Merge pull request #3195 from eseiler/feature/clang

[FEATURE] Clang support

.github/workflows/ci_linux.yml

@@ -31,6 +31,11 @@ jobs:
       fail-fast: true
       matrix:
         include:
+          - name: "clang17"
+            compiler: "clang-17"
+            build: unit
+            build_type: Release
+
           - name: "gcc13"
             compiler: "gcc-13"
             build: unit

build_system/seqan3-config.cmake

@@ -196,16 +196,8 @@ if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU" AND CMAKE_CXX_COMPILER_VERSION VER
     message (FATAL_ERROR "GCC < 10 is not supported. The detected compiler version is ${CMAKE_CXX_COMPILER_VERSION}.")
 endif ()
 
-option (SEQAN3_DISABLE_COMPILER_CHECK "Skips the check for supported compilers." OFF)
-
-if (NOT SEQAN3_DISABLE_COMPILER_CHECK)
-    if (NOT "${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
-        message (FATAL_ERROR "Only GCC is supported. "
-                             "The detected compiler version is ${CMAKE_CXX_COMPILER_ID} ${CMAKE_CXX_COMPILER_VERSION}. "
-                             "You can disable this error by passing -DSEQAN3_DISABLE_COMPILER_CHECK=ON to CMake.")
-    endif ()
-else ()
-    set (SEQAN3_DEFINITIONS ${SEQAN3_DEFINITIONS} "-DSEQAN3_DISABLE_COMPILER_CHECK")
+if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 17)
+    message (FATAL_ERROR "Clang < 17 is not supported. The detected compiler version is ${CMAKE_CXX_COMPILER_VERSION}.")
 endif ()
 
 # ----------------------------------------------------------------------------

include/seqan3/alignment/configuration/align_config_on_result.hpp

@@ -54,7 +54,7 @@ class on_result : private seqan3::pipeable_config_element
 {
 public:
     //!\brief The stored callable which will be invoked with the alignment result.
-    seqan3::detail::copyable_wrapper_t<callback_t> callback{}; // Allows lambdas with capture blocks.
+    seqan3::detail::copyable_wrapper_t<callback_t> callback; // Allows lambdas with capture blocks.
 
     /*!\name Constructors, destructor and assignment
      * \{

include/seqan3/alignment/matrix/detail/trace_matrix_full.hpp

@@ -289,7 +289,7 @@ class trace_matrix_full<trace_t>::iterator::column_proxy : public std::ranges::v
 {
 private:
     //!\brief The represented column.
-    matrix_column_type column{};
+    matrix_column_type column;
 
 public:
     /*!\name Constructor, assignment and destructor

include/seqan3/alignment/pairwise/alignment_algorithm.hpp

@@ -742,7 +742,6 @@ class alignment_algorithm :
         // if traceback is enabled.
         if constexpr (traits_t::compute_sequence_alignment)
         {
-            auto trace_matrix_it = trace_debug_matrix.begin() + offset;
             std::ranges::copy(
                 column
                     | std::views::transform(

include/seqan3/alignment/pairwise/alignment_result.hpp

@@ -24,7 +24,7 @@ namespace seqan3::detail
 
 // forward declaration for friend declaration in alignment_result.
 template <typename configuration_t>
-    requires is_type_specialisation_of_v<configuration_t, configuration>
+    requires seqan3::detail::is_type_specialisation_of_v<configuration_t, configuration>
 class policy_alignment_result_builder;
 
 /*!\brief A struct that contains the actual alignment result data.
@@ -170,7 +170,7 @@ class alignment_result
 
