[FIX] Use std::ranges:: instead of ranges:: (#3005)

* [FIX] Use std::ranges:: instead of ranges::

* [MISC] clang-format

Co-authored-by: seqan-actions[bot] <seqan-actions@users.noreply.github.com>

doc/tutorial/07_sequence_file/index.md

@@ -249,7 +249,7 @@ If no 10 records are available any more, it will just print the remaining record
 
 On some occasions, you are only interested in sequence records that fulfill a certain criteria,
 e.g. having a minimum sequence length or a minimum average quality.
-Just like in the example with *ranges::view::chunk* you can use *std::ranges::filter* for this purpose:
+Just like in the example with *seqan3::views::chunk* you can use *std::ranges::filter* for this purpose:
 
 \snippet doc/tutorial/07_sequence_file/sequence_file_quality_filter.cpp main
 

include/seqan3/alignment/pairwise/edit_distance_unbanded.hpp

@@ -874,8 +874,8 @@ class edit_distance_unbanded :
         query{std::forward<query_t>(_query)},
         config{std::forward<align_config_t>(_config)},
         _score{static_cast<score_type>(std::ranges::size(query))},
-        database_it{ranges::begin(database)},
-        database_it_end{ranges::end(database)}
+        database_it{std::ranges::begin(database)},
+        database_it_end{std::ranges::end(database)}
     {
         static constexpr size_t alphabet_size_ = alphabet_size<query_alphabet_type>;
 

include/seqan3/alphabet/range/hash.hpp

@@ -26,7 +26,7 @@ namespace std
  * \details
  * \experimentalapi{Experimental since version 3.1.}
  */
-template <ranges::input_range urng_t>
+template <std::ranges::input_range urng_t>
     requires seqan3::semialphabet<std::ranges::range_reference_t<urng_t>>
 struct hash<urng_t>
 {
@@ -38,7 +38,7 @@ struct hash<urng_t>
      * \details
      * \experimentalapi{Experimental since version 3.1.}
      */
-    template <ranges::input_range urng2_t>
+    template <std::ranges::input_range urng2_t>
         requires seqan3::semialphabet<std::ranges::range_reference_t<urng2_t>>
     size_t operator()(urng2_t && range) const noexcept
     {

include/seqan3/core/detail/persist_view.hpp

@@ -39,7 +39,7 @@ namespace seqan3::detail
  *
  * \details
  *
- * Note that most members of this class are generated by ranges::view_interface which is not yet documented here.
+ * Note that most members of this class are generated by std::ranges::view_interface which is not yet documented here.
  */
 template <std::ranges::input_range urng_t>
 class view_persist : public std::ranges::view_interface<view_persist<urng_t>>

include/seqan3/io/sam_file/format_sam.hpp

@@ -958,7 +958,7 @@ inline void format_sam::read_sam_dict_vector(seqan3::detail::sam_tag_variant & v
                                              value_type value)
 {
     std::vector<value_type> tmp_vector;
-    while (std::ranges::begin(stream_view) != ranges::end(stream_view)) // not fully consumed yet
+    while (std::ranges::begin(stream_view) != std::ranges::end(stream_view)) // not fully consumed yet
     {
         read_arithmetic_field(stream_view | detail::take_until(is_char<','>), value);
         tmp_vector.push_back(value);
@@ -988,7 +988,7 @@ inline void format_sam::read_sam_byte_vector(seqan3::detail::sam_tag_variant & v
     std::vector<std::byte> tmp_vector;
     std::byte value;
 
-    while (std::ranges::begin(stream_view) != ranges::end(stream_view)) // not fully consumed yet
+    while (std::ranges::begin(stream_view) != std::ranges::end(stream_view)) // not fully consumed yet
     {
         try
         {

include/seqan3/io/sequence_file/format_embl.hpp

@@ -228,7 +228,7 @@ class format_embl
         }
         else
         {
-            if (ranges::empty(id)) //[[unlikely]]
+            if (std::ranges::empty(id)) //[[unlikely]]
                 throw std::runtime_error{"The ID field may not be empty when writing embl files."};
 
             if (options.embl_genbank_complete_header)

include/seqan3/io/sequence_file/format_genbank.hpp

@@ -201,14 +201,14 @@ class format_genbank
         size_t sequence_size{0};
         [[maybe_unused]] char buffer[50];
         if constexpr (!detail::decays_to_ignore_v<seq_type>)
-            sequence_size = ranges::size(sequence);
+            sequence_size = std::ranges::size(sequence);
 
