}
         | seqan3::search_cfg::hit_all_best{};
 
     for (auto && record : query_file_in | std::views::take(20))
     {
+        (void)storage; // Silence warning about unused parameter. We are not yet using `storage`.
+
         seqan3::debug_stream << "Hits:" << '\n';
         for (auto && result : search(record.sequence(), index, search_config))
             seqan3::debug_stream << result << '\n';
         seqan3::debug_stream << "======================" << '\n';
     }
-    (void)sam_path; // prevent unused parameter warning
-    (void)storage;  // prevent unused parameter warning
 }
 
 void run_program(std::filesystem::path const & reference_path,

doc/tutorial/11_read_mapper/read_mapper_step3.cpp

@@ -47,6 +47,8 @@ void map_reads(std::filesystem::path const & query_path,
 
     seqan3::sequence_file_input query_file_in{query_path};
 
+    (void)sam_path; // Silence warning about unused parameter. We are not yet using `sam_path`.
+
     seqan3::configuration const search_config =
         seqan3::search_cfg::max_error_total{seqan3::search_cfg::error_count{errors}}
         | seqan3::search_cfg::hit_all_best{};
@@ -79,7 +81,6 @@ void map_reads(std::filesystem::path const & query_path,
             }
         }
     }
-    (void)sam_path; // prevent unused parameter warning
 }
 //! [solution]
 

include/seqan3/utility/char_operations/predicate_detail.hpp

@@ -19,6 +19,7 @@
 #include <stdexcept>
 #include <string>
 
+#include <seqan3/utility/concept.hpp>
 #include <seqan3/utility/detail/type_name_as_string.hpp>
 #include <seqan3/utility/type_traits/basic.hpp>
 
@@ -194,7 +195,21 @@ struct char_predicate_base
     constexpr bool operator()(value_t const val) const noexcept
         requires (sizeof(value_t) != 1)
     {
-        using char_trait = std::char_traits<value_t>;
+        // std::char_traits is only guaranteed to be defined for character types.
+        // libc++ deprecates other specialisations in llvm-17, and removes them in llvm-18.
+        // We map the non-character types to corresponding chracter types.
+        // For example, `seqan3::is_eof(EOF)` will call this function with `value_t == int`.
+        // clang-format off
+        using char_value_t = std::conditional_t<seqan3::builtin_character<value_t>, value_t,
+                             std::conditional_t<std::same_as<value_t, std::char_traits<char>::int_type>, char,
+                             std::conditional_t<std::same_as<value_t, std::char_traits<wchar_t>::int_type>, wchar_t,
+                             std::conditional_t<std::same_as<value_t, std::char_traits<char8_t>::int_type>, char8_t,
+                             std::conditional_t<std::same_as<value_t, std::char_traits<char16_t>::int_type>, char16_t,
+                             std::conditional_t<std::same_as<value_t, std::char_traits<char32_t>::int_type>, char32_t,
+                             void>>>>>>;
+        // clang-format on
+        static_assert(!std::same_as<char_value_t, void>, "There is no valid character representation.");
+        using char_trait = std::char_traits<char_value_t>;
         return (static_cast<std::make_unsigned_t<value_t>>(val) < 256) ? operator()(static_cast<uint8_t>(val))
              : (char_trait::eq_int_type(val, char_trait::eof()))       ? derived_t::data[256]
                                                                        : false;

include/seqan3/utility/tuple/pod_tuple.hpp

@@ -39,9 +39,7 @@ struct pod_tuple
  * actually enforces this on all types in the tuple (if you want to add non POD types, just use
  * std::tuple instead).
  *
- * It (only) supports [aggregate initialization](https://en.cppreference.com/w/cpp/language/aggregate_initialization),
- * i.e. you must use brace-initializiers and cannot
- * use paranthesis. You can use seqan3::get or std::get and also
+ * You can use seqan3::get or std::get and also
  * [structured bindings](https://en.cppreference.com/w/cpp/language/declarations#Structured_binding_declaration)
  * to access the elements in the tuple.
  *
@@ -57,6 +55,17 @@ struct pod_tuple<type0, types...>
     type0 _head;
     //!\brief The rest of the elements defined as a "recursive member".
     pod_tuple<types...> _tail;
+
+    constexpr pod_tuple() noexcept = default;                              //!< Defaulted.
+    constexpr pod_tuple(pod_tuple const &) noexcept = default;             //!< Defaulted.
+    constexpr pod_tuple & operator=(pod_tuple const &) noexcept = default; //!< Defaulted.
+    constexpr pod_tuple(pod_tuple &&) noexcept = default;                  //!< Defaulted.
+    constexpr pod_tuple & operator=(pod_tuple &&) noexcept = default;      //!< Defaulted.
+    constexpr ~pod_tuple() noexcept = default;                             //!< Defaulted.
+
+    //!\brief Construct from arguments.
+    constexpr pod_tuple(type0 v0, types... args) noexcept : _head{v0}, _tail{args...}
+    {}
     //!\endcond
 
