[PATCH] deprecate core_language.hpp (#2351)

* [PATCH] deprecate core_language.hpp - Move content of core/concept/core_language.hpp to utility/detail/exposition_only_concept.hpp - Added deprecation to core_language.hpp and a forward include to exposition_only_concept.hpp - Changed all header files to new include path - Changed all unittest to new include path * [FIX] rename unittest to utility/detail/exposition_only_concept_test.cpp * [FIX] doxygen - adjusting template_specicialisation_of • remove from `concept` group • add missing `detail::` namespace scope * [FIX] introducing to doxygen * [FIX] reorder of includes Co-authored-by: Marcel <marehr@users.noreply.github.com> * [FIX] more reordering of includes Co-authored-by: Marcel <marehr@users.noreply.github.com>
seqan · Feb 15, 2021 · a1d5d4d · a1d5d4d
1 parent 94a4e22
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Showing 44 changed files with 273 additions and 249 deletions.
diff --git a/include/seqan3/alignment/configuration/align_config_output.hpp b/include/seqan3/alignment/configuration/align_config_output.hpp
@@ -15,7 +15,7 @@
 #include <seqan3/alignment/configuration/detail.hpp>
 #include <seqan3/alignment/pairwise/alignment_result.hpp>
 #include <seqan3/core/algorithm/pipeable_config_element.hpp>
-#include <seqan3/core/concept/core_language.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 
 namespace seqan3::align_cfg
 {

diff --git a/include/seqan3/alignment/configuration/align_config_score_type.hpp b/include/seqan3/alignment/configuration/align_config_score_type.hpp
@@ -14,7 +14,7 @@
 
 #include <seqan3/alignment/configuration/detail.hpp>
 #include <seqan3/core/algorithm/pipeable_config_element.hpp>
-#include <seqan3/core/concept/core_language.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 
 namespace seqan3::align_cfg
 {

diff --git a/include/seqan3/alignment/matrix/alignment_optimum.hpp b/include/seqan3/alignment/matrix/alignment_optimum.hpp
@@ -16,8 +16,8 @@
 #include <type_traits>
 
 #include <seqan3/alignment/matrix/detail/matrix_coordinate.hpp>
-#include <seqan3/core/concept/core_language.hpp>
 #include <seqan3/core/detail/template_inspection.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 #include <seqan3/utility/simd/algorithm.hpp>
 #include <seqan3/utility/simd/concept.hpp>
 #include <seqan3/utility/simd/simd_traits.hpp>

diff --git a/include/seqan3/alignment/matrix/detail/affine_cell_proxy.hpp b/include/seqan3/alignment/matrix/detail/affine_cell_proxy.hpp
@@ -17,8 +17,8 @@
 #include <type_traits>
 
 #include <seqan3/alignment/matrix/trace_directions.hpp>
-#include <seqan3/core/concept/core_language.hpp>
 #include <seqan3/core/detail/empty_type.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 #include <seqan3/utility/simd/concept.hpp>
 #include <seqan3/utility/tuple_utility.hpp>
 

diff --git a/include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column.hpp b/include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column.hpp
@@ -19,7 +19,7 @@
 #include <seqan3/alignment/matrix/detail/alignment_matrix_column_major_range_base.hpp>
 #include <seqan3/alignment/matrix/detail/alignment_score_matrix_one_column_base.hpp>
 #include <seqan3/alignment/matrix/detail/alignment_score_matrix_proxy.hpp>
-#include <seqan3/core/concept/core_language.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 #include <seqan3/utility/simd/concept.hpp>
 
 namespace seqan3::detail

diff --git a/include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column_base.hpp b/include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column_base.hpp
@@ -16,8 +16,8 @@
 #include <utility>
 #include <vector>
 
-#include <seqan3/core/concept/core_language.hpp>
 #include <seqan3/range/container/aligned_allocator.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 #include <seqan3/utility/simd/concept.hpp>
 
 namespace seqan3::detail

diff --git a/include/seqan3/alignment/matrix/detail/alignment_score_matrix_proxy.hpp b/include/seqan3/alignment/matrix/detail/alignment_score_matrix_proxy.hpp
@@ -12,7 +12,7 @@
 
 #pragma once
 
-#include <seqan3/core/concept/core_language.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 #include <seqan3/utility/simd/concept.hpp>
 
 namespace seqan3::detail

diff --git a/include/seqan3/alignment/matrix/detail/combined_score_and_trace_matrix.hpp b/include/seqan3/alignment/matrix/detail/combined_score_and_trace_matrix.hpp
@@ -16,9 +16,9 @@
 
