From 5fec3543dc040c43621478ff1de25755b316d515 Mon Sep 17 00:00:00 2001 From: "seqan-actions[bot]" Date: Thu, 6 Jun 2024 20:08:24 +0200 Subject: [PATCH] [MISC] IWYU --- include/hibf/build/update_parent_kmers.hpp | 5 ++-- .../hierarchical_interleaved_bloom_filter.hpp | 17 ++++++------ include/hibf/misc/bit_vector.hpp | 19 +++++++------ include/hibf/misc/divide_and_ceil.hpp | 1 + include/hibf/misc/insert_iterator.hpp | 15 ++++++----- include/hibf/misc/timer.hpp | 4 +-- src/build/construct_ibf.cpp | 13 ++++----- src/build/insert_into_ibf.cpp | 11 ++++---- src/config.cpp | 5 ++-- src/hierarchical_interleaved_bloom_filter.cpp | 25 ++++++++--------- src/layout/compute_layout.cpp | 10 +++---- src/misc/print.cpp | 11 ++++---- src/sketch/toolbox.cpp | 25 ++++++++--------- test/include/hibf/test/sandboxed_path.hpp | 1 - .../interleaved_bloom_filter_benchmark.cpp | 27 ++++++++++--------- test/unit/hibf/counting_vector_test.cpp | 5 ++-- test/unit/hibf/sketch/hyperloglog_test.cpp | 11 ++++---- test/unit/hibf/sketch/toolbox_test.cpp | 19 ++++++------- .../unit/test/temporary_snippet_file_test.cpp | 3 ++- 19 files changed, 116 insertions(+), 111 deletions(-) diff --git a/include/hibf/build/update_parent_kmers.hpp b/include/hibf/build/update_parent_kmers.hpp index 35c28e00..7b2da7e7 100644 --- a/include/hibf/build/update_parent_kmers.hpp +++ b/include/hibf/build/update_parent_kmers.hpp @@ -8,9 +8,10 @@ */ #pragma once -#include // for uint64_t +#include // for uint64_t +#include // for equal_to -#include // for unordered_flat_set +#include // for unordered_flat_set, hash #include // for serial_timer, concurrent_timer #include diff --git a/include/hibf/hierarchical_interleaved_bloom_filter.hpp b/include/hibf/hierarchical_interleaved_bloom_filter.hpp index ede835ba..51b9c025 100644 --- a/include/hibf/hierarchical_interleaved_bloom_filter.hpp +++ b/include/hibf/hierarchical_interleaved_bloom_filter.hpp @@ -4,15 +4,14 @@ #pragma once -#include // for __fn, fill, sort -#include // for assert -#include // for int64_t, uint16_t -#include // for integral, unsigned_integral -#include // for size_t -#include // for less, identity -#include // for addressof -#include // for forward_range, range, range_value_t -#include // for vector, operator== +#include // for __fn, fill, sort +#include // for assert +#include // for int64_t, uint16_t +#include // for integral, unsigned_integral +#include // for size_t +#include // for addressof +#include // for forward_range, range_value_t, range +#include // for vector, operator== #include // for CEREAL_SERIALIZE_FUNCTION_NAME #include // IWYU pragma: keep diff --git a/include/hibf/misc/bit_vector.hpp b/include/hibf/misc/bit_vector.hpp index 07a3e1ff..4294c44d 100644 --- a/include/hibf/misc/bit_vector.hpp +++ b/include/hibf/misc/bit_vector.hpp @@ -21,7 +21,7 @@ #pragma once -#include // for max, __for_each_fn, for_each, __all_of_fn, __any_of_fn, __fill_fn +#include // for __fn, for_each, all_of, any_of, copy, fill #include // for countr_zero #include // for assert #include // for uint64_t @@ -29,24 +29,23 @@ #include // for strong_ordering, operator== #include // for assignable_from #include // for size_t, ptrdiff_t -#include // for identity #include // for initializer_list -#include // for back_inserter, iter_reference_t, random_access_iterator_tag -#include // for allocator, assume_aligned, allocator_traits -#include // for __next_fn, distance, next, _Begin, _End, __distance_fn, begin +#include // for iter_reference_t, __fn, back_inserter, distance, iter_differen... +#include // for allocator, assume_aligned, allocator_traits, __compressed_pair +#include // for __fn, begin, end #include // for out_of_range -#include // for operator+, char_traits, to_string, operator""s +#include // for char_traits, operator+, to_string, operator""s #include // for conditional_t #include // for swap #include // for vector -#include // for CEREAL_SERIALIZE_FUNCTION_NAME -#include // for CEREAL_SERIALIZE_FUNCTION_NAME +#include // for binary_data +#include // for CEREAL_LOAD_FUNCTION_NAME, CEREAL_SAVE_FUNCTION_NAME #include // for specialization, specialize -#include // for cereal_archive +#include // for cereal_archive, cereal_text_archive #include // for aligned_allocator -#include // for HIBF_CONSTEXPR_VECTOR +#include // for HIBF_CONSTEXPR_VECTOR, _LIBCPP_HAS_NO_ASAN, _LIBCPP_VERSION namespace seqan::hibf { diff --git a/include/hibf/misc/divide_and_ceil.hpp b/include/hibf/misc/divide_and_ceil.hpp index 77083e69..2a963836 100644 --- a/include/hibf/misc/divide_and_ceil.hpp +++ b/include/hibf/misc/divide_and_ceil.hpp @@ -7,6 +7,7 @@ #include // for assert #include // for unsigned_integral #include // for size_t +#include // for numeric_limits #include diff --git a/include/hibf/misc/insert_iterator.hpp b/include/hibf/misc/insert_iterator.hpp index ccebc3e1..903869a0 100644 --- a/include/hibf/misc/insert_iterator.hpp +++ b/include/hibf/misc/insert_iterator.hpp @@ -4,14 +4,15 @@ #pragma once -#include // for assert -#include // for uint64_t -#include // for ptrdiff_t -#include // for output_iterator_tag -#include // for addressof -#include // for vector +#include // for assert +#include // for uint64_t +#include // for ptrdiff_t +#include // for equal_to +#include // for output_iterator_tag +#include // for addressof +#include // for vector -#include // for unordered_flat_set +#include // for unordered_flat_set, hash #include // IWYU pragma: private, include diff --git a/include/hibf/misc/timer.hpp b/include/hibf/misc/timer.hpp index af6a4590..41e1428b 100644 --- a/include/hibf/misc/timer.hpp +++ b/include/hibf/misc/timer.hpp @@ -12,10 +12,10 @@ #include // for max #include // for atomic, __atomic_base, memory_order_relaxed #include // for assert -#include // for duration, time_point, operator-, steady_clock +#include // for duration, time_point, operator-, operator<=>, steady_clock #include // for uint64_t +#include // for operator>=, strong_ordering #include // for same_as -#include // for move #include diff --git a/src/build/construct_ibf.cpp b/src/build/construct_ibf.cpp index a6550f97..d44e7cca 100644 --- a/src/build/construct_ibf.cpp +++ b/src/build/construct_ibf.cpp @@ -2,11 +2,12 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: BSD-3-Clause -#include // for assert -#include // for uint64_t -#include // for ceil -#include // for size_t -#include // for vector +#include // for assert +#include // for uint64_t +#include // for ceil +#include // for size_t +#include // for equal_to +#include // for vector #include // for bin_size_in_bits #include // for build_data @@ -14,7 +15,7 @@ #include // for insert_into_ibf #include // for update_parent_kmers #include // for config -#include // for unordered_flat_set +#include // for unordered_flat_set, hash #include // for interleaved_bloom_filter, bin_count, bin_size, hash_function_c... #include // for graph #include // for divide_and_ceil diff --git a/src/build/insert_into_ibf.cpp b/src/build/insert_into_ibf.cpp index e2e3ff4c..4a5b0784 100644 --- a/src/build/insert_into_ibf.cpp +++ b/src/build/insert_into_ibf.cpp @@ -5,18 +5,17 @@ #include // for assert #include // for uint64_t #include // for size_t -#include // for function +#include // for equal_to, function #include // for counted_iterator -#include // for all_t, operator== #include // for vector #include // for build_data #include // for insert_into_ibf -#include // for config, insert_iterator -#include // for unordered_flat_set -#include // for chunk_view, operator==, chunk, chunk_fn +#include // for insert_iterator, config +#include // for Table, hash, unordered_flat_set +#include // for chunk, chunk_fn, chunk_view #include // for operator| -#include // for interleaved_bloom_filter, bin_index +#include // for bin_index, interleaved_bloom_filter #include // for layout #include // for divide_and_ceil #include // for serial_timer, concurrent_timer diff --git a/src/config.cpp b/src/config.cpp index 1e27d498..b82069d6 100644 --- a/src/config.cpp +++ b/src/config.cpp @@ -3,12 +3,13 @@ // SPDX-License-Identifier: BSD-3-Clause #include // for assert -#include // for sqrt, ceil +#include // for ceil, sqrt #include // for function #include // for operator<<, basic_ostream, basic_istream, getline, stringstream +#include // for basic_stringstream #include // for invalid_argument #include // for char_traits, string -#include // for operator==, basic_string_view +#include // for operator==, basic_string_view, string_view #include // for JSONInputArchive, JSONOutputArchive #include // for make_nvp, InputArchive, OutputArchive diff --git a/src/hierarchical_interleaved_bloom_filter.cpp b/src/hierarchical_interleaved_bloom_filter.cpp index 9044df4f..f4078300 100644 --- a/src/hierarchical_interleaved_bloom_filter.cpp +++ b/src/hierarchical_interleaved_bloom_filter.cpp @@ -2,16 +2,17 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: BSD-3-Clause -#include // for max, fill_n, shuffle -#include // for assert -#include // for uint64_t, int64_t -#include // for size_t -#include // for mutex, lock_guard -#include // for iota -#include // for optional -#include // for random_device, mt19937_64 -#include // for move -#include // for vector, erase +#include // for shuffle, __fn, none_of +#include // for assert +#include // for uint64_t, int64_t +#include // for size_t +#include // for equal_to +#include // for mutex, lock_guard +#include // for iota +#include // for optional +#include // for random_device, mt19937_64 +#include // for move +#include // for vector, erase #include // for build_data #include // for compute_kmers @@ -20,7 +21,7 @@ #include // for update_parent_kmers #include // for update_user_bins #include // for config -#include // for unordered_flat_set +#include // for unordered_flat_set, hash #include // for hierarchical_interleaved_bloom_filter #include // for interleaved_bloom_filter #include // for compute_fpr_correction @@ -28,7 +29,7 @@ #include // for graph #include // for layout #include // for divide_and_ceil -#include // for timer +#include // for concurrent_timer #include // for compute_sketches #include // for hyperloglog diff --git a/src/layout/compute_layout.cpp b/src/layout/compute_layout.cpp index 3d7dee02..b7786b49 100644 --- a/src/layout/compute_layout.cpp +++ b/src/layout/compute_layout.cpp @@ -2,12 +2,10 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: BSD-3-Clause -#include // for __fn, sort -#include // for size_t -#include // for identity -#include // for addressof -#include // for stringstream -#include // for vector +#include // for __fn, sort +#include // for size_t +#include // for addressof +#include // for vector #include // for config #include // for compute_fpr_correction diff --git a/src/misc/print.cpp b/src/misc/print.cpp index 77834373..0df227f6 100644 --- a/src/misc/print.cpp +++ b/src/misc/print.cpp @@ -2,11 +2,12 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: BSD-3-Clause -#include // for uint16_t, int16_t, int64_t, int8_t, uint8_t, int32_t, uint32_t, uin... -#include // for size_t -#include // for basic_ostream::operator<<, ostream, operator<<, basic_ostream -#include // for range_value_t, empty -#include // for vector +#include // for uint16_t, int16_t, int64_t, int8_t, uint8_t, int32_t, uint32_t, uin... +#include // for size_t +#include // for ostream, operator<<, basic_ostream +#include // for range_value_t, empty +#include // for conditional +#include // for vector #include // for bit_vector #include // for counting_vector diff --git a/src/sketch/toolbox.cpp b/src/sketch/toolbox.cpp index e13cea40..a7c03995 100644 --- a/src/sketch/toolbox.cpp +++ b/src/sketch/toolbox.cpp @@ -2,18 +2,19 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: BSD-3-Clause -#include // for sort -#include // for assert -#include // for uint64_t, int64_t -#include // for sqrt, floor -#include // for size_t -#include // for numeric_limits -#include // for omp_get_thread_num -#include // for uniform_int_distribution, mt19937_64 -#include // for swap, move -#include // for vector - -#include // for unordered_flat_map, pair +#include // for sort +#include // for assert +#include // for uint64_t, int64_t +#include // for floor, sqrt +#include // for size_t +#include // for equal_to +#include // for numeric_limits +#include // for omp_get_thread_num +#include // for uniform_int_distribution, mt19937_64 +#include // for swap, move +#include // for vector + +#include // for hash, unordered_flat_map #include // for hyperloglog #include // for clustering_node, entry, neighbor, prio_queue, distance_matrix, cluste... diff --git a/test/include/hibf/test/sandboxed_path.hpp b/test/include/hibf/test/sandboxed_path.hpp index d217e908..701350a1 100644 --- a/test/include/hibf/test/sandboxed_path.hpp +++ b/test/include/hibf/test/sandboxed_path.hpp @@ -11,7 +11,6 @@ #include // for path, filesystem_error, operator/ #include // for errc, make_error_code -#include // for __libcpp_remove_reference_t #include // for move, forward #include diff --git a/test/performance/ibf/interleaved_bloom_filter_benchmark.cpp b/test/performance/ibf/interleaved_bloom_filter_benchmark.cpp index 065dc41e..1edaea89 100644 --- a/test/performance/ibf/interleaved_bloom_filter_benchmark.cpp +++ b/test/performance/ibf/interleaved_bloom_filter_benchmark.cpp @@ -4,21 +4,22 @@ #include // for State, Benchmark, AddCustomContext, Counter, BENCHMARK -#include // for copy, fill_n, __generate_fn, generate -#include // for log, ceil, exp -#include // for size_t -#include // for uniform_int_distribution, mt19937_64 -#include // for all_t, transform_view, iterator_t, iota_view, _Partial -#include // for allocator, to_string, basic_string -#include // for tuple, make_tuple -#include // for move, pair -#include // for vector - -#include // for pair, unordered_map -#include // for chunk_view, operator==, chunk, chunk_fn +#include // for __fn, generate +#include // for log, ceil, exp +#include // for size_t +#include // for equal_to +#include // for uniform_int_distribution, mt19937_64 +#include // for transform_view, iota_view, __range_adaptor_closure_t, __fn +#include // for to_string, basic_string +#include // for tuple, make_tuple +#include // for move, pair +#include // for vector + +#include // for hash, unordered_map +#include // for chunk, chunk_fn, chunk_view #include // for operator| #include // for to -#include // for interleaved_bloom_filter, bin_index, bin_count, bin_size +#include // for bin_index, interleaved_bloom_filter, bin_count, bin_size #include // for divide_and_ceil #include // for HIBF_HAS_AVX512 #include // for operator""_MiB diff --git a/test/unit/hibf/counting_vector_test.cpp b/test/unit/hibf/counting_vector_test.cpp