     //!\brief Befriend alignment result builder.
     template <typename configuration_t>
-        requires detail::is_type_specialisation_of_v<configuration_t, configuration>
+        requires seqan3::detail::is_type_specialisation_of_v<configuration_t, configuration>
     friend class detail::policy_alignment_result_builder;
 
 public:

include/seqan3/alignment/pairwise/detail/concept.hpp

@@ -105,7 +105,7 @@ concept indexed_sequence_pair_range =
 //!\cond
 template <typename t>
 concept align_pairwise_single_input =
-    sequence_pair<std::remove_reference_t<t>> && std::is_lvalue_reference_v<t>
+    (sequence_pair<std::remove_reference_t<t>> && std::is_lvalue_reference_v<t>)
     || (std::ranges::viewable_range<std::tuple_element_t<0, std::remove_reference_t<t>>>
         && std::ranges::viewable_range<std::tuple_element_t<1, std::remove_reference_t<t>>>);
 //!\endcond

include/seqan3/alignment/pairwise/detail/policy_alignment_result_builder.hpp

@@ -32,7 +32,7 @@ namespace seqan3::detail
  * Implements the interfaces to build the alignment result based on the previously selected output configurations.
  */
 template <typename alignment_configuration_t>
-    requires is_type_specialisation_of_v<alignment_configuration_t, configuration>
+    requires seqan3::detail::is_type_specialisation_of_v<alignment_configuration_t, configuration>
 class policy_alignment_result_builder
 {
 protected:

include/seqan3/alphabet/composite/alphabet_variant.hpp

@@ -17,6 +17,7 @@
 #include <algorithm>
 #include <array>
 #include <cassert>
+#include <span>
 #include <utility>
 #include <variant>
 
@@ -28,6 +29,17 @@
 namespace seqan3::detail
 {
 
+//!\brief Helper to determine whether a type is a std::span.
+template <typename t, size_t extent = std::dynamic_extent>
+struct is_span : std::false_type
+{};
+
+//!\cond
+template <typename t, size_t extent>
+struct is_span<std::span<t, extent>> : std::true_type
+{};
+//!\endcond
+
 //!\brief Prevents wrong instantiations of std::alphabet_variant's constructors.
 template <typename other_t, typename... alternative_types>
 inline constexpr bool variant_general_guard =
@@ -193,7 +205,7 @@ class alphabet_variant :
      * \stableapi{Since version 3.1.}
      */
     template <typename alternative_t>
-        requires (!std::same_as<alternative_t, alphabet_variant>)
+        requires (!std::same_as<alternative_t, alphabet_variant>) && (!detail::is_span<alternative_t>::value)
               && (!std::is_base_of_v<alphabet_variant, alternative_t>)
               && (!list_traits::contains<
                   alphabet_variant,
@@ -223,10 +235,11 @@ class alphabet_variant :
      * \experimentalapi{Experimental since version 3.1.}
      */
     template <typename indirect_alternative_t>
-        requires (
-            (detail::instantiate_if_v<detail::lazy<std::is_convertible, indirect_alternative_t, alternative_types>,
-                                      detail::variant_general_guard<indirect_alternative_t, alternative_types...>>
-             || ...))
+        requires (!detail::is_span<indirect_alternative_t>::value)
+              && ((
+                  detail::instantiate_if_v<detail::lazy<std::is_convertible, indirect_alternative_t, alternative_types>,
+                                           detail::variant_general_guard<indirect_alternative_t, alternative_types...>>
+                  || ...))
     constexpr alphabet_variant(indirect_alternative_t const rhs) noexcept
     {
         using alternative_predicate = detail::implicitly_convertible_from<indirect_alternative_t>;
@@ -403,10 +416,12 @@ class alphabet_variant :
      * \stableapi{Since version 3.1.}
      */
     template <typename alphabet_variant_t, typename indirect_alternative_type>
-    friend constexpr auto
-    operator==(alphabet_variant_t const lhs, indirect_alternative_type const rhs) noexcept -> std::enable_if_t<
-        detail::variant_comparison_guard<alphabet_variant_t, indirect_alternative_type, false, alternative_types...>,
-        bool>
+        requires (!detail::is_span<alphabet_variant_t>::value)
+              && (detail::variant_comparison_guard<alphabet_variant_t,
+                                                   indirect_alternative_type,
+                                                   false,
+                                                   alternative_types...>)
+    friend constexpr bool operator==(alphabet_variant_t const lhs, indirect_alternative_type const rhs) noexcept
     {
         using alternative_predicate = detail::weakly_equality_comparable_with_<indirect_alternative_type>;
         constexpr auto alternative_position =
@@ -428,10 +443,12 @@ class alphabet_variant :
 