 #include <seqan3/alignment/matrix/detail/affine_cell_proxy.hpp>
 #include <seqan3/alignment/matrix/detail/matrix_coordinate.hpp>
-#include <seqan3/core/concept/core_language.hpp>
 #include <seqan3/core/range/type_traits.hpp>
 #include <seqan3/range/views/zip.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 
 namespace seqan3::detail
 {

diff --git a/include/seqan3/alignment/matrix/detail/matrix_coordinate.hpp b/include/seqan3/alignment/matrix/detail/matrix_coordinate.hpp
@@ -15,8 +15,8 @@
 #include <seqan3/std/concepts>
 #include <type_traits>
 
-#include <seqan3/core/concept/core_language.hpp>
 #include <seqan3/core/detail/strong_type.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 #include <seqan3/utility/simd/algorithm.hpp>
 #include <seqan3/utility/simd/concept.hpp>
 

diff --git a/include/seqan3/alignment/matrix/detail/score_matrix_single_column.hpp b/include/seqan3/alignment/matrix/detail/score_matrix_single_column.hpp
@@ -17,10 +17,10 @@
 
 #include <seqan3/alignment/matrix/detail/affine_cell_proxy.hpp>
 #include <seqan3/alignment/matrix/detail/matrix_coordinate.hpp>
-#include <seqan3/core/concept/core_language.hpp>
 #include <seqan3/range/container/aligned_allocator.hpp>
 #include <seqan3/range/views/repeat_n.hpp>
 #include <seqan3/range/views/zip.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 #include <seqan3/utility/simd/concept.hpp>
 
 namespace seqan3::detail

diff --git a/include/seqan3/alignment/matrix/detail/trace_matrix_full.hpp b/include/seqan3/alignment/matrix/detail/trace_matrix_full.hpp
@@ -20,11 +20,11 @@
 #include <seqan3/alignment/matrix/detail/trace_iterator.hpp>
 #include <seqan3/alignment/matrix/detail/two_dimensional_matrix.hpp>
 #include <seqan3/alignment/matrix/trace_directions.hpp>
-#include <seqan3/core/concept/core_language.hpp>
 #include <seqan3/core/detail/template_inspection.hpp>
 #include <seqan3/range/container/aligned_allocator.hpp>
 #include <seqan3/range/views/repeat_n.hpp>
 #include <seqan3/range/views/zip.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 
 namespace seqan3::detail
 {

diff --git a/include/seqan3/alignment/pairwise/detail/alignment_algorithm_state.hpp b/include/seqan3/alignment/pairwise/detail/alignment_algorithm_state.hpp
@@ -14,7 +14,7 @@
 
 #include <seqan3/alignment/matrix/alignment_coordinate.hpp>
 #include <seqan3/alignment/matrix/alignment_optimum.hpp>
-#include <seqan3/core/concept/core_language.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 #include <seqan3/utility/simd/concept.hpp>
 
 namespace seqan3::detail

diff --git a/include/seqan3/alignment/pairwise/policy/affine_gap_policy.hpp b/include/seqan3/alignment/pairwise/policy/affine_gap_policy.hpp
@@ -15,7 +15,7 @@
 #include <seqan3/alignment/configuration/align_config_gap_cost_affine.hpp>
 #include <seqan3/alignment/matrix/trace_directions.hpp>
 #include <seqan3/alignment/pairwise/detail/alignment_algorithm_state.hpp>
-#include <seqan3/core/concept/core_language.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 
 namespace seqan3::detail
 {

diff --git a/include/seqan3/alignment/pairwise/policy/simd_affine_gap_policy.hpp b/include/seqan3/alignment/pairwise/policy/simd_affine_gap_policy.hpp
@@ -19,8 +19,8 @@
 #include <seqan3/alignment/matrix/alignment_optimum.hpp>
 #include <seqan3/alignment/matrix/trace_directions.hpp>
 #include <seqan3/alignment/pairwise/detail/alignment_algorithm_state.hpp>
-#include <seqan3/core/concept/core_language.hpp>
 #include <seqan3/core/configuration/configuration.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 #include <seqan3/utility/simd/algorithm.hpp>
 #include <seqan3/utility/simd/concept.hpp>
 #include <seqan3/utility/simd/simd_traits.hpp>

diff --git a/include/seqan3/alignment/scoring/gap_scheme.hpp b/include/seqan3/alignment/scoring/gap_scheme.hpp
@@ -12,12 +12,12 @@
 
 #pragma once
 
+#include <seqan3/std/concepts>
 #include <stdexcept>
 
 #include <seqan3/core/concept/cereal.hpp>
-#include <seqan3/core/concept/core_language.hpp>
 #include <seqan3/core/detail/strong_type.hpp>
-#include <seqan3/std/concepts>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 
 namespace seqan3
 {

diff --git a/include/seqan3/alignment/scoring/scoring_scheme_base.hpp b/include/seqan3/alignment/scoring/scoring_scheme_base.hpp
@@ -17,8 +17,8 @@
 