index 2eda550b..9d37b804 100644 --- a/test/unit/hibf/counting_vector_test.cpp +++ b/test/unit/hibf/counting_vector_test.cpp @@ -6,18 +6,17 @@ # define HIBF_HAS_AVX512 0 #endif -#include // for TYPED_TEST, Message, TestPartResult, ASSERT_EQ, EXPECT_EQ, TYPED_TE... +#include // for Message, TYPED_TEST, TestPartResult, ASSERT_EQ, EXPECT_EQ, Types #include // for fill, fill_n #include // for int16_t, int32_t, int64_t, int8_t, uint16_t, uint32_t, uint64_t #include // for signed_integral #include // for size_t #include // for numeric_limits -#include // for __sanitizer_annotate_contiguous_container #include // for bit_vector #include // for counting_vector -#include // for _LIBCPP_VERSION +#include // for _LIBCPP_HAS_NO_ASAN, _LIBCPP_VERSION template class counting_vector_test : public ::testing::Test diff --git a/test/unit/hibf/sketch/hyperloglog_test.cpp b/test/unit/hibf/sketch/hyperloglog_test.cpp index 6a6f21d1..aaca9ae1 100644 --- a/test/unit/hibf/sketch/hyperloglog_test.cpp +++ b/test/unit/hibf/sketch/hyperloglog_test.cpp @@ -4,19 +4,20 @@ #include // for Test, Message, TestInfo, TestPartResult, TEST, EXPECT_EQ -#include // for __generate_fn, generate +#include // for __fn, generate #include // for uint64_t, uint8_t #include // for size_t #include // for path #include // for basic_ofstream, basic_ifstream, ofstream, ifstream, basi... +#include // for equal_to #include // for uniform_int_distribution, mt19937_64 -#include // for iterator_t, all_t, iota_view, operator==, _Iota, iota +#include // for __fn, iota, iota_view, views #include // for runtime_error, invalid_argument -#include // for allocator, basic_string, char_traits +#include // for basic_string #include // for vector -#include // for unordered_flat_set -#include // for chunk_view, operator==, chunk, chunk_fn +#include // for hash, unordered_flat_set +#include // for chunk, chunk_fn, chunk_view #include // for operator| #include // for divide_and_ceil #include // for hyperloglog diff --git a/test/unit/hibf/sketch/toolbox_test.cpp b/test/unit/hibf/sketch/toolbox_test.cpp index 36e6af19..b5ef43db 100644 --- a/test/unit/hibf/sketch/toolbox_test.cpp +++ b/test/unit/hibf/sketch/toolbox_test.cpp @@ -4,15 +4,16 @@ #include // for Message, TestPartResult, EXPECT_EQ, TestInfo, TEST_F, Test -#include // for uint64_t -#include // for size_t -#include // for numeric_limits -#include // for uniform_int_distribution, mt19937_64 -#include // for basic_string, string -#include // for tie, make_tuple -#include // for vector - -#include // for unordered_flat_map +#include // for uint64_t +#include // for size_t +#include // for equal_to +#include // for numeric_limits +#include // for uniform_int_distribution, mt19937_64 +#include // for basic_string, string +#include // for tie, make_tuple +#include // for vector + +#include // for hash, pair, unordered_flat_map #include // for _LIBCPP_VERSION #include // for hyperloglog #include // for clustering_node, entry, precompute_union_estimates_for, cluster_bins diff --git a/test/unit/test/temporary_snippet_file_test.cpp b/test/unit/test/temporary_snippet_file_test.cpp index cb61a010..6e5b536d 100644 --- a/test/unit/test/temporary_snippet_file_test.cpp +++ b/test/unit/test/temporary_snippet_file_test.cpp @@ -5,8 +5,9 @@ #include // for Test, AssertionResult, Message, TestInfo, TestPartResult #include // for path, current_path, operator/, exists -#include // for char_traits, basic_filebuf, basic_ostream, ifstream, strings... +#include // for char_traits, basic_ifstream, basic_filebuf, basic_ostream #include // for allocator +#include // for basic_stringstream #include // for temporary_snippet_file