Merge pull request #2255 from Irallia/INFRA/core/move_header_algorith…

…m_to_configuration

[INFRA] Move core/algorithm into core/configuration

include/seqan3/alignment/configuration/align_config_debug.hpp

@@ -13,8 +13,8 @@
 #pragma once
 
 #include <seqan3/alignment/configuration/detail.hpp>
-#include <seqan3/core/algorithm/configuration_element_debug_mode.hpp>
 #include <seqan3/core/algorithm/pipeable_config_element.hpp>
+#include <seqan3/core/configuration/detail/configuration_element_debug_mode.hpp>
 
 namespace seqan3::align_cfg::detail
 {

include/seqan3/alignment/configuration/align_config_edit.hpp

@@ -15,7 +15,7 @@
 #include <seqan3/alignment/configuration/align_config_gap_cost_affine.hpp>
 #include <seqan3/alignment/configuration/align_config_scoring_scheme.hpp>
 #include <seqan3/alignment/scoring/nucleotide_scoring_scheme.hpp>
-#include <seqan3/core/algorithm/configuration.hpp>
+#include <seqan3/core/configuration/configuration.hpp>
 
 namespace seqan3::align_cfg
 {

include/seqan3/alignment/configuration/align_config_parallel.hpp

@@ -15,7 +15,7 @@
 #pragma once
 
 #include <seqan3/alignment/configuration/detail.hpp>
-#include <seqan3/core/algorithm/configuration_element_parallel_mode.hpp>
+#include <seqan3/core/configuration/detail/configuration_element_parallel_mode.hpp>
 
 namespace seqan3::align_cfg
 {

include/seqan3/alignment/configuration/detail.hpp

@@ -12,7 +12,7 @@
 
 #pragma once
 
-#include <seqan3/core/algorithm/configuration_utility.hpp>
+#include <seqan3/core/configuration/detail/configuration_utility.hpp>
 
 namespace seqan3::detail
 {

include/seqan3/alignment/pairwise/align_result_selector.hpp

@@ -23,7 +23,7 @@
 #include <seqan3/alignment/matrix/trace_directions.hpp>
 #include <seqan3/alignment/pairwise/detail/type_traits.hpp>
 #include <seqan3/alphabet/gap/gapped.hpp>
-#include <seqan3/core/algorithm/configuration.hpp>
+#include <seqan3/core/configuration/configuration.hpp>
 #include <seqan3/core/detail/template_inspection.hpp>
 #include <seqan3/core/range/type_traits.hpp>
 #include <seqan3/range/decorator/gap_decorator.hpp>

include/seqan3/alignment/pairwise/alignment_result.hpp

@@ -15,7 +15,7 @@
 
 #include <optional>
 
-#include <seqan3/core/algorithm/configuration.hpp>
+#include <seqan3/core/configuration/configuration.hpp>
 #include <seqan3/core/detail/debug_stream_type.hpp>
 #include <seqan3/core/detail/template_inspection.hpp>
 

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

@@ -17,7 +17,7 @@
 #include <seqan3/alignment/exception.hpp>
 #include <seqan3/alignment/matrix/detail/coordinate_matrix.hpp>
 #include <seqan3/alignment/pairwise/detail/type_traits.hpp>
-#include <seqan3/core/algorithm/configuration.hpp>
+#include <seqan3/core/configuration/configuration.hpp>
 #include <seqan3/core/detail/template_inspection.hpp>
 
 namespace seqan3::detail

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

@@ -14,7 +14,7 @@
 
 #include <seqan3/alignment/matrix/detail/aligned_sequence_builder.hpp>
 #include <seqan3/alignment/pairwise/detail/type_traits.hpp>
-#include <seqan3/core/algorithm/configuration.hpp>
+#include <seqan3/core/configuration/configuration.hpp>
 #include <seqan3/core/detail/empty_type.hpp>
 #include <seqan3/core/detail/template_inspection.hpp>
 