 #include <seqan3/alphabet/concept.hpp>
 #include <seqan3/core/concept/cereal.hpp>
-#include <seqan3/core/concept/core_language.hpp>
 #include <seqan3/core/detail/strong_type.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 
 #if SEQAN3_WITH_CEREAL
 #include <cereal/types/array.hpp>

diff --git a/include/seqan3/alphabet/composite/alphabet_tuple_base.hpp b/include/seqan3/alphabet/composite/alphabet_tuple_base.hpp
@@ -18,11 +18,11 @@
 
 #include <meta/meta.hpp>
 
-#include <seqan3/alphabet/concept.hpp>
-#include <seqan3/alphabet/composite/detail.hpp>
 #include <seqan3/alphabet/alphabet_base.hpp>
+#include <seqan3/alphabet/composite/detail.hpp>
+#include <seqan3/alphabet/concept.hpp>
 #include <seqan3/alphabet/detail/alphabet_proxy.hpp>
-#include <seqan3/core/concept/core_language.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 #include <seqan3/utility/detail/integer_traits.hpp>
 #include <seqan3/utility/tuple/concept.hpp>
 #include <seqan3/utility/type_list/traits.hpp>

diff --git a/include/seqan3/alphabet/composite/detail.hpp b/include/seqan3/alphabet/composite/detail.hpp
@@ -13,7 +13,7 @@
 #pragma once
 
 #include <seqan3/alphabet/concept.hpp>
-#include <seqan3/core/concept/core_language.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 #include <seqan3/utility/type_list/type_list.hpp>
 #include <seqan3/utility/type_traits/lazy_conditional.hpp>
 

diff --git a/include/seqan3/alphabet/concept.hpp b/include/seqan3/alphabet/concept.hpp
@@ -16,8 +16,8 @@
 
 #include <seqan3/alphabet/exception.hpp>
 #include <seqan3/core/concept/cereal.hpp>
-#include <seqan3/core/concept/core_language.hpp>
 #include <seqan3/core/detail/customisation_point.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 #include <seqan3/utility/detail/type_name_as_string.hpp>
 #include <seqan3/utility/type_traits/basic.hpp>
 

diff --git a/include/seqan3/alphabet/detail/alphabet_proxy.hpp b/include/seqan3/alphabet/detail/alphabet_proxy.hpp
@@ -17,8 +17,8 @@
 #include <seqan3/alphabet/alphabet_base.hpp>
 #include <seqan3/alphabet/nucleotide/concept.hpp>
 #include <seqan3/alphabet/quality/concept.hpp>
-#include <seqan3/core/concept/core_language.hpp>
 #include <seqan3/core/detail/template_inspection.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 #include <seqan3/utility/type_traits/basic.hpp>
 
 namespace seqan3

diff --git a/include/seqan3/argument_parser/validators.hpp b/include/seqan3/argument_parser/validators.hpp
@@ -21,13 +21,13 @@
 #include <sstream>
 
 #include <seqan3/argument_parser/exceptions.hpp>
-#include <seqan3/core/concept/core_language.hpp>
 #include <seqan3/core/debug_stream/detail/to_string.hpp>
 #include <seqan3/core/detail/debug_stream_range.hpp>
 #include <seqan3/io/detail/misc.hpp>
 #include <seqan3/io/detail/safe_filesystem_entry.hpp>
 #include <seqan3/range/container/concept.hpp>
 #include <seqan3/range/views/join.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 #include <seqan3/utility/type_list/traits.hpp>
 #include <seqan3/utility/type_pack/traits.hpp>
 #include <seqan3/utility/type_traits/basic.hpp>

diff --git a/include/seqan3/core/algorithm/bound.hpp b/include/seqan3/core/algorithm/bound.hpp
@@ -14,8 +14,8 @@
 
 #pragma once
 
-#include <seqan3/core/concept/core_language.hpp>
 #include <seqan3/core/detail/strong_type.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 
 SEQAN3_DEPRECATED_HEADER("This header is deprecated and will be removed in SeqAn-3.1.0. The contained functionality has been replaced by the seqan3::align_cfg::band_fixed_size configuration.")
 

diff --git a/include/seqan3/core/concept/all.hpp b/include/seqan3/core/concept/all.hpp
@@ -13,14 +13,5 @@
 #pragma once
 
 #include <seqan3/core/concept/cereal.hpp>
-#include <seqan3/core/concept/core_language.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 #include <seqan3/utility/tuple/concept.hpp>
-
-/*!\defgroup concept Concept
- * \ingroup core
- * \brief Additional concepts that are not specific to a SeqAn module.
- *
- * \details
- *
- * \todo write me.
- */