diff --git a/include/hibf/build/compute_kmers.hpp b/include/hibf/build/compute_kmers.hpp index 062ad275..ce178127 100644 --- a/include/hibf/build/compute_kmers.hpp +++ b/include/hibf/build/compute_kmers.hpp @@ -9,7 +9,7 @@ #pragma once -#include // for uint64_t +#include // for uint64_t #include // for build_data #include // for unordered_flat_set diff --git a/include/hibf/build/construct_ibf.hpp b/include/hibf/build/construct_ibf.hpp index f68cd4c0..66215550 100644 --- a/include/hibf/build/construct_ibf.hpp +++ b/include/hibf/build/construct_ibf.hpp @@ -4,13 +4,13 @@ #pragma once -#include // for uint64_t -#include // for size_t +#include // for size_t +#include // for uint64_t #include // for build_data #include // for unordered_flat_set #include // for interleaved_bloom_filter -#include +#include // for graph namespace seqan::hibf::build { diff --git a/include/hibf/build/insert_into_ibf.hpp b/include/hibf/build/insert_into_ibf.hpp index e8d41853..853b9c92 100644 --- a/include/hibf/build/insert_into_ibf.hpp +++ b/include/hibf/build/insert_into_ibf.hpp @@ -4,14 +4,14 @@ #pragma once -#include // for uint64_t -#include // for size_t +#include // for size_t +#include // for uint64_t #include // for build_data #include // for unordered_flat_set #include // for interleaved_bloom_filter #include // for layout -#include // for concurrent, timer +#include // for concurrent_timer namespace seqan::hibf::build { diff --git a/include/hibf/build/update_parent_kmers.hpp b/include/hibf/build/update_parent_kmers.hpp index 7b2da7e7..53f6e1f6 100644 --- a/include/hibf/build/update_parent_kmers.hpp +++ b/include/hibf/build/update_parent_kmers.hpp @@ -8,7 +8,7 @@ */ #pragma once -#include // for uint64_t +#include // for uint64_t #include // for equal_to #include // for unordered_flat_set, hash diff --git a/include/hibf/build/update_user_bins.hpp b/include/hibf/build/update_user_bins.hpp index e343534e..de10f7c4 100644 --- a/include/hibf/build/update_user_bins.hpp +++ b/include/hibf/build/update_user_bins.hpp @@ -5,7 +5,7 @@ #pragma once #include // for fill_n -#include // for int64_t +#include // for uint64_t #include // for vector #include // for layout diff --git a/include/hibf/cereal/concepts.hpp b/include/hibf/cereal/concepts.hpp index 65a97342..b0ef6752 100644 --- a/include/hibf/cereal/concepts.hpp +++ b/include/hibf/cereal/concepts.hpp @@ -4,8 +4,10 @@ #pragma once -#include // for InputArchiveBase, OutputArchiveBase -#include // for InputArchiveBase, OutputArchiveBase +#include // for is_base_of_v + +#include // for OutputArchiveBase, InputArchiveBase, BinaryInputArchive, BinaryOutputA... +#include // for TextArchive #include diff --git a/include/hibf/config.hpp b/include/hibf/config.hpp index 20b0a322..424d4ca4 100644 --- a/include/hibf/config.hpp +++ b/include/hibf/config.hpp @@ -4,8 +4,8 @@ #pragma once -#include // for uint32_t, uint8_t #include // for size_t +#include // for uint32_t, uint8_t #include // for function #include // for istream, ostream diff --git a/include/hibf/hierarchical_interleaved_bloom_filter.hpp b/include/hibf/hierarchical_interleaved_bloom_filter.hpp index e8f8899a..8d75972d 100644 --- a/include/hibf/hierarchical_interleaved_bloom_filter.hpp +++ b/include/hibf/hierarchical_interleaved_bloom_filter.hpp @@ -6,9 +6,9 @@ #include // for __fn, fill, sort #include // for assert -#include // for uint64_t, uint16_t, uint32_t #include // for integral, unsigned_integral #include // for size_t +#include // for uint64_t, uint16_t, uint32_t #include // for numeric_limits #include // for addressof #include // for forward_range, range_value_t, range diff --git a/include/hibf/interleaved_bloom_filter.hpp b/include/hibf/interleaved_bloom_filter.hpp index 998092e3..c01cc151 100644 --- a/include/hibf/interleaved_bloom_filter.hpp +++ b/include/hibf/interleaved_bloom_filter.hpp @@ -12,8 +12,8 @@ #include // for fill #include // for array #include // for assert -#include // for uint32_t, uint16_t, uint64_t #include // for integral, same_as, unsigned_integral +#include // for uint32_t, uint16_t, uint64_t #include // for size_t #include // for addressof #include // for range, range_reference_t, range_value_t, forward_range, input_... diff --git a/include/hibf/layout/data_store.hpp b/include/hibf/layout/data_store.hpp index f38b20af..f24928ad 100644 --- a/include/hibf/layout/data_store.hpp +++ b/include/hibf/layout/data_store.hpp @@ -4,12 +4,12 @@ #pragma once -#include // for assert -#include // for uint64_t -#include // for size_t -#include // for iota -#include // for string -#include // for vector +#include // for assert +#include // for size_t +#include // for uint64_t +#include // for iota +#include // for basic_string, string +#include // for vector #include // for layout #include // for concurrent_timer diff --git a/include/hibf/misc/bit_vector.hpp b/include/hibf/misc/bit_vector.hpp index 3d437415..a43b3fda 100644 --- a/include/hibf/misc/bit_vector.hpp +++ b/include/hibf/misc/bit_vector.hpp @@ -24,17 +24,17 @@ #include // for __fn, for_each, all_of, any_of, copy, fill #include // for countr_zero #include // for assert -#include // for uint64_t #include // for CHAR_BIT #include // for strong_ordering, operator== #include // for assignable_from #include // for size_t, ptrdiff_t +#include // for uint64_t #include // for initializer_list #include // for iter_reference_t, __fn, back_inserter, distance, iter_differen... -#include // for allocator, assume_aligned, allocator_traits, __compressed_pair +#include // for allocator, allocator_traits, assume_aligned, __compressed_pair #include // for __fn, begin, end #include // for out_of_range -#include // for char_traits, operator+, to_string, operator""s +#include // for char_traits, operator+, to_string, operator""s, basic_string #include // for conditional_t #include // for swap #include // for vector diff --git a/include/hibf/misc/counting_vector.hpp b/include/hibf/misc/counting_vector.hpp index f8814625..6129b4ea 100644 --- a/include/hibf/misc/counting_vector.hpp +++ b/include/hibf/misc/counting_vector.hpp @@ -12,12 +12,12 @@ #include // for transform #include // for countr_zero #include // for assert -#include // for uint64_t #include // for CHAR_BIT #include // for integral +#include // for uint64_t, uint8_t #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 6ad2c993..30212b82 100644 --- a/include/hibf/misc/insert_iterator.hpp +++ b/include/hibf/misc/insert_iterator.hpp @@ -5,8 +5,8 @@ #pragma once #include // for assert -#include // for uint64_t, uint8_t #include // for size_t, ptrdiff_t +#include // for uint64_t, uint8_t #include // for function, equal_to #include // for output_iterator_tag #include // for addressof diff --git a/include/hibf/misc/print.hpp b/include/hibf/misc/print.hpp index d9d27be5..b37e2a05 100644 --- a/include/hibf/misc/print.hpp +++ b/include/hibf/misc/print.hpp @@ -4,9 +4,9 @@ #pragma once -#include // for int64_t, int16_t, int32_t, int8_t, uint16_t, uint32_t, uint64_t -#include // for cout, ostream -#include // for vector +#include // for uint64_t, int16_t, int32_t, int64_t, int8_t, uint16_t, uint32_t +#include // for cout, ostream +#include // for vector #include // for bit_vector #include // for counting_vector diff --git a/include/hibf/misc/timer.hpp b/include/hibf/misc/timer.hpp index 41e1428b..1f60c40e 100644 --- a/include/hibf/misc/timer.hpp +++ b/include/hibf/misc/timer.hpp @@ -13,9 +13,9 @@ #include // for atomic, __atomic_base, memory_order_relaxed #include // for assert #include // for duration, time_point, operator-, operator<=>, steady_clock -#include // for uint64_t #include // for operator>=, strong_ordering #include // for same_as +#include // for uint64_t #include diff --git a/include/hibf/sketch/hyperloglog.hpp b/include/hibf/sketch/hyperloglog.hpp index acaccd56..5545e31f 100644 --- a/include/hibf/sketch/hyperloglog.hpp +++ b/include/hibf/sketch/hyperloglog.hpp @@ -11,11 +11,11 @@ #pragma once -#include // for array -#include // for uint64_t, uint8_t, uint32_t -#include // for size_t -#include // for istream, ostream -#include // for vector +#include // for array +#include // for size_t +#include // for uint64_t, uint8_t, uint32_t +#include // for istream, ostream +#include // for vector #include // for access #include // for make_nvp, CEREAL_NVP diff --git a/include/hibf/sketch/toolbox.hpp b/include/hibf/sketch/toolbox.hpp index 9c3a6042..ac107255 100644 --- a/include/hibf/sketch/toolbox.hpp +++ b/include/hibf/sketch/toolbox.hpp @@ -4,8 +4,8 @@ #pragma once -#include // for uint64_t, int64_t #include // for size_t +#include // for uint64_t, int64_t #include // for greater #include // for priority_queue #include // for vector diff --git a/include/hibf/version.hpp b/include/hibf/version.hpp index 621a7261..dfc750f8 100644 --- a/include/hibf/version.hpp +++ b/include/hibf/version.hpp @@ -6,8 +6,8 @@ // IWYU pragma: always_keep -#include // for uint8_t -#include // for size_t +#include // for size_t +#include // for uint8_t /*!\file * \brief Provides version macros and global variables. diff --git a/src/build/compute_kmers.cpp b/src/build/compute_kmers.cpp index 727569a9..884b4cc3 100644 --- a/src/build/compute_kmers.cpp +++ b/src/build/compute_kmers.cpp @@ -7,12 +7,12 @@ * \author Enrico Seiler */ -#include // for uint64_t +#include // for uint64_t #include // for function #include // for build_data #include // for compute_kmers -#include // for config, insert_iterator +#include // for insert_iterator, config #include // for unordered_flat_set #include // for layout #include // for serial_timer, concurrent_timer diff --git a/src/build/construct_ibf.cpp b/src/build/construct_ibf.cpp index 5328c3f4..2fc7846c 100644 --- a/src/build/construct_ibf.cpp +++ b/src/build/construct_ibf.cpp @@ -3,9 +3,9 @@ // SPDX-License-Identifier: BSD-3-Clause #include // for assert -#include // for uint64_t #include // for ceil #include // for size_t +#include // for uint64_t #include // for equal_to #include // for vector diff --git a/src/build/insert_into_ibf.cpp b/src/build/insert_into_ibf.cpp index 7615dfda..27082891 100644 --- a/src/build/insert_into_ibf.cpp +++ b/src/build/insert_into_ibf.cpp @@ -4,10 +4,11 @@ #include // for __fn, all_of, fill_n #include // for