[MISC] rename align_cfg::vectorise to align_cfg::vectorised

CHANGELOG.md

@@ -84,6 +84,7 @@ Note that 3.1.0 will be the first API stable release and interfaces in this rele
 * The seqan3::align_cfg::mode configuration has been adapted. The algorithm can now be configured using one of the
   pipeable configuration elements seqan3::align_cfg::method_global or seqan3::align_cfg::method_local
   ([\#1918](https://github.com/seqan/seqan3/pull/1918).
+* The `seqan3::align_cfg::vectorise` configuration has been renamed to `seqan3::align_cfg::vectorised`.
 
 ### Core
 

include/seqan3/alignment/configuration/align_config_vectorise.hpp → include/seqan3/alignment/configuration/align_config_vectorised.hpp

@@ -6,7 +6,7 @@
 // -----------------------------------------------------------------------------------------------------
 
 /*!\file
- * \brief Provides seqan3::align_cfg::vectorise configuration.
+ * \brief Provides seqan3::align_cfg::vectorised configuration.
  * \author Jörg Winkler <j.winkler AT fu-berlin.de>
  * \author Lydia Buntrock <lydia.buntrock AT fu-berlin.de>
  */
@@ -23,10 +23,10 @@ namespace seqan3::detail
 /*!\brief A tag to select the vectorised alignment algorithm.
  * \ingroup alignment_configuration
  */
-struct vectorise_tag : public pipeable_config_element<vectorise_tag>
+struct vectorised_tag : public pipeable_config_element<vectorised_tag>
 {
     //!\brief Internal id to check for consistent configuration settings.
-    static constexpr detail::align_config_id id{detail::align_config_id::vectorise};
+    static constexpr detail::align_config_id id{detail::align_config_id::vectorised};
 };
 
 } // namespace seqan3::detail
@@ -50,8 +50,8 @@ namespace seqan3::align_cfg
  *
  * ### Example
  *
- * \include test/snippet/alignment/configuration/align_cfg_vectorise_example.cpp
+ * \include test/snippet/alignment/configuration/align_cfg_vectorised_example.cpp
  */
-inline constexpr detail::vectorise_tag vectorise{};
+inline constexpr detail::vectorised_tag vectorised{};
 
 } // namespace seqan3::align_cfg

include/seqan3/alignment/configuration/all.hpp

@@ -24,7 +24,7 @@
 #include <seqan3/alignment/configuration/align_config_parallel.hpp>
 #include <seqan3/alignment/configuration/align_config_result.hpp>
 #include <seqan3/alignment/configuration/align_config_scoring.hpp>
-#include <seqan3/alignment/configuration/align_config_vectorise.hpp>
+#include <seqan3/alignment/configuration/align_config_vectorised.hpp>
 #include <seqan3/alignment/configuration/detail.hpp>
 
 /*!\namespace seqan3::align_cfg

include/seqan3/alignment/configuration/detail.hpp

@@ -35,7 +35,7 @@ enum struct align_config_id : uint8_t
     parallel,     //!< ID for the \ref seqan3::align_cfg::parallel "parallel" option.
     result,       //!< ID for the \ref seqan3::align_cfg::result "result" option.
     scoring,      //!< ID for the \ref seqan3::align_cfg::scoring "scoring" option.
-    vectorise,    //!< ID for the \ref seqan3::align_cfg::vectorise "vectorise" option.
+    vectorised,   //!< ID for the \ref seqan3::align_cfg::vectorised "vectorised" option.
     SIZE          //!< Represents the number of configuration elements.
 };
 
@@ -65,7 +65,7 @@ inline constexpr std::array<std::array<bool, static_cast<uint8_t>(align_config_i
         { 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1}, //  9: parallel
         { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1}, // 10: result
         { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1}, // 11: scoring
-        { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0}  // 12: vectorise
+        { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0}  // 12: vectorised
     }
 };
 

include/seqan3/alignment/pairwise/align_pairwise.hpp

@@ -71,10 +71,10 @@ namespace seqan3
  * ### Accessing the alignment results
  *
  * For each sequence pair one or more \ref seqan3::alignment_result "seqan3::alignment_result"s can be computed.
- * The seqan3::align_pairwise function returns an seqan3::algorithm_result_generator_range which can be used to iterate over the
- * alignments. If the `vectorise` configurations are omitted the alignments are computed on-demand when iterating over
- * the results. In case of a parallel execution all alignments are computed at once in parallel when calling `begin` on
- * the associated seqan3::algorithm_result_generator_range.
+ * The seqan3::align_pairwise function returns an seqan3::algorithm_result_generator_range which can be used to iterate
+ * over the alignments. If the `vectorised` configurations are omitted the alignments are computed on-demand when
+ * iterating over the results. In case of a parallel execution all alignments are computed at once in parallel when
+ * calling `begin` on the associated seqan3::algorithm_result_generator_range.
  *
  * The following snippets demonstrate the single element and the range based interface.
  *