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

@@ -18,8 +18,8 @@
 #include <seqan3/alignment/matrix/detail/coordinate_matrix.hpp>
 #include <seqan3/alignment/matrix/detail/matrix_coordinate.hpp>
 #include <seqan3/alignment/pairwise/detail/type_traits.hpp>
-#include <seqan3/core/algorithm/configuration.hpp>
 #include <seqan3/core/concept/tuple.hpp>
+#include <seqan3/core/configuration/configuration.hpp>
 #include <seqan3/core/detail/template_inspection.hpp>
 
 namespace seqan3::detail

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

@@ -28,8 +28,8 @@
 #include <seqan3/alignment/matrix/detail/matrix_coordinate.hpp>
 #include <seqan3/alignment/matrix/trace_directions.hpp>
 #include <seqan3/alignment/pairwise/detail/concept.hpp>
-#include <seqan3/core/algorithm/configuration.hpp>
 #include <seqan3/core/bit_manipulation.hpp>
+#include <seqan3/core/configuration/configuration.hpp>
 #include <seqan3/core/detail/empty_type.hpp>
 #include <seqan3/core/detail/template_inspection.hpp>
 #include <seqan3/core/simd/simd_traits.hpp>

include/seqan3/alignment/pairwise/edit_distance_unbanded.hpp

@@ -24,7 +24,7 @@
 #include <seqan3/alignment/matrix/matrix_concept.hpp>
 #include <seqan3/alignment/pairwise/alignment_result.hpp>
 #include <seqan3/alignment/pairwise/edit_distance_fwd.hpp>
-#include <seqan3/core/algorithm/configuration.hpp>
+#include <seqan3/core/configuration/configuration.hpp>
 
 namespace seqan3::detail
 {

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/algorithm/configuration.hpp>
 #include <seqan3/core/concept/core_language.hpp>
+#include <seqan3/core/configuration/configuration.hpp>
 #include <seqan3/core/simd/concept.hpp>
 #include <seqan3/core/simd/simd_algorithm.hpp>
 #include <seqan3/core/simd/simd_traits.hpp>

include/seqan3/core/algorithm/all.hpp

@@ -15,67 +15,11 @@
 /*!\defgroup algorithm Algorithm
  * \ingroup core
  * \brief Provides core functionality used to configure algorithms.
- *
- * \details
- *
- * In SeqAn there are many algorithms, e.g. alignment or search algorithms, that can be configured through
- * many different settings and policies that alter the execution of the respective algorithm.
- * These configurations can be orthogonal or might be mutually exclusive and can make interfaces very difficult to use.
- * This module provides a basic system to manage the configurations of algorithms using a unified interface.
- *
- * ### Usage
- *
- * The basis of any algorithm configuration are configuration elements. These are objects that handle a specific
- * setting and must satisfy the seqan3::detail::config_element_specialisation. The following snippet demonstrates a
- * basic setup for such configuration elements.
- *
- * \include test/snippet/core/algorithm/configuration_setup.cpp
- *
- * Here, two classes with the name `bar` and `foo` are created. They can be normal or template classes and must
- * inherit from seqan3::pipeable_config_element and contain a member with the name `value` to satisfy the respective
- * concept. The separate `value` member is used for a proper encapsulation from the actual setting parameter.
- * For example the alignment algorithms require a scoring scheme, but the scoring scheme itself should not be pipeable
- * with other settings.
- *
- * In addition an enum type was defined that will be used later to allow for compatibility checks when combining
- * settings in a configuration object. This enum assigns every configuration element a unique id.
- * To provide compatibility checks the `seqan3::detail::compatibility_table` must be overloaded for the specific
- * algorithm configuration.
- *
- * \include test/snippet/core/algorithm/configuration_compatibility.cpp
- *
- * The type for the configuration element ids is used to overload the bool table. In the example above, both
- * elements can be combined with each other but not with themselves, to avoid inconsistent settings.
- *
- * ### Combining Configurations
- *
- * To enable easy creation of algorithm settings the seqan3::configuration supports a pipeable interface for the
- * different configuration elements which are added through the seqan3::pipeable_config_element base class.
- * The following snippet demonstrates how `bar` and `foo` can be combined.
- *
- * \include test/snippet/core/algorithm/configuration_combine.cpp
-
- * ### Access the data
- *
- * The configuration inherits from a std::tuple and exposes a tuple like interface using the standard
- * position-based and type-based `get` interfaces. The `get` interface was extended to also support
- * template template types as input template parameters to query the correct element:
- *
- * \include test/snippet/core/algorithm/configuration_get.cpp
- *
- * The get interface returns a reference to the stored configuration element. In some cases, e.g. the implementor
- * of the actual algorithm, one wants to have an easy access to the actual value of the setting. Since, the
- * configuration must not contain all possible configuration elements the seqan3::configuration provides a
- * seqan3::configuration::get_or interface. Using this interface one can call get with a specific configuration element.
- * If this configuration element or a specialisation of it is already stored inside of the configuration, the respective
- * element is returned. Otherwise, the passed argument will be returned as the alternative.
- *
- * \include test/snippet/core/algorithm/configuration_get_or.cpp
  */
 #include <seqan3/core/algorithm/algorithm_result_generator_range.hpp>
 #include <seqan3/core/algorithm/bound.hpp>
-#include <seqan3/core/algorithm/concept.hpp>
-#include <seqan3/core/algorithm/configuration_utility.hpp>
-#include <seqan3/core/algorithm/configuration.hpp>
-#include <seqan3/core/detail/pack_algorithm.hpp>
 #include <seqan3/core/algorithm/pipeable_config_element.hpp>
+#include <seqan3/core/configuration/all.hpp>
+#if SEQAN3_VERSION_MAJOR == 3 && SEQAN3_VERSION_MINOR == 1
+  #pragma warning "Remove #include <seqan3/core/configuration/all.hpp> from this header."
+#endif