assert -#include // for uint64_t #include // for size_t +#include // for uint64_t #include // for equal_to, function #include // for counted_iterator +#include // for subrange #include // for vector #include // for build_data diff --git a/src/hierarchical_interleaved_bloom_filter.cpp b/src/hierarchical_interleaved_bloom_filter.cpp index 90eef301..1456e2af 100644 --- a/src/hierarchical_interleaved_bloom_filter.cpp +++ b/src/hierarchical_interleaved_bloom_filter.cpp @@ -4,8 +4,8 @@ #include // for shuffle, __fn, none_of #include // for assert -#include // for uint64_t, int64_t #include // for size_t +#include // for uint64_t #include // for equal_to #include // for mutex, lock_guard #include // for iota @@ -22,18 +22,18 @@ #include // for update_user_bins #include // for config #include // for unordered_flat_set, hash -#include // for hierarchical_interleaved_bloom_filter +#include // for hierarchical_interleaved_bloom_filter, merged #include // for interleaved_bloom_filter #include // for compute_fpr_correction #include // for compute_layout #include // for graph #include // for layout #include // for divide_and_ceil -#include -#include // for concurrent_timer -#include // for compute_sketches -#include -#include // for hyperloglog +#include // for iota_vector +#include // for concurrent_timer +#include // for compute_sketches +#include // for estimate_kmer_counts +#include // for hyperloglog namespace seqan::hibf { diff --git a/src/interleaved_bloom_filter.cpp b/src/interleaved_bloom_filter.cpp index 5b0de811..b418e89e 100644 --- a/src/interleaved_bloom_filter.cpp +++ b/src/interleaved_bloom_filter.cpp @@ -6,7 +6,7 @@ #include // for array #include // for bit_ceil, countl_zero #include // for assert -#include // for uint64_t +#include // for uint64_t #include // for size_t, memcpy #include // for equal_to, function #include // for logic_error, invalid_argument diff --git a/src/misc/print.cpp b/src/misc/print.cpp index 439918f8..4afbb622 100644 --- a/src/misc/print.cpp +++ b/src/misc/print.cpp @@ -2,9 +2,9 @@ // 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 ostream, operator<<, basic_ostream +#include // for uint16_t, int16_t, int8_t, uint64_t, uint8_t, int32_t, int64_t, uin... +#include // for ostream, basic_ostream, operator<< #include // for range_value_t, empty #include // for conditional #include // for vector diff --git a/src/sketch/compute_sketches.cpp b/src/sketch/compute_sketches.cpp index c6d4f19a..fbef5889 100644 --- a/src/sketch/compute_sketches.cpp +++ b/src/sketch/compute_sketches.cpp @@ -2,16 +2,16 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: BSD-3-Clause -#include // for __fn, sort_heap, fill, make_heap +#include // for __fn, sort_heap, all_of, fill, make_heap #include // for atomic_flag #include // for assert -#include // for uint64_t #include // for size_t +#include // for uint64_t, uint8_t #include // for equal_to, function #include // for numeric_limits #include // for span #include // for runtime_error -#include // for allocator, char_traits, operator+, to_string +#include // for operator+, allocator, char_traits, to_string, basic_string #include // for move #include // for vector diff --git a/src/sketch/hyperloglog.cpp b/src/sketch/hyperloglog.cpp index 16239f5b..76b1ac3e 100644 --- a/src/sketch/hyperloglog.cpp +++ b/src/sketch/hyperloglog.cpp @@ -7,9 +7,9 @@ #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 uint64_t, uint8_t, uint32_t #include // for basic_ostream, basic_istream, istream, ostream #include // for addressof #include // for runtime_error, invalid_argument diff --git a/src/sketch/minhashes.cpp b/src/sketch/minhashes.cpp index cdc35fe8..fc8f35b0 100644 --- a/src/sketch/minhashes.cpp +++ b/src/sketch/minhashes.cpp @@ -4,7 +4,7 @@ #include // for __fn, is_sorted, all_of, find, pop_heap, push_heap #include // for assert -#include // for uint64_t +#include // for uint64_t #include // for span #include // for vector diff --git a/src/sketch/toolbox.cpp b/src/sketch/toolbox.cpp index ac0e7cea..f228573e 100644 --- a/src/sketch/toolbox.cpp +++ b/src/sketch/toolbox.cpp @@ -4,9 +4,9 @@ #include // for sort #include // for assert -#include // for uint64_t, int64_t #include // for floor, sqrt #include // for size_t +#include // for uint64_t, int64_t #include // for equal_to #include // for numeric_limits #include // for omp_get_thread_num diff --git a/test/include/hibf/test/cereal.hpp b/test/include/hibf/test/cereal.hpp index 714066f3..c110f6ce 100644 --- a/test/include/hibf/test/cereal.hpp +++ b/test/include/hibf/test/cereal.hpp @@ -9,9 +9,10 @@ #pragma once -#include // for AssertionResult, EXPECT_TRUE, Message, TestPartResult +#include // for AssertionResult, Message, EXPECT_TRUE, TestPartResult -#include // for basic_ios, ios, basic_ifstream, basic_ofstream, ifstream, ofs... +#include // for basic_ifstream, basic_ios, basic_ofstream, ios, ifstream, ofs... +#include // for basic_string #include // for remove_cvref_t #include // for BinaryInputArchive, BinaryOutputArchive diff --git a/test/include/hibf/test/iterator_test_template.hpp b/test/include/hibf/test/iterator_test_template.hpp