     //!\copydoc operator==(alphabet_variant_t const lhs, indirect_alternative_type const rhs)
     template <typename alphabet_variant_t, typename indirect_alternative_type, typename = void>
-    friend constexpr auto operator==(indirect_alternative_type const lhs, alphabet_variant_t const rhs) noexcept
-        -> std::enable_if_t<
-            detail::variant_comparison_guard<alphabet_variant_t, indirect_alternative_type, true, alternative_types...>,
-            bool>
+        requires (!detail::is_span<alphabet_variant_t>::value)
+              && (detail::variant_comparison_guard<alphabet_variant_t,
+                                                   indirect_alternative_type,
+                                                   true,
+                                                   alternative_types...>)
+    friend constexpr bool operator==(indirect_alternative_type const lhs, alphabet_variant_t const rhs) noexcept
     {
         return rhs == lhs;
     }

include/seqan3/alphabet/composite/semialphabet_any.hpp

@@ -71,8 +71,9 @@ class semialphabet_any : public alphabet_base<semialphabet_any<size>, size, void
      * \details
      * \stableapi{Since version 3.1.}
      */
-    template <semialphabet other_alph_t>
-        requires (alphabet_size<other_alph_t> == size)
+    template <typename other_alph_t>
+        requires (!std::same_as<other_alph_t, semialphabet_any>)
+              && semialphabet<other_alph_t> && (alphabet_size<other_alph_t> == size)
     explicit semialphabet_any(other_alph_t const other)
     {
         assign_rank(seqan3::to_rank(other));
@@ -83,8 +84,9 @@ class semialphabet_any : public alphabet_base<semialphabet_any<size>, size, void
      * \details
      * \stableapi{Since version 3.1.}
      */
-    template <semialphabet other_alph_t>
-        requires ((alphabet_size<other_alph_t> == size) && std::regular<other_alph_t>)
+    template <typename other_alph_t>
+        requires (!std::same_as<other_alph_t, semialphabet_any>)
+              && semialphabet<other_alph_t> && (alphabet_size<other_alph_t> == size) && std::regular<other_alph_t>
     explicit operator other_alph_t() const
     {
         other_alph_t other{};

include/seqan3/alphabet/views/translate_join.hpp

@@ -68,7 +68,7 @@ class view_translate_join : public std::ranges::view_base
     //!\}
 
     //!\brief Befriend the following class s.t. iterator and const_iterator can be defined for this type.
-    template <typename, template <typename...> typename>
+    template <typename range_type, template <typename...> typename derived_t_template, typename... args_t>
     friend class detail::random_access_iterator_base;
 
 public:

include/seqan3/argument_parser/argument_parser.hpp

@@ -150,11 +150,11 @@ class argument_parser
     /*!\name Constructors, destructor and assignment
      * \{
      */
-    argument_parser() = delete;                                     //!< Deleted.
-    argument_parser(argument_parser const &) = default;             //!< Defaulted.
-    argument_parser & operator=(argument_parser const &) = default; //!< Defaulted.
-    argument_parser(argument_parser &&) = default;                  //!< Defaulted.
-    argument_parser & operator=(argument_parser &&) = default;      //!< Defaulted.
+    argument_parser() = delete;                                    //!< Deleted.
+    argument_parser(argument_parser const &) = delete;             //!< Deleted. Holds std::future.
+    argument_parser & operator=(argument_parser const &) = delete; //!< Deleted. Holds std::future.
+    argument_parser(argument_parser &&) = default;                 //!< Defaulted.
+    argument_parser & operator=(argument_parser &&) = default;     //!< Defaulted.
 