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

@@ -23,7 +23,7 @@
 #include <seqan3/alignment/configuration/align_config_parallel.hpp>
 #include <seqan3/alignment/configuration/align_config_result.hpp>
 #include <seqan3/alignment/configuration/align_config_scoring.hpp>
-#include <seqan3/alignment/configuration/align_config_vectorise.hpp>
+#include <seqan3/alignment/configuration/align_config_vectorised.hpp>
 #include <seqan3/alignment/matrix/detail/matrix_coordinate.hpp>
 #include <seqan3/alignment/matrix/trace_directions.hpp>
 #include <seqan3/alignment/pairwise/detail/concept.hpp>
@@ -117,7 +117,7 @@ struct alignment_configuration_traits
 public:
     //!\brief Flag to indicate vectorised mode.
     static constexpr bool is_vectorised =
-        configuration_t::template exists<remove_cvref_t<decltype(align_cfg::vectorise)>>();
+        configuration_t::template exists<remove_cvref_t<decltype(align_cfg::vectorised)>>();
     //!\brief Flag indicating whether parallel alignment mode is enabled.
     static constexpr bool is_parallel = configuration_t::template exists<align_cfg::parallel>();
     //!\brief Flag indicating whether global alignment method is enabled.

test/performance/alignment/global_affine_alignment_simd_benchmark.cpp

@@ -77,29 +77,29 @@ void seqan3_affine_dna4_accelerated(benchmark::State & state, align_configs_t &&
 BENCHMARK_CAPTURE(seqan3_affine_dna4_accelerated,
                   simd_with_score,
                   seqan3::align_cfg::result{seqan3::with_score, seqan3::using_score_type<int16_t>},
-                  seqan3::align_cfg::vectorise)
+                  seqan3::align_cfg::vectorised)
                         ->UseRealTime()
                         ->DenseRange(deviation_begin, deviation_end, deviation_step);
 
 BENCHMARK_CAPTURE(seqan3_affine_dna4_accelerated,
                   simd_with_end_position,
                   seqan3::align_cfg::result{seqan3::with_end_positions, seqan3::using_score_type<int16_t>},
-                  seqan3::align_cfg::vectorise)
+                  seqan3::align_cfg::vectorised)
                         ->UseRealTime()
                         ->DenseRange(deviation_begin, deviation_end, deviation_step);
 
 BENCHMARK_CAPTURE(seqan3_affine_dna4_accelerated,
                   simd_parallel_with_score,
                   seqan3::align_cfg::result{seqan3::with_score, seqan3::using_score_type<int16_t>},
-                  seqan3::align_cfg::vectorise,
+                  seqan3::align_cfg::vectorised,
                   seqan3::align_cfg::parallel{get_number_of_threads()})
                         ->UseRealTime()
                         ->DenseRange(deviation_begin, deviation_end, deviation_step);
 
 BENCHMARK_CAPTURE(seqan3_affine_dna4_accelerated,
                   simd_parallel_with_end_position,
                   seqan3::align_cfg::result{seqan3::with_end_positions, seqan3::using_score_type<int16_t>},
-                  seqan3::align_cfg::vectorise,
+                  seqan3::align_cfg::vectorised,
                   seqan3::align_cfg::parallel{get_number_of_threads()})
                         ->UseRealTime()
                         ->DenseRange(deviation_begin, deviation_end, deviation_step);

test/snippet/alignment/configuration/align_cfg_vectorised_example.cpp

@@ -0,0 +1,7 @@
+#include <seqan3/alignment/configuration/align_config_vectorised.hpp>
+
+int main()
+{
+    // Enable SIMD vectorised alignment computation.
+    auto cfg = seqan3::align_cfg::vectorised;
+}