index c3e1d2f7..26e68ced 100644 --- a/test/include/hibf/test/iterator_test_template.hpp +++ b/test/include/hibf/test/iterator_test_template.hpp @@ -10,11 +10,12 @@ #include // for derived_from, same_as, copy_constructible, equality_comparable_with #include // for size_t -#include // for random_access_iterator_tag, forward_iterator_tag, bidirectional_iterator_tag, input... -#include // for to_address -#include // for begin, cbegin, next, end, cend, distance, iterator_t, range_difference_t +#include // for next, random_access_iterator_tag, forward_iterator_tag, distance, bidirectional_ite... +#include // for to_address, addressof +#include // for begin, cbegin, end, cend, iterator_t, range_difference_t +#include // for basic_string #include // for remove_reference_t, conditional_t -#include // for as_const, addressof, pair +#include // for as_const, forward, pair #include diff --git a/test/include/hibf/test/sandboxed_path.hpp b/test/include/hibf/test/sandboxed_path.hpp index 701350a1..0a588d71 100644 --- a/test/include/hibf/test/sandboxed_path.hpp +++ b/test/include/hibf/test/sandboxed_path.hpp @@ -10,6 +10,7 @@ #pragma once #include // for path, filesystem_error, operator/ +#include // for basic_string #include // for errc, make_error_code #include // for move, forward diff --git a/test/include/hibf/test/tmp_directory.hpp b/test/include/hibf/test/tmp_directory.hpp index 8acf43c8..0e52267e 100644 --- a/test/include/hibf/test/tmp_directory.hpp +++ b/test/include/hibf/test/tmp_directory.hpp @@ -21,8 +21,9 @@ #endif #include // for assert -#include // for path, exists, is_empty, remove_all, temp_directory_path, filesystem_... -#include // for optional, nullopt +#include // for path, exists, filesystem_error, is_empty, remove_all, temp_directory... +#include // for optional, nullopt, nullopt_t +#include // for basic_string #include // for errc, make_error_code #include // for exchange diff --git a/test/include/hibf/test/type_name_as_string.hpp b/test/include/hibf/test/type_name_as_string.hpp index 919f8380..c5a92f6c 100644 --- a/test/include/hibf/test/type_name_as_string.hpp +++ b/test/include/hibf/test/type_name_as_string.hpp @@ -15,9 +15,10 @@ #include // for free #include // for function -#include // for allocator, addressof, unique_ptr -#include // for char_traits, operator+, string, to_string -#include // for remove_reference_t +#include // for allocator, unique_ptr, addressof +#include // for char_traits, basic_string, operator+, string, to_string +#include // for tuple +#include // for remove_reference_t, is_const_v, is_lvalue_reference_v, is_rvalue_reference_v #include // for type_info #include diff --git a/test/performance/ibf/bit_vector_benchmark.cpp b/test/performance/ibf/bit_vector_benchmark.cpp index 79dfb54a..2f1100b0 100644 --- a/test/performance/ibf/bit_vector_benchmark.cpp +++ b/test/performance/ibf/bit_vector_benchmark.cpp @@ -4,12 +4,13 @@ // Authored by: Rene Rahn -#include // for Benchmark, State, BENCHMARK_CAPTURE, DoNotOptimize, BENCHMARK_MAIN +#include // for Benchmark, BENCHMARK_CAPTURE, DoNotOptimize, State, BENCHMARK_MAIN #include // for __fn, generate -#include // for int32_t, uint8_t #include // for size_t +#include // for int32_t, uint8_t #include // for uniform_int_distribution, mt19937_64 +#include // for basic_string #include // for invoke_result_t #include // for move, pair diff --git a/test/performance/ibf/bit_vector_serialisation_benchmark.cpp b/test/performance/ibf/bit_vector_serialisation_benchmark.cpp index 0539924e..78bc0235 100644 --- a/test/performance/ibf/bit_vector_serialisation_benchmark.cpp +++ b/test/performance/ibf/bit_vector_serialisation_benchmark.cpp @@ -2,16 +2,16 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: BSD-3-Clause -#include // for State, Counter, DoNotOptimize, Benchmark, BENCHMARK, BENCHMARK_MAIN +#include // for State, Counter, Benchmark, DoNotOptimize, BENCHMARK, BENCHMARK_MAIN -#include // for __generate_fn, generate -#include // for int32_t, uint8_t, int64_t +#include // for __fn, generate #include // for size_t +#include // for int32_t, uint8_t, int64_t #include // for exists, file_size -#include // for basic_ifstream, basic_ios, basic_ofstream, ios, ifstream, ofstream +#include // for basic_ifstream, basic_ofstream, basic_ios, ios, ifstream, ofstream #include // for uniform_int_distribution, mt19937_64 #include // for logic_error -#include // for allocator, to_string, basic_string +#include // for basic_string, to_string #include // for BinaryInputArchive, BinaryOutputArchive #include // for InputArchive, OutputArchive diff --git a/test/performance/sketch/compute_sketches_benchmark.cpp b/test/performance/sketch/compute_sketches_benchmark.cpp index 1f64d518..c42f0cdf 100644 --- a/test/performance/sketch/compute_sketches_benchmark.cpp +++ b/test/performance/sketch/compute_sketches_benchmark.cpp @@ -4,10 +4,10 @@ #include // for Counter, State, BENCHMARK_TEMPLATE, Benchmark, ClobberMemory -#include // for uint64_t, uint8_t -#include // for size_t -#include // for basic_string -#include // for vector +#include // for size_t +#include // for