         // ID
         if constexpr (detail::decays_to_ignore_v<id_type>)
         {
             throw std::logic_error{"The ID field may not be set to ignore when writing genbank files."};
         }
-        else if (ranges::empty(id)) //[[unlikely]]
+        else if (std::ranges::empty(id)) //[[unlikely]]
         {
             throw std::runtime_error{"The ID field may not be empty when writing genbank files."};
         }

include/seqan3/io/views/detail/take_exactly_view.hpp

@@ -46,7 +46,7 @@ namespace seqan3::detail
  *
  * \details
  *
- * Note that most members of this class are generated by ranges::view_interface which is not yet documented here.
+ * Note that most members of this class are generated by std::ranges::view_interface which is not yet documented here.
  */
 template <std::ranges::view urng_t, bool or_throw>
 class view_take_exactly : public std::ranges::view_interface<view_take_exactly<urng_t, or_throw>>

include/seqan3/io/views/detail/take_until_view.hpp

@@ -45,7 +45,7 @@ namespace seqan3::detail
  *
  * \details
  *
- * Note that most members of this class are generated by ranges::view_interface which is not yet documented here.
+ * Note that most members of this class are generated by std::ranges::view_interface which is not yet documented here.
  */
 template <std::ranges::view urng_t, typename fun_t, bool or_throw, bool and_consume>
 class view_take_until : public std::ranges::view_interface<view_take_until<urng_t, fun_t, or_throw, and_consume>>

include/seqan3/search/views/kmer_hash.hpp

@@ -33,7 +33,7 @@ namespace seqan3::detail
  *
  * \details
  *
- * Note that most members of this class are generated by ranges::view_interface which is not yet documented here.
+ * Note that most members of this class are generated by std::ranges::view_interface which is not yet documented here.
  */
 template <std::ranges::view urng_t>
 class kmer_hash_view : public std::ranges::view_interface<kmer_hash_view<urng_t>>

include/seqan3/search/views/minimiser.hpp

@@ -114,7 +114,7 @@ class minimiser_view : public std::ranges::view_interface<minimiser_view<urng1_t
     */
     template <typename other_urng1_t>
         requires (std::ranges::viewable_range<other_urng1_t>
-                  && std::constructible_from<urng1_t, ranges::ref_view<std::remove_reference_t<other_urng1_t>>>)
+                  && std::constructible_from<urng1_t, std::ranges::ref_view<std::remove_reference_t<other_urng1_t>>>)
     minimiser_view(other_urng1_t && urange1, size_t const window_size) :
         urange1{std::views::all(std::forward<other_urng1_t>(urange1))},
         urange2{default_urng2_t{}},

include/seqan3/utility/views/interleave.hpp

@@ -41,7 +41,7 @@ namespace seqan3::detail
  *
  * \details
  *
- * Note that most members of this class are generated by ranges::view_interface which is not yet documented here.
+ * Note that most members of this class are generated by std::ranges::view_interface which is not yet documented here.
  */
 template <std::ranges::random_access_range urng_t, std::ranges::random_access_range inserted_rng_t>
     requires std::ranges::view<urng_t> && std::ranges::sized_range<urng_t> && std::ranges::view<inserted_rng_t>
@@ -65,13 +65,13 @@ class view_interleave : public std::ranges::view_interface<view_interleave<urng_
     //!\brief This resolves to range_type::size_type as the underlying range is guaranteed to be sized.
     using size_type = std::ranges::range_size_t<urng_t>;
     //!\brief The reference_type.
-    using reference = ranges::common_reference_t<std::ranges::range_reference_t<urng_t>,
-                                                 std::ranges::range_reference_t<inserted_rng_t>>;
+    using reference =
+        std::common_reference_t<std::ranges::range_reference_t<urng_t>, std::ranges::range_reference_t<inserted_rng_t>>;
     //!\brief The const_reference type is equal to the reference type.
-    using const_reference = detail::transformation_trait_or_t<
-        ranges::common_reference<std::ranges::range_reference_t<urng_t const>,
-                                 std::ranges::range_reference_t<inserted_rng_t const>>,
-        void>;
+    using const_reference =
+        detail::transformation_trait_or_t<std::common_reference<std::ranges::range_reference_t<urng_t const>,
+                                                                std::ranges::range_reference_t<inserted_rng_t const>>,
+                                          void>;
     //!\brief The value_type (which equals the reference_type with any references removed).
     using value_type = std::ranges::range_value_t<urng_t>;
     //!\brief A signed integer type, usually std::ptrdiff_t.

include/seqan3/utility/views/repeat.hpp

@@ -38,7 +38,7 @@ namespace seqan3::detail
  * This class models an infinite range over a given value, although "infinity" is limited by the maximum value of
  * `difference_type` of which the iterator stores a member variable to represent distances.
  *
- * Note that most members of this class are generated by ranges::view_interface which is not yet documented here.
+ * Note that most members of this class are generated by std::ranges::view_interface which is not yet documented here.
  */
 template <std::copy_constructible value_t>
 class repeat_view : public std::ranges::view_interface<repeat_view<value_t>>