include/seqan3/core/algorithm/concept.hpp

@@ -6,180 +6,15 @@
 // -----------------------------------------------------------------------------------------------------
 
 /*!\file
- * \brief Provides concepts for the configuration classes.
+ * \brief [DEPRECATED] Provides concepts for the configuration classes.
  * \author Rene Rahn <rene.rahn AT fu-berlin.de>
+ * \deprecated This header will be removed in 3.1.0; Please \#include <seqan3/core/configuration/detail/concept.hpp>
+ *             instead.
  */
 
 #pragma once
 
-#include <seqan3/std/concepts>
-#include <functional>
-#include <type_traits>
+#include <seqan3/core/configuration/detail/concept.hpp>
 
-#include <meta/meta.hpp>
-
-#include <seqan3/core/detail/template_inspection.hpp>
-
-namespace seqan3
-{
-//!\cond
-// Forward declarations
-template <typename derived_t, typename value_t = void>
-struct pipeable_config_element;
-//!\endcond
-}
-
-namespace seqan3::detail
-{
-
-// ----------------------------------------------------------------------------
-// compatibility_table
-// ----------------------------------------------------------------------------
-
-/*!\brief Declaration of algorithm specific compatibility table.
- * \ingroup algorithm
- * \tparam algorithm_id_type The type of the algorithm specific id. Algorithm configurations must maintain
- *                           this table to allow validation checks.
- */
-template <typename algorithm_id_type>
-inline constexpr std::array<std::array<void *, 0>, 0> compatibility_table{};
-
-// ----------------------------------------------------------------------------
-// Concept config_element_specialisation
-// ----------------------------------------------------------------------------
-
-#if SEQAN3_WORKAROUND_GCC_PIPEABLE_CONFIG_CONCEPT
-/*!\brief A helper class to check if a type has a static member called `id`.
- * \ingroup algorithm
- *
- * \details
- *
- * This class is needed for gcc versions older than 11. It adds a SFINAE check to test if a type
- * has a static member called `id`, which is needed for the concept defintions around the
- * pipeable configuration element concepts.
- */
-struct config_id_accessor
-{
-private:
-    //!\brief Helper variable template to convert the configuration enum identifier to an integer.
-    template <typename config_t>
-    static constexpr int32_t as_int = static_cast<int32_t>(std::remove_cvref_t<config_t>::id);
-
-    //!\brief Helper function to check if static id member exists.
-    template <typename config_t>
-    static constexpr auto has_id_member(int) -> decltype((static_cast<void>(config_t::id), true))
-    {
-        return true;
-    }
-
-    //!\overload
-    template <typename config_t>
-    static constexpr bool has_id_member(...)
-    {
-        return false;
-    }
-
-public:
-    //!\brief Type alias for the internal enumeration type that represents the id.
-    template <typename config_t>
-    using id_type = std::remove_cvref_t<decltype(config_t::id)>;
-
-    /*!\brief Checks if two configuration types are compatible.
-     *
-     * \tparam config1_t The type of the first configuration to check against the second.
-     * \tparam config2_t The type of the second configuration.
-     *
-     * \details
-     *
-     * Uses the seqan3::detail::compatibility_table of the corresponding configuration element domain to check
-     * if both configurations can be combined.
-     */
-    template <typename config1_t, typename config2_t>
-    static constexpr auto is_compatible()
-    {
-        if constexpr (has_id_member<config1_t>(0) && has_id_member<config2_t>(0)) // needed for gcc <= 9
-        {