uint64_t, uint8_t +#include // for basic_string +#include // for vector #include // for config, insert_iterator #include // for compute_sketches diff --git a/test/performance/sketch/hyperloglog_benchmark.cpp b/test/performance/sketch/hyperloglog_benchmark.cpp index 9fa3dcb6..68290bcf 100644 --- a/test/performance/sketch/hyperloglog_benchmark.cpp +++ b/test/performance/sketch/hyperloglog_benchmark.cpp @@ -2,9 +2,10 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: BSD-3-Clause -#include // for State, DoNotOptimize, Benchmark, BENCHMARK, BENCHMARK_MAIN +#include // for DoNotOptimize, State, Benchmark, BENCHMARK, BENCHMARK_MAIN -#include // for uint8_t +#include // for uint8_t +#include // for basic_string #include // for hyperloglog diff --git a/test/snippet/hibf/config_input_fn_file.cpp b/test/snippet/hibf/config_input_fn_file.cpp index eb426f98..1937c145 100644 --- a/test/snippet/hibf/config_input_fn_file.cpp +++ b/test/snippet/hibf/config_input_fn_file.cpp @@ -2,13 +2,14 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: CC0-1.0 -#include // for uint64_t -#include // for size_t -#include // for path -#include // for basic_ifstream, ifstream -#include // for function -#include // for getline, string -#include // for vector +#include // for size_t +#include // for uint64_t +#include // for path +#include // for basic_ifstream, getline, ifstream +#include // for function +#include // for basic_string, string +#include // for basic_string_view +#include // for vector #include // for temporary_snippet_file @@ -16,7 +17,7 @@ seqan::hibf::test::temporary_snippet_file file1{"file1.fa", "ACGT"}; seqan::hibf::test::temporary_snippet_file file2{"file2.fa", "ACGT"}; //![main] -#include // for config, insert_iterator +#include // for insert_iterator, config int main() { diff --git a/test/snippet/hibf/config_input_fn_vector.cpp b/test/snippet/hibf/config_input_fn_vector.cpp index e67e385b..d2020f78 100644 --- a/test/snippet/hibf/config_input_fn_vector.cpp +++ b/test/snippet/hibf/config_input_fn_vector.cpp @@ -2,12 +2,12 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: CC0-1.0 -#include // for uint64_t #include // for size_t +#include // for uint64_t #include // for function #include // for vector -#include // for config, insert_iterator +#include // for insert_iterator, config struct dna { diff --git a/test/snippet/ibf/counting_agent.cpp b/test/snippet/ibf/counting_agent.cpp index 6e10974f..7cdee448 100644 --- a/test/snippet/ibf/counting_agent.cpp +++ b/test/snippet/ibf/counting_agent.cpp @@ -2,10 +2,10 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: CC0-1.0 -#include // for uint8_t -#include // for size_t -#include // for iota_view, operator==, __fn, iota, views -#include // for vector +#include // for size_t +#include // for uint8_t +#include // for iota_view, __fn, iota, views +#include // for vector #include // for interleaved_bloom_filter, bin_index, bin_count, bin_size, hash_... #include // for print, print_t diff --git a/test/snippet/ibf/counting_vector.cpp b/test/snippet/ibf/counting_vector.cpp index 21172688..990f6339 100644 --- a/test/snippet/ibf/counting_vector.cpp +++ b/test/snippet/ibf/counting_vector.cpp @@ -2,7 +2,7 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: CC0-1.0 -#include // for uint16_t +#include // for uint16_t #include // for interleaved_bloom_filter, bin_index, bin_count, bin_size #include // for counting_vector diff --git a/test/snippet/readme.cpp b/test/snippet/readme.cpp index d228399a..2d60df29 100644 --- a/test/snippet/readme.cpp +++ b/test/snippet/readme.cpp @@ -2,10 +2,10 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: CC0-1.0 -#include // for uint64_t, int64_t #include // for size_t +#include // for uint64_t #include // for function -#include // for operator<<, basic_ostream, cout +#include // for basic_ostream, operator<<, cout #include // for __fn, iota, views #include // for vector diff --git a/test/unit/hibf/bit_vector_test.cpp b/test/unit/hibf/bit_vector_test.cpp index 1734b39b..97b645c3 100644 --- a/test/unit/hibf/bit_vector_test.cpp +++ b/test/unit/hibf/bit_vector_test.cpp @@ -11,10 +11,11 @@ #include // for size_t #include // for initializer_list #include // for output_iterator, random_access_iterator_tag -#include // for _CBegin, _CEnd, cbegin, cend +#include // for __fn, cbegin, cend #include // for out_of_range +#include // for basic_string #include // for as_const, move -#include // for allocator, vector +#include // for vector #include // for bit_vector, operator&, operator^, operator| #include // for test_serialisation diff --git a/test/unit/hibf/build/bin_size_in_bits_test.cpp b/test/unit/hibf/build/bin_size_in_bits_test.cpp index c7d9fb3e..e3a28ec3 100644 --- a/test/unit/hibf/build/bin_size_in_bits_test.cpp +++ b/test/unit/hibf/build/bin_size_in_bits_test.cpp @@ -2,7 +2,9 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: BSD-3-Clause -#include // for Test, TestInfo, EXPECT_EQ, Message, TEST, TestPartResult +#include // for Test, Message, DeathTest, TestInfo, TestPartResult, EXPECT_DEATH + +#include // for basic_string #include // for