     /*!\name Comparison operators

test/snippet/CMakeLists.txt

@@ -16,6 +16,7 @@ option (SEQAN3_GENERATE_SNIPPETS "Whether seqan3 snippets should be generated an
 
 add_library (snippet_main snippet_main.cpp)
 target_link_libraries (snippet_main PUBLIC seqan3::test gtest)
+target_compile_options (snippet_main PUBLIC "-Wno-unused-variable" "-Wno-unused-but-set-variable")
 
 macro (seqan3_snippet test_name_prefix snippet snippet_base_path)
     seqan3_test_component (snippet_target_name "${snippet}" TARGET_NAME)
@@ -24,7 +25,7 @@ macro (seqan3_snippet test_name_prefix snippet snippet_base_path)
     set (target "${snippet_target_name}_snippet")
 
     add_executable (${target} "${snippet_base_path}/${snippet}")
-    target_link_libraries (${target} PUBLIC snippet_main)
+    target_link_libraries (${target} PUBLIC seqan3::test snippet_main)
     set_target_properties (${target} PROPERTIES RUNTIME_OUTPUT_DIRECTORY
                                                 "${CMAKE_CURRENT_BINARY_DIR}/${snippet_target_path}")
     collect_used_snippet (${target})

test/snippet/alphabet/nucleotide/@target_alphabet@_implicit_conversion_from_@source_alphabet@_views.cpp.in

@@ -15,7 +15,7 @@ int main()
 
     auto ${source_alphabet}_view = vector | seqan3::views::convert<seqan3::${source_alphabet}>;
 
-    for (auto && chr: ${source_alphabet}_view) // converts lazily on-the-fly
+    for (auto && chr : ${source_alphabet}_view) // converts lazily on-the-fly
     {
         static_assert(std::same_as<decltype(chr), seqan3::${source_alphabet} &&>);
     }

test/snippet/io/views/detail/take_line_view_adaptor_def.cpp

@@ -6,7 +6,7 @@
 int main()
 {
     //![usage]
-    std::views::take_while(
+    auto v = std::views::take_while(
         [](auto const & l)
         {
             return (l != '\r') && (l != '\n');

test/snippet/utility/char_operations/char_predicate.cpp

@@ -4,55 +4,55 @@
 int main()
 {
     //! [is_eof]
-    seqan3::is_eof(EOF); // returns true
-    seqan3::is_eof('C'); // returns false
+    static_assert(seqan3::is_eof(EOF));
+    static_assert(!seqan3::is_eof('C'));
     //! [is_eof]
 
     //! [is_cntrl]
-    seqan3::is_cntrl('\0'); // returns true.
+    static_assert(seqan3::is_cntrl('\0'));
     //! [is_cntrl]
 
     //! [is_print]
-    seqan3::is_print(' '); // returns true.
+    static_assert(seqan3::is_print(' '));
     //! [is_print]
 
     //! [is_space]
-    seqan3::is_space('\n'); // returns true.
+    static_assert(seqan3::is_space('\n'));
     //! [is_space]
 
     //! [is_blank]
-    seqan3::is_blank('\t'); // returns true.
+    static_assert(seqan3::is_blank('\t'));
     //! [is_blank]
 
     //! [is_graph]
-    seqan3::is_graph('%'); // returns true.
+    static_assert(seqan3::is_graph('%'));
     //! [is_graph]
 
     //! [is_punct]
-    seqan3::is_punct(':'); // returns true.
+    static_assert(seqan3::is_punct(':'));
     //! [is_punct]
 
     //! [is_alnum]
-    seqan3::is_alnum('9'); // returns true.
+    static_assert(seqan3::is_alnum('9'));
     //! [is_alnum]
 
     //! [is_alpha]
-    seqan3::is_alpha('z'); // returns true.
+    static_assert(seqan3::is_alpha('z'));
     //! [is_alpha]
 
     //! [is_upper]
-    seqan3::is_upper('K'); // returns true.
+    static_assert(seqan3::is_upper('K'));
     //! [is_upper]
 
     //! [is_lower]
-    seqan3::is_lower('a'); // returns true.
+    static_assert(seqan3::is_lower('a'));
     //! [is_lower]
 
     //! [is_digit]
-    seqan3::is_digit('1'); // returns true.
+    static_assert(seqan3::is_digit('1'));
     //! [is_digit]
 
     //! [is_xdigit]
-    seqan3::is_xdigit('e'); // returns true.
+    static_assert(seqan3::is_xdigit('e'));
     //! [is_xdigit]
 }

test/snippet/utility/type_pack/detail/type_pack_algorithm_all_of.cpp

@@ -17,7 +17,7 @@ auto fn = [](auto value)
     else if constexpr (std::is_same_v<value_t, int>)
         return value == 3;
     else if constexpr (std::is_same_v<value_t, double>)
-        return std::abs(value - 1.2) < 0.00001;
+        return value - 1.2 < 0.00001;
     else
         return false;
 };