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[PATCH] deprecate core_language.hpp #2351

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Feb 15, 2021
Merged

[PATCH] deprecate core_language.hpp #2351

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d8b8490
[PATCH] deprecate core_language.hpp
SGSSGene Jan 25, 2021
5dbb7c7
[FIX] rename unittest to utility/detail/exposition_only_concept_test.cpp
SGSSGene Jan 27, 2021
a93d692
[FIX] doxygen - adjusting template_specicialisation_of
SGSSGene Feb 5, 2021
c6bc2ea
[FIX] introducing to doxygen
SGSSGene Feb 5, 2021
23a21b9
[FIX] reorder of includes
SGSSGene Feb 14, 2021
7b01ba2
[FIX] more reordering of includes
SGSSGene Feb 14, 2021
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/configuration/align_config_output.hpp
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#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
{
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/configuration/align_config_score_type.hpp
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#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
{
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/matrix/alignment_optimum.hpp
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#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>
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/matrix/detail/affine_cell_proxy.hpp
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#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>

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2 changes: 1 addition & 1 deletion include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column.hpp
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#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
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/matrix/detail/alignment_score_matrix_one_column_base.hpp
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#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
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/matrix/detail/alignment_score_matrix_proxy.hpp
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#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
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/matrix/detail/combined_score_and_trace_matrix.hpp
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#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
{
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/matrix/detail/matrix_coordinate.hpp
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#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>

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2 changes: 1 addition & 1 deletion include/seqan3/alignment/matrix/detail/score_matrix_single_column.hpp
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#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
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/matrix/detail/trace_matrix_full.hpp
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#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
{
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/pairwise/detail/alignment_algorithm_state.hpp
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#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
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/pairwise/policy/affine_gap_policy.hpp
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#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
{
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/pairwise/policy/simd_affine_gap_policy.hpp
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#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>
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4 changes: 2 additions & 2 deletions include/seqan3/alignment/scoring/gap_scheme.hpp
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#pragma once

#include <seqan3/std/concepts>
#include <stdexcept>
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#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
{
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2 changes: 1 addition & 1 deletion include/seqan3/alignment/scoring/scoring_scheme_base.hpp
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#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>
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6 changes: 3 additions & 3 deletions include/seqan3/alphabet/composite/alphabet_tuple_base.hpp
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#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>
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2 changes: 1 addition & 1 deletion include/seqan3/alphabet/composite/detail.hpp
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#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>

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2 changes: 1 addition & 1 deletion include/seqan3/alphabet/concept.hpp
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#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>

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2 changes: 1 addition & 1 deletion include/seqan3/alphabet/detail/alphabet_proxy.hpp
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#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
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2 changes: 1 addition & 1 deletion include/seqan3/argument_parser/validators.hpp
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#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>
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2 changes: 1 addition & 1 deletion include/seqan3/core/algorithm/bound.hpp
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#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.")

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11 changes: 1 addition & 10 deletions include/seqan3/core/concept/all.hpp
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#pragma once

#include <seqan3/core/concept/cereal.hpp>
#include <seqan3/core/concept/core_language.hpp>
#include <seqan3/utility/detail/exposition_only_concept.hpp>
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So far I know, we don't put detail things into all.hpp files.
@seqan/core is that correct?

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Some question came up:

1. where to put the `\defgroup utility_concept Concept`. Everywhere else it is inside an all.hpp, but I don't really have one. I have put it for now into `utility/all.hpp`

2. core/all.hpp had an unuseful `concept` description. I for now removed it.

utility_concept

For detail folder there is no all.hpp.
We actually want to establish to never just include 'all.hpp' but only what you need. The 'all.hpp' are for the user, who is not so familiar with the different modules etc.
Things in detail are functionalities that are there for us and not for the user, so there is no 'all.hpp'.

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So far I know, we don't put detail things into all.hpp files.
@seqan/core is that correct?

In general, you are right, but I think it is okay in this case. In the long-run we will remove that header.

#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.
*/
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