bin_size_in_bits diff --git a/test/unit/hibf/counting_vector_test.cpp b/test/unit/hibf/counting_vector_test.cpp index 248061d1..71ed8af6 100644 --- a/test/unit/hibf/counting_vector_test.cpp +++ b/test/unit/hibf/counting_vector_test.cpp @@ -9,14 +9,15 @@ #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 int16_t, int32_t, int64_t, int8_t, uint16_t, uint32_t, uint64_t #include // for numeric_limits +#include // for basic_string #include // for bit_vector #include // for counting_vector -#include // for _LIBCPP_HAS_NO_ASAN, _LIBCPP_VERSION +#include // for HIBF_COMPILER_IS_GCC, _LIBCPP_HAS_NO_ASAN, _LIBCPP_VERSION template class counting_vector_test : public ::testing::Test diff --git a/test/unit/hibf/hierarchical_interleaved_bloom_filter_test.cpp b/test/unit/hibf/hierarchical_interleaved_bloom_filter_test.cpp index 0fa25638..2184c656 100644 --- a/test/unit/hibf/hierarchical_interleaved_bloom_filter_test.cpp +++ b/test/unit/hibf/hierarchical_interleaved_bloom_filter_test.cpp @@ -2,13 +2,14 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: BSD-3-Clause -#include // for Test, Message, TestPartResult, TestInfo, EXPECT_EQ +#include // for Test, Message, TestPartResult, TestInfo, CmpHelperEQ -#include // for uint32_t #include // for size_t +#include // for uint32_t #include // for function -#include // for _Iota, iota, views -#include // for basic_stringstream, char_traits, stringstream +#include // for __fn, iota, views +#include // for char_traits, basic_stringstream, stringstream +#include // for basic_string #include // for move #include // for vector, allocator diff --git a/test/unit/hibf/insert_iterator_test.cpp b/test/unit/hibf/insert_iterator_test.cpp index e8036597..c6657096 100644 --- a/test/unit/hibf/insert_iterator_test.cpp +++ b/test/unit/hibf/insert_iterator_test.cpp @@ -2,13 +2,14 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: BSD-3-Clause -#include // for Test, Message, TestInfo, TEST, TestPartResult, EXPECT_EQ, EXPEC... +#include // for Test, Message, TestInfo, TEST, TestPartResult, CmpHelperEQ, Cmp... #include // for __fn, copy #include // for array -#include // for uint64_t, uint8_t #include // for size_t +#include // for uint64_t, uint8_t #include // for equal_to, function +#include // for basic_string #include // for vector #include // for insert_iterator diff --git a/test/unit/hibf/interleaved_bloom_filter_test.cpp b/test/unit/hibf/interleaved_bloom_filter_test.cpp index 547148cc..ea25c2b4 100644 --- a/test/unit/hibf/interleaved_bloom_filter_test.cpp +++ b/test/unit/hibf/interleaved_bloom_filter_test.cpp @@ -6,19 +6,20 @@ # define HIBF_HAS_AVX512 0 #endif -#include // for Message, Test, AssertionResult, TestPartResult, TestInfo, EXPEC... +#include // for Message, Test, AssertionResult, TestPartResult, CmpHelperEQ -#include // for __fn, all_of, for_each +#include // for __fn, fill, all_of, for_each #include // for array -#include // for uint64_t #include // for operator<, strong_ordering #include // for size_t +#include // for uint64_t #include // for function #include // for iota_view, __fn, iota, views, operator== #include // for logic_error, invalid_argument +#include // for basic_string #include // for is_copy_assignable_v, is_copy_constructible_v, is_default_const... #include // for move -#include // for vector +#include // for vector, __bit_iterator, operator- #include // for insert_iterator, config #include // for interleaved_bloom_filter, bin_index, bin_count, bin_size, hash_... diff --git a/test/unit/hibf/layout/compute_layout_test.cpp b/test/unit/hibf/layout/compute_layout_test.cpp index 17a2c9cf..ec5157ab 100644 --- a/test/unit/hibf/layout/compute_layout_test.cpp +++ b/test/unit/hibf/layout/compute_layout_test.cpp @@ -2,20 +2,21 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: BSD-3-Clause -#include // for Test, AssertionResult, TestInfo, EXPECT_TRUE, Message, TEST, Tes... +#include // for Test, AssertionResult, Message, TestInfo, EXPECT_TRUE, TEST #include // for size_t #include // for function -#include // for vector, allocator - -#include // for insert_iterator, config -#include // for compute_layout -#include // for layout -#include -#include // for concurrent_timer -#include // for compute_sketches -#include -#include // for hyperloglog +#include // for basic_string +#include // for vector + +#include // for insert_iterator, config +#include // for compute_layout +#include // for layout +#include // for iota_vector +#include // for concurrent_timer +#include // for compute_sketches +#include // for estimate_kmer_counts +#include // for hyperloglog TEST(compute_layout, dispatch) { diff --git a/test/unit/hibf/layout/fpr_correction_test.cpp b/test/unit/hibf/layout/fpr_correction_test.cpp index 6e753b10..f4a1e207 100644 --- a/test/unit/hibf/layout/fpr_correction_test.cpp +++ b/test/unit/hibf/layout/fpr_correction_test.cpp @@ -2,10 +2,11 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: BSD-3-Clause -#include // for Test, Message, TestPartResult, EXPECT_NEAR, TestInfo +#include // for Message, Test, TestPartResult, EXPECT_NEAR, TestInfo, CmpH... #include // for size_t -#include // for vector, allocator +#include // for basic_string +#include // for vector #include // for compute_fpr_correction diff --git a/test/unit/hibf/layout/graph_test.cpp b/test/unit/hibf/layout/graph_test.cpp index 34903846..12d7459d 100644 --- a/test/unit/hibf/layout/graph_test.cpp +++ b/test/unit/hibf/layout/graph_test.cpp @@ -2,11 +2,12 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: BSD-3-Clause -#include // for Message, TestPartResult, EXPECT_EQ, Test, ASSERT_EQ, TestInfo, TEST +#include // for Message, TestPartResult, CmpHelperEQ, CmpHelperEQFailure, EXPECT_EQ, Test #include // for size_t #include // for optional -#include // for vector, allocator +#include // for basic_string +#include // for vector #include // for graph #include // for layout diff --git a/test/unit/hibf/layout/hierarchical_binning_test.cpp b/test/unit/hibf/layout/hierarchical_binning_test.cpp index 4b0e49aa..73766863 100644 --- a/test/unit/hibf/layout/hierarchical_binning_test.cpp +++ b/test/unit/hibf/layout/hierarchical_binning_test.cpp @@ -2,10 +2,11 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: BSD-3-Clause -#include // for Test, Message, TestPartResult, TestInfo, TEST, EXP... +#include // for Test, Message, TestPartResult, TestInfo, TEST, Cmp... #include // for size_t #include // for invalid_argument +#include // for basic_string #include // for vector #include // for config diff --git a/test/unit/hibf/layout/simple_binning_test.cpp b/test/unit/hibf/layout/simple_binning_test.cpp index edf7a9d7..78f88daa 100644 --- a/test/unit/hibf/layout/simple_binning_test.cpp +++ b/test/unit/hibf/layout/simple_binning_test.cpp @@ -2,11 +2,12 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: BSD-3-Clause -#include // for Test, TestInfo, Message, TestPartResult, TEST, EXPECT_EQ +#include // for Test, Message, TestInfo, TestPartResult, TEST, CmpHelperEQ, CmpHel... #include // for size_t #include // for runtime_error -#include // for allocator, vector +#include // for basic_string +#include // for vector #include // for data_store #include // for layout diff --git a/test/unit/hibf/path_test.cpp b/test/unit/hibf/path_test.cpp index 51866ff1..b088e1db 100644 --- a/test/unit/hibf/path_test.cpp +++ b/test/unit/hibf/path_test.cpp @@ -5,6 +5,7 @@ #include // for Test, TestInfo, TEST #include // for path +#include // for basic_string #include // for move #include // for specialization diff --git a/test/unit/hibf/print_test.cpp b/test/unit/hibf/print_test.cpp index 758254dc..e51cac67 100644 --- a/test/unit/hibf/print_test.cpp +++ b/test/unit/hibf/print_test.cpp @@ -2,13 +2,14 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: BSD-3-Clause -#include // for EXPECT_EQ, GetCapturedStderr, GetCapturedStdout, Message, TestPartR... +#include // for Message, CmpHelperEQ, CmpHelperEQFailure, EXPECT_EQ, GetCapturedStderr -#include // for int64_t, int16_t, int32_t, int8_t, uint16_t, uint32_t, uint64_t -#include // for same_as, unsigned_integral -#include // for cerr -#include // for range_value_t -#include // for allocator, vector +#include // for same_as, unsigned_integral +#include // for uint64_t, int16_t, int32_t, int64_t, int8_t, uint16_t, uint32_t +#include // for cerr +#include // for range_value_t +#include // for basic_string +#include // for vector #include // for bit_vector #include // for counting_vector diff --git a/test/unit/hibf/sketch/compute_sketches_test.cpp b/test/unit/hibf/sketch/compute_sketches_test.cpp index 065362c4..d47e7df3 100644 --- a/test/unit/hibf/sketch/compute_sketches_test.cpp +++ b/test/unit/hibf/sketch/compute_sketches_test.cpp @@ -2,12 +2,13 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: BSD-3-Clause -#include // for Message, TestPartResult, TestInfo, AssertionResult, ASSERT_EQ +#include // for Message, TestPartResult, CmpHelperEQ, CmpHelperEQFailure, Assert... #include // for size_t #include // for function #include // for __fn, iota, views #include // for runtime_error +#include // for basic_string #include // for vector #include // for config, insert_iterator diff --git a/test/unit/hibf/sketch/estimate_kmer_counts_test.cpp b/test/unit/hibf/sketch/estimate_kmer_counts_test.cpp index 96d99e51..ddab4564 100644 --- a/test/unit/hibf/sketch/estimate_kmer_counts_test.cpp +++ b/test/unit/hibf/sketch/estimate_kmer_counts_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, Message, TestPartResult, EXPECT_EQ, TestInfo, ASSERT_EQ +#include // for Test, Message, CmpHelperEQ, CmpHelperEQFailure, TestPartResult -#include // for uint64_t -#include // for size_t -#include // for uniform_int_distribution, mt19937_64 -#include // for allocator, vector +#include // for size_t +#include // for uint64_t +#include // for uniform_int_distribution, mt19937_64 +#include // for basic_string +#include // for vector #include // for estimate_kmer_counts #include // for hyperloglog diff --git a/test/unit/hibf/sketch/hyperloglog_test.cpp b/test/unit/hibf/sketch/hyperloglog_test.cpp index aaca9ae1..7ad2ee48 100644 --- a/test/unit/hibf/sketch/hyperloglog_test.cpp +++ b/test/unit/hibf/sketch/hyperloglog_test.cpp @@ -2,13 +2,13 