     /*!\brief Initializes an seqan3::argument_parser object from the command line arguments.
      *
@@ -773,7 +773,7 @@ class argument_parser
                 {
                     if (argv_len <= i + 1)
                         throw too_few_arguments{"Option --export-help must be followed by a value."};
-                    export_format = {argv[i + 1]};
+                    export_format = argv[i + 1];
                 }
 
                 if (export_format == "html")

include/seqan3/argument_parser/detail/format_parse.hpp

@@ -64,10 +64,9 @@ class format_parse : public format_base
     ~format_parse() = default;                                   //!< Defaulted.
 
     /*!\brief The constructor of the parse format.
-     * \param[in] argc_ The number of command line arguments.
      * \param[in] argv_ The command line arguments to parse.
      */
-    format_parse(int const argc_, std::vector<std::string> argv_) : argc{argc_ - 1}, argv{std::move(argv_)}
+    format_parse(int const, std::vector<std::string> argv_) : argv{std::move(argv_)}
     {}
     //!\}
 
@@ -822,8 +821,6 @@ class format_parse : public format_base
     std::vector<std::function<void()>> positional_option_calls;
     //!\brief Keeps track of the number of specified positional options.
     unsigned positional_option_count{0};
-    //!\brief Number of command line arguments.
-    int argc;
     //!\brief Vector of command line arguments.
     std::vector<std::string> argv;
     //!\brief Artificial end of argv if \-- was seen.

include/seqan3/contrib/parallel/serialised_resource_pool.hpp

@@ -43,11 +43,8 @@ struct ResourcePool
     {
         unlockWriting(recycled);
         TValue * ptr = NULL;
-        unsigned count = 0;
         while (popBack(ptr, recycled))
         {
-            if (ptr != NULL)
-                count++;
             delete ptr;
         }
     }

include/seqan3/contrib/stream/bz2_ostream.hpp

@@ -233,7 +233,7 @@ bool basic_bz2_ostreambuf<
         std::streamsize buffer_size_
         )
 {
-    std::streamsize written_byte_size=0, total_written_byte_size = 0;
+    std::streamsize written_byte_size=0;
 
     m_bzip2_stream.next_in=(byte_buffer_type)buffer_;
     m_bzip2_stream.avail_in=buffer_size_*sizeof(char_type);
@@ -248,7 +248,6 @@ bool basic_bz2_ostreambuf<
         if (m_err == BZ_RUN_OK  || m_err == BZ_STREAM_END)
         {
             written_byte_size= static_cast<std::streamsize>(m_output_buffer.size()) - m_bzip2_stream.avail_out;
-            total_written_byte_size+=written_byte_size;
             // output buffer is full, dumping to ostream
             m_ostream.write(
                 (const char_type*) &(m_output_buffer[0]),

include/seqan3/contrib/stream/gz_ostream.hpp

@@ -221,7 +221,7 @@ bool basic_gz_ostreambuf<Elem, Tr, ElemA, ByteT, ByteAT>::zip_to_stream(
     typename basic_gz_ostreambuf<Elem, Tr, ElemA, ByteT, ByteAT>::char_type * buffer_,
     std::streamsize buffer_size_)
 {
-    std::streamsize written_byte_size = 0, total_written_byte_size = 0;
+    std::streamsize written_byte_size = 0;
 
     m_zip_stream.next_in = (byte_buffer_type)buffer_;
     m_zip_stream.avail_in = static_cast<uInt>(buffer_size_ * sizeof(char_type));
@@ -236,7 +236,6 @@ bool basic_gz_ostreambuf<Elem, Tr, ElemA, ByteT, ByteAT>::zip_to_stream(
         if (m_err == Z_OK  || m_err == Z_STREAM_END)
         {
             written_byte_size = static_cast<std::streamsize>(m_output_buffer.size()) - m_zip_stream.avail_out;
-            total_written_byte_size += written_byte_size;
 