-            if constexpr (std::same_as<id_type<config1_t>, id_type<config2_t>>)
-            {
-                return std::bool_constant<compatibility_table<id_type<config1_t>>[as_int<config1_t>]
-                                                                                 [as_int<config2_t>]>{};
-            }
-            else
-            {
-                return std::false_type{};
-            }
-        }
-        else
-        {
-            return std::bool_constant<compatibility_table<id_type<config1_t>>[as_int<config1_t>][as_int<config2_t>]>{};
-        }
-    }
-
-    //!\brief Variable template that evaluates to `true` if the type has a static id member, otherwise `false`.
-    template <typename config_t>
-    static constexpr bool has_id = has_id_member<config_t>(0);
-};
-#endif // SEQAN3_WORKAROUND_GCC_PIPEABLE_CONFIG_CONCEPT
-
-/*!\interface seqan3::detail::config_element_specialisation <>
- * \brief Concept for an algorithm configuration element.
- * \ingroup algorithm
- *
- * \extends std::semiregular
- * \implements seqan3::pipeable_config_element
- */
-
-/*!\name Requirements for seqan3::detail::config_element_specialisation
- * \relates seqan3::detail::config_element_specialisation
- * \brief   You can expect this member on all types that satisfy seqan3::detail::config_element_specialisation.
- * \{
- */
-/*!\var id
- * \brief Algorithm specific static id used for internal validation checks.
- */
-//!\}
-//!\cond
-template <typename config_t>
-SEQAN3_CONCEPT config_element_specialisation = requires
-{
-    requires std::is_base_of_v<seqan3::pipeable_config_element<config_t>, config_t>;
-    requires std::semiregular<config_t>;
-#if SEQAN3_WORKAROUND_GCC_PIPEABLE_CONFIG_CONCEPT
-    requires config_id_accessor::has_id<config_t>;
-#else // ^^^ workaround / no workaround vvv
-    { config_t::id };
-#endif // SEQAN3_WORKAROUND_GCC_PIPEABLE_CONFIG_CONCEPT
-};
-//!\endcond
-
-/*!\interface seqan3::detail::config_element_pipeable_with <>
- * \brief Concept to check if one configuration element can be combined with another configuration element.
- * \ingroup algorithm
- *
- * \tparam config1_t The type of the first configuration element.
- * \tparam config2_t The type of the second configuration element.
- *
- * \details
- *
- * This concept is fulfilled if:
- *  * both configurations model seqan3::detail::config_element_specialisation,
- *  * are defined within the same algorithm configuration domain,
- *  * a seqan3::detail::compatibility_table is defined for the configuration elements and
- *    returns `true` for both configurations.
- */
-//!\cond
-template <typename config1_t, typename config2_t>
-SEQAN3_CONCEPT config_element_pipeable_with =
-    config_element_specialisation<config1_t> &&
-    config_element_specialisation<config2_t> &&
-#if SEQAN3_WORKAROUND_GCC_PIPEABLE_CONFIG_CONCEPT
-    std::same_as<config_id_accessor::id_type<config1_t>, config_id_accessor::id_type<config2_t>> &&
-    decltype(config_id_accessor::is_compatible<config1_t, config2_t>())::value;
-#else // ^^^ workaround / no workaround vvv
-    std::same_as<std::remove_cvref_t<decltype(config1_t::id)>, std::remove_cvref_t<decltype(config2_t::id)>> &&
-    compatibility_table<std::remove_cvref_t<decltype(config1_t::id)>>[static_cast<int32_t>(config1_t::id)]
-                                                                     [static_cast<int32_t>(config2_t::id)];
-#endif // SEQAN3_WORKAROUND_GCC_PIPEABLE_CONFIG_CONCEPT
-//!\endcond
-
-} // namespace seqan3::detail
+SEQAN3_DEPRECATED_HEADER(
+   "This header is deprecated and will be removed in SeqAn-3.1.0; Please #include <seqan3/core/configuration/detail/concept.hpp> instead.")