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: BSD-3-Clause -#include // for Test, Message, TestInfo, TestPartResult, TEST, EXPECT_EQ +#include // for Test, Message, TestInfo, TestPartResult, TEST, CmpHelperEQ #include // for __fn, generate -#include // for uint64_t, uint8_t #include // for size_t +#include // for uint64_t, uint8_t #include // for path -#include // for basic_ofstream, basic_ifstream, ofstream, ifstream, basi... +#include // for basic_ofstream, basic_ifstream, basic_ios, ofstream, ifs... #include // for equal_to #include // for uniform_int_distribution, mt19937_64 #include // for __fn, iota, iota_view, views diff --git a/test/unit/hibf/sketch/minhashes_test.cpp b/test/unit/hibf/sketch/minhashes_test.cpp index 8a8732aa..c239ef0a 100644 --- a/test/unit/hibf/sketch/minhashes_test.cpp +++ b/test/unit/hibf/sketch/minhashes_test.cpp @@ -5,10 +5,11 @@ #include // for AssertionResult, Message, Test, TestPartResult, EXPECT_FALSE, TestInfo #include // for __fn, equal, make_heap -#include // for uint64_t #include // for size_t +#include // for uint64_t #include // for __fn, iota, views #include // for span +#include // for basic_string #include // for move #include // for vector diff --git a/test/unit/hibf/sketch/toolbox_test.cpp b/test/unit/hibf/sketch/toolbox_test.cpp index b5ef43db..7de6ab20 100644 --- a/test/unit/hibf/sketch/toolbox_test.cpp +++ b/test/unit/hibf/sketch/toolbox_test.cpp @@ -2,10 +2,10 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: BSD-3-Clause -#include // for Message, TestPartResult, EXPECT_EQ, TestInfo, TEST_F, Test +#include // for Message, TestPartResult, CmpHelperEQ, CmpHelperEQFailure, EXPECT_EQ -#include // for uint64_t #include // for size_t +#include // for uint64_t #include // for equal_to #include // for numeric_limits #include // for uniform_int_distribution, mt19937_64 diff --git a/test/unit/hibf/timer_test.cpp b/test/unit/hibf/timer_test.cpp index ffb3fad4..3762b0ee 100644 --- a/test/unit/hibf/timer_test.cpp +++ b/test/unit/hibf/timer_test.cpp @@ -2,10 +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, CmpHelper... -#include // for operator""ms -#include // for sleep_for +#include // for operator""ms +#include // for basic_string +#include // for sleep_for +#include // for is_copy_assignable_v, is_copy_constructible_v, is_default_constructible_v #include // for concurrent_timer, serial_timer diff --git a/test/unit/test/expect_range_eq_test.cpp b/test/unit/test/expect_range_eq_test.cpp index 69a8116d..0e40c7d3 100644 --- a/test/unit/test/expect_range_eq_test.cpp +++ b/test/unit/test/expect_range_eq_test.cpp @@ -8,7 +8,8 @@ #include // for ptrdiff_t #include // for input_range #include // for span -#include // for string_view +#include // for basic_string +#include // for basic_string_view, string_view #include // for vector #include // for expect_range_eq, EXPECT_RANGE_EQ diff --git a/test/unit/test/expect_same_type_test.cpp b/test/unit/test/expect_same_type_test.cpp index ad62c457..5518834d 100644 --- a/test/unit/test/expect_same_type_test.cpp +++ b/test/unit/test/expect_same_type_test.cpp @@ -3,8 +3,9 @@ // SPDX-License-Identifier: BSD-3-Clause #include // for EXPECT_NONFATAL_FAILURE -#include // for Test, AssertionResult, Message, TestPartResult, TestInfo, TEST +#include // for Test, Message, AssertionResult, TestPartResult, TestInfo, TEST +#include // for basic_string #include // for tuple #include // for type_identity diff --git a/test/unit/test/file_access_test.cpp b/test/unit/test/file_access_test.cpp index f7cecc74..e6095338 100644 --- a/test/unit/test/file_access_test.cpp +++ b/test/unit/test/file_access_test.cpp @@ -2,10 +2,11 @@ // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik // SPDX-License-Identifier: BSD-3-Clause -#include // for AssertionResult, TestInfo, Message, TEST_F, TestPartResult, EXPECT_EQ +#include // for AssertionResult, Message, TestInfo, TEST_F, TestPartResult, CmpHelperEQ -#include // for remove, path, temp_directory_path, perm_options, permissions, perms -#include // for basic_ios, fstream, ios, ofstream +#include // for path, remove, temp_directory_path, perm_options, permissions, perms +#include // for basic_fstream, basic_ios, basic_ofstream, fstream, ios, ofstream +#include // for basic_string #include // for write_access, read_access diff --git a/test/unit/test/temporary_snippet_file_test.cpp b/test/unit/test/temporary_snippet_file_test.cpp index 6e5b536d..83c261d5 100644 --- a/test/unit/test/temporary_snippet_file_test.cpp +++ b/test/unit/test/temporary_snippet_file_test.cpp @@ -4,10 +4,11 @@ #include // for Test, AssertionResult, Message, TestInfo, TestPartResult -#include // for path, current_path, operator/, exists -#include // for char_traits, basic_ifstream, basic_filebuf, basic_ostream -#include // for allocator -#include // for basic_stringstream +#include // for path, current_path, operator/, exists +#include // for char_traits, basic_ifstream, basic_filebuf, basic_ostream +#include // for basic_stringstream +#include // for allocator, basic_string +#include // for basic_string_view #include // for temporary_snippet_file