             // output buffer is full, dumping to ostream
             m_ostream.write((const char_type *) &(m_output_buffer[0]),

include/seqan3/core/algorithm/detail/execution_handler_parallel.hpp

@@ -213,14 +213,14 @@ class execution_handler_parallel
     {
     public:
         /*!\name Constructors, destructor and assignment
-        * \brief Instances of this class are not copyable.
+        * \brief Instances of this class are not copyable and not movable.
         * \{
         */
         internal_state() = default;                                  //!< Defaulted.
         internal_state(internal_state const &) = delete;             //!< Deleted.
-        internal_state(internal_state &&) = default;                 //!< Defaulted.
+        internal_state(internal_state &&) = delete;                  //!< Deleted.
         internal_state & operator=(internal_state const &) = delete; //!< Deleted.
-        internal_state & operator=(internal_state &&) = default;     //!< Defaulted.
+        internal_state & operator=(internal_state &&) = delete;      //!< Deleted.
 
         //!\brief Waits for threads to finish.
         ~internal_state()

include/seqan3/core/platform.hpp

@@ -86,13 +86,21 @@
 #        endif // (__GNUC__ > 13)
 #    endif     // SEQAN3_DISABLE_NEWER_COMPILER_DIAGNOSTIC
 
+// ============================================================================
+//  Compiler support Clang
+// ============================================================================
+
+#elif defined(__clang__)
+#    if __clang_major__ < 17
+#        error "Only Clang >= 17 is supported."
+#    endif
+
 // ============================================================================
 //  Compiler support other
 // ============================================================================
 
 #elif !defined(SEQAN3_DISABLE_COMPILER_CHECK)
-#    error                                                                                                             \
-        "Your compiler is not supported. Currently, only GCC is known to work. You can disable this error by setting -DSEQAN3_DISABLE_COMPILER_CHECK."
+#    error "Your compiler is not supported. You can disable this error by setting -DSEQAN3_DISABLE_COMPILER_CHECK."
 #endif // SEQAN3_COMPILER_IS_GCC
 
 // ============================================================================

include/seqan3/io/sam_file/detail/format_sam_base.hpp

@@ -338,7 +338,7 @@ inline void format_sam_base::read_header(stream_view_type && stream_view,
         read_forward_range_field(string_buffer, value);
     };
 
-    auto print_cerr_of_unspported_tag = [&it](char const * const header_tag, std::array<char, 2> raw_tag)
+    auto print_cerr_of_unspported_tag = [](char const * const header_tag, std::array<char, 2> raw_tag)
     {
         std::cerr << "Unsupported SAM header tag in @" << header_tag << ": " << raw_tag[0] << raw_tag[1] << '\n';
     };

include/seqan3/io/sam_file/format_sam.hpp

@@ -111,12 +111,12 @@ class format_sam : protected detail::format_sam_base
      * \{
      */
     // construction cannot be noexcept because this class has a std::string variable as a quality string buffer.
-    format_sam() = default;                               //!< Defaulted.
-    format_sam(format_sam const &) = default;             //!< Defaulted.
-    format_sam & operator=(format_sam const &) = default; //!< Defaulted.
-    format_sam(format_sam &&) = default;                  //!< Defaulted.
-    format_sam & operator=(format_sam &&) = default;      //!< Defaulted.
-    ~format_sam() = default;                              //!< Defaulted.
+    format_sam() = default;                              //!< Defaulted.
+    format_sam(format_sam const &) = delete;             //!< Deleted. Header holds a unique_ptr.
+    format_sam & operator=(format_sam const &) = delete; //!< Deleted. Header holds a unique_ptr.
+    format_sam(format_sam &&) = default;                 //!< Defaulted.
+    format_sam & operator=(format_sam &&) = default;     //!< Defaulted.
+    ~format_sam() = default;                             //!< Defaulted.
 
     //!\}
 
@@ -224,9 +224,6 @@ class format_sam : protected detail::format_sam_base
     //!\brief The default header for the alignment format.
     sam_file_header<> default_header{};
 
-    //!\brief Tracks whether reference information (\@SR tag) were found in the SAM header
-    bool ref_info_present_in_header{false};
-
     //!\brief A buffer to store a raw record pointing into the stream buffer of the input.
     std::array<std::string_view, 11> raw_record{};