test/unit/alignment/configuration/CMakeLists.txt

@@ -9,4 +9,4 @@ seqan3_test(align_config_method_test.cpp)
 seqan3_test(align_config_on_result_test.cpp)
 seqan3_test(align_config_result_test.cpp)
 seqan3_test(align_config_scoring_test.cpp)
-seqan3_test(align_config_vectorise_test.cpp)
+seqan3_test(align_config_vectorised_test.cpp)

test/unit/alignment/configuration/align_config_common_test.cpp

@@ -27,7 +27,7 @@ using test_types = ::testing::Types<seqan3::align_cfg::aligned_ends<std::remove_
                                     seqan3::align_cfg::parallel,
                                     seqan3::align_cfg::result<>,
                                     seqan3::align_cfg::scoring<seqan3::nucleotide_scoring_scheme<int8_t>>,
-                                    seqan3::detail::vectorise_tag,
+                                    seqan3::detail::vectorised_tag,
                                     seqan3::detail::alignment_result_capture_element<alignment_result_t>>;
 
 TYPED_TEST_SUITE(alignment_configuration_test, test_types, );

test/unit/alignment/configuration/align_config_vectorise_test.cpp → test/unit/alignment/configuration/align_config_vectorised_test.cpp

@@ -10,11 +10,11 @@
 #include <functional>
 #include <type_traits>
 
-#include <seqan3/alignment/configuration/align_config_vectorise.hpp>
+#include <seqan3/alignment/configuration/align_config_vectorised.hpp>
 #include <seqan3/core/algorithm/configuration.hpp>
 
-TEST(align_config_vectorise, config_element)
+TEST(align_config_vectorised, config_element)
 {
-    seqan3::configuration cfg{seqan3::align_cfg::vectorise};
-    EXPECT_TRUE(decltype(cfg)::template exists<seqan3::detail::vectorise_tag>());
+    seqan3::configuration cfg{seqan3::align_cfg::vectorised};
+    EXPECT_TRUE(decltype(cfg)::template exists<seqan3::detail::vectorised_tag>());
 }

test/unit/alignment/pairwise/align_pairwise_test.cpp

@@ -29,13 +29,13 @@ using seqan3::operator""_dna4;
 template <typename t>
 struct align_pairwise_test : ::testing::Test
 {
-    // two helper variables to check if the TypeParam contains vectorise.
+    // two helper variables to check if the TypeParam contains vectorised.
     using dummy_cfg_t = std::conditional_t<std::is_same_v<void, t>,
                                            decltype(seqan3::align_cfg::max_error{1}),
                                            t>;
     using config_t = decltype(seqan3::align_cfg::method_global{} | seqan3::align_cfg::edit_scheme | dummy_cfg_t{});
 
-    static constexpr bool is_vectorised = config_t::template exists<seqan3::detail::vectorise_tag>();
+    static constexpr bool is_vectorised = config_t::template exists<seqan3::detail::vectorised_tag>();
 };
 
 using testing_types = ::testing::Types<void,

test/unit/alignment/pairwise/global_affine_unbanded_collection_simd_test.cpp

@@ -26,7 +26,7 @@ static auto dna4_all_same = []()
     for (size_t i = 0; i < 100; ++i)
         data.push_back(base_fixture);
 
-    return alignment_fixture_collection{base_fixture.config | seqan3::align_cfg::vectorise, data};
+    return alignment_fixture_collection{base_fixture.config | seqan3::align_cfg::vectorised, data};
 }();
 
 static auto dna4_different_length = []()
@@ -47,7 +47,7 @@ static auto dna4_different_length = []()
         data.push_back(base_fixture_04);
     }
 
-    return alignment_fixture_collection{base_fixture_01.config | seqan3::align_cfg::vectorise, data};
+    return alignment_fixture_collection{base_fixture_01.config | seqan3::align_cfg::vectorised, data};
 }();
 
 static auto dna4_with_empty_sequences = []()
@@ -72,7 +72,7 @@ static auto dna4_with_empty_sequences = []()
         data.push_back(base_fixture_06);
     }
 
-    return alignment_fixture_collection{base_fixture_01.config | seqan3::align_cfg::vectorise, data};
+    return alignment_fixture_collection{base_fixture_01.config | seqan3::align_cfg::vectorised, data};
 }();
 
 } // namespace seqan3::test::alignment::collection::simd::global::affine::unbanded