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..986aa0c9 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 __sort_fn, fill, sort +#include // for assert +#include // for int64_t, uint16_t +#include // for integral, unsigned_integral +#include // for size_t +#include // for forward_range, range_value_t, range +#include // for addressof +#include // for vector, operator== #include // for CEREAL_SERIALIZE_FUNCTION_NAME #include // IWYU pragma: keep diff --git a/include/hibf/interleaved_bloom_filter.hpp b/include/hibf/interleaved_bloom_filter.hpp index f5be675e..3eec7e60 100644 --- a/include/hibf/interleaved_bloom_filter.hpp +++ b/include/hibf/interleaved_bloom_filter.hpp @@ -15,9 +15,9 @@ #include // for uint16_t, uint64_t #include // for integral, same_as, unsigned_integral #include // for size_t -#include // for addressof -#include // for range, forward_range, input_range, range_reference_t, range_va... +#include // for range, range_reference_t, range_value_t, forward_range, input_... #include // for remove_cvref_t +#include // for addressof #include // for operator==, vector #include // for CEREAL_SERIALIZE_FUNCTION_NAME diff --git a/include/hibf/layout/hierarchical_binning.hpp b/include/hibf/layout/hierarchical_binning.hpp index 652f7f27..38671bc6 100644 --- a/include/hibf/layout/hierarchical_binning.hpp +++ b/include/hibf/layout/hierarchical_binning.hpp @@ -6,8 +6,7 @@ #include // for assert #include // for size_t -#include // for addressof -#include // for pair +#include // for addressof, pair #include // for vector #include // for bin_size_in_bits diff --git a/include/hibf/layout/simple_binning.hpp b/include/hibf/layout/simple_binning.hpp index 23b8a8c5..bf7b2e9f 100644 --- a/include/hibf/layout/simple_binning.hpp +++ b/include/hibf/layout/simple_binning.hpp @@ -6,8 +6,8 @@ #include // for assert #include // for size_t -#include // for addressof #include // for runtime_error +#include // for addressof #include // for vector #include // for data_store diff --git a/include/hibf/misc/bit_vector.hpp b/include/hibf/misc/bit_vector.hpp index a957ff8f..e02e96ad 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 __for_each_fn, for_each, __all_of_fn, __any_of_fn, __fill_fn #include // for countr_zero #include // for assert #include // for uint64_t @@ -29,22 +29,21 @@ #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 iter_reference_t, back_inserter, iter_difference_t, iter_value_t #include // for allocator, assume_aligned, allocator_traits #include // for __next_fn, distance, next, _Begin, _End, __distance_fn, begin #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 diff --git a/include/hibf/misc/counting_vector.hpp b/include/hibf/misc/counting_vector.hpp index f82068b1..94732c22 100644 --- a/include/hibf/misc/counting_vector.hpp +++ b/include/hibf/misc/counting_vector.hpp @@ -9,7 +9,6 @@ #pragma once -#include // for transform #include // for countr_zero #include // for assert #include // for uint64_t @@ -17,7 +16,7 @@ #include // for integral #include // for size_t #include // for minus, plus -#include // for conditional_t +#include // for conditional, conditional_t #include // for vector #include // for aligned_allocator diff --git a/include/hibf/misc/insert_iterator.hpp b/include/hibf/misc/insert_iterator.hpp index ccebc3e1..b2d5d4f4 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 05d9fba3..0db61e25 100644 --- a/include/hibf/misc/timer.hpp +++ b/include/hibf/misc/timer.hpp @@ -12,11 +12,12 @@ #include // for max #include // for atomic, __atomic_base, memory_order_relaxed #include // for assert -#include // for duration, time_point, operator-, steady_clock #include // for uint64_t #include // for same_as #include // for move +#include // for duration, time_point, operator-, steady_clock + #include namespace seqan::hibf 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/config.cpp b/src/config.cpp index 1e27d498..bf6f6c43 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_ostream, basic_istream, operator<<, stringstream, cerr +#include // for basic_stringstream #include // for invalid_argument -#include // for char_traits, string -#include // for operator==, basic_string_view +#include // for char_traits, getline, operator<<, string +#include // for operator<<, operator==, basic_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..8889425b 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 +#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 d170c1f1..8f41c233 100644 --- a/src/layout/compute_layout.cpp +++ b/src/layout/compute_layout.cpp @@ -2,12 +2,11 @@ // 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 __sort_fn, sort +#include // for size_t +#include // for basic_stringstream, stringstream +#include // for addressof +#include // for vector #include // for config #include // for compute_fpr_correction diff --git a/src/layout/graph.cpp b/src/layout/graph.cpp index c1da014c..91291517 100644 --- a/src/layout/graph.cpp +++ b/src/layout/graph.cpp @@ -6,8 +6,8 @@ #include // for assert #include // for size_t #include // for initializer_list -#include // for __fn, prev -#include // for optional, nullopt +#include // for optional, nullopt, nullopt_t +#include // for __prev_fn, prev #include // for vector #include // for graph diff --git a/src/misc/print.cpp b/src/misc/print.cpp index 77834373..7849f1a4 100644 --- a/src/misc/print.cpp +++ b/src/misc/print.cpp @@ -2,11 +2,13 @@ // 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, basic_ostream::operator<<, operator<<, basic_ostream +#include // for __iter_traits_impl +#include // for range_value_t, empty +#include // for remove_cvref +#include // for vector #include // for bit_vector #include // for counting_vector diff --git a/src/sketch/hyperloglog.cpp b/src/sketch/hyperloglog.cpp index 459b0d83..250ecd63 100644 --- a/src/sketch/hyperloglog.cpp +++ b/src/sketch/hyperloglog.cpp @@ -3,17 +3,16 @@ // SPDX-FileCopyrightText: 2013 Hideaki Ohno // SPDX-License-Identifier: BSD-3-Clause AND MIT -#include // for max, __fn, fill +#include // for max, __fill_fn, fill #include // for array #include // for countl_zero #include // for assert #include // for uint64_t, uint8_t, uint32_t #include // for log #include // for size_t -#include // for basic_ostream, basic_istream, istream, ostream -#include // for addressof +#include // for basic_ostream, basic_istream, basic_istream::read, basic_ostre... #include // for runtime_error, invalid_argument -#include // for swap +#include // for addressof, swap #include // for vector #include // for simde__m256i, simde_mm256_add_ps, simde_mm256_set1_ps, simde_m... diff --git a/src/sketch/toolbox.cpp b/src/sketch/toolbox.cpp index e13cea40..f97856c4 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, greater +#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 6cbe760e..4d4eec79 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/include/hibf/test/type_name_as_string.hpp b/test/include/hibf/test/type_name_as_string.hpp index 4fdbdde0..d9f0ce0e 100644 --- a/test/include/hibf/test/type_name_as_string.hpp +++ b/test/include/hibf/test/type_name_as_string.hpp @@ -15,10 +15,11 @@ #include // for free #include // for function -#include // for allocator, addressof, unique_ptr +#include // for allocator, unique_ptr #include // for char_traits, operator+, string, to_string #include // for remove_reference_t #include // for type_info +#include // for addressof #include diff --git a/test/performance/ibf/interleaved_bloom_filter_benchmark.cpp b/test/performance/ibf/interleaved_bloom_filter_benchmark.cpp index 065dc41e..5bda0dda 100644 --- a/test/performance/ibf/interleaved_bloom_filter_benchmark.cpp +++ b/test/performance/ibf/interleaved_bloom_filter_benchmark.cpp @@ -4,18 +4,19 @@ #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 __generate_fn, generate +#include // for log, ceil, exp +#include // for size_t +#include // for equal_to +#include // for uniform_int_distribution, mt19937_64 +#include // for iota_view, transform_view, _Partial, _Transform, operator| +#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 diff --git a/test/unit/hibf/counting_vector_test.cpp b/test/unit/hibf/counting_vector_test.cpp index 2eda550b..1b9713d0 100644 --- a/test/unit/hibf/counting_vector_test.cpp +++ b/test/unit/hibf/counting_vector_test.cpp @@ -6,14 +6,13 @@ # 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 diff --git a/test/unit/hibf/layout/layout_test.cpp b/test/unit/hibf/layout/layout_test.cpp index 8662cdeb..73b61357 100644 --- a/test/unit/hibf/layout/layout_test.cpp +++ b/test/unit/hibf/layout/layout_test.cpp @@ -2,12 +2,13 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: BSD-3-Clause -#include // for Test, AssertionResult, Message, TestPartResult, EXPECT_EQ, TestInfo, TEST +#include // for Test, Message, AssertionResult, TestPartResult, EXPECT_EQ, TestInfo, TEST -#include // for size_t -#include // for operator<<, basic_ostream, stringstream, basic_stringstream, basic_iostream -#include // for char_traits, allocator, string -#include // for vector +#include // for size_t +#include // for basic_stringstream, operator<<, basic_ostream, stringstream, basic_ios +#include // for allocator, char_traits, string +#include // for operator<< +#include // for vector #include // for layout, operator<< diff --git a/test/unit/hibf/sketch/hyperloglog_test.cpp b/test/unit/hibf/sketch/hyperloglog_test.cpp index 6a6f21d1..96e269ef 100644 --- a/test/unit/hibf/sketch/hyperloglog_test.cpp +++ b/test/unit/hibf/sketch/hyperloglog_test.cpp @@ -9,14 +9,15 @@ #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 _Iota, iota, iota_view, views #include // for runtime_error, invalid_argument #include // for allocator, basic_string, char_traits #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..b1dc1008 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, greater +#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/hibf/timer_test.cpp b/test/unit/hibf/timer_test.cpp index ffb3fad4..8b59a172 100644 --- a/test/unit/hibf/timer_test.cpp +++ b/test/unit/hibf/timer_test.cpp @@ -2,11 +2,12 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: BSD-3-Clause -#include // for AssertionResult, Message, TestPartResult, CmpHelperGE, CmpHelperGT, EXPECT_TRUE +#include // for Message, AssertionResult, TestPartResult, CmpHelperGE, EXPECT_TRUE, CmpHelperGT -#include // for operator""ms #include // for sleep_for +#include // for operator""ms + #include // for concurrent_timer, serial_timer static inline void waste_time() diff --git a/test/unit/test/temporary_snippet_file_test.cpp b/test/unit/test/temporary_snippet_file_test.cpp index fd8374c0..1dfc1f33 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_ostream::operator<<, basi... #include // for allocator +#include // for basic_stringstream #include // for temporary_snippet_file