[MISC] IWYU

include/hibf/build/update_parent_kmers.hpp

@@ -8,9 +8,10 @@
  */
 #pragma once
 
-#include <cinttypes> // for uint64_t
+#include <cinttypes>  // for uint64_t
+#include <functional> // for equal_to
 
-#include <hibf/contrib/robin_hood.hpp> // for unordered_flat_set
+#include <hibf/contrib/robin_hood.hpp> // for unordered_flat_set, hash
 #include <hibf/misc/timer.hpp>         // for serial_timer, concurrent_timer
 #include <hibf/platform.hpp>
 

include/hibf/hierarchical_interleaved_bloom_filter.hpp

@@ -4,15 +4,14 @@
 
 #pragma once
 
-#include <algorithm>  // for __fn, fill, sort
-#include <cassert>    // for assert
-#include <cinttypes>  // for int64_t, uint16_t
-#include <concepts>   // for integral, unsigned_integral
-#include <cstddef>    // for size_t
-#include <functional> // for less, identity
-#include <memory>     // for addressof
-#include <ranges>     // for forward_range, range, range_value_t
-#include <vector>     // for vector, operator==
+#include <algorithm> // for __fn, fill, sort
+#include <cassert>   // for assert
+#include <cinttypes> // for int64_t, uint16_t
+#include <concepts>  // for integral, unsigned_integral
+#include <cstddef>   // for size_t
+#include <memory>    // for addressof
+#include <ranges>    // for forward_range, range_value_t, range
+#include <vector>    // for vector, operator==
 
 #include <cereal/macros.hpp>       // for CEREAL_SERIALIZE_FUNCTION_NAME
 #include <cereal/types/vector.hpp> // IWYU pragma: keep

include/hibf/misc/bit_vector.hpp

@@ -21,32 +21,31 @@
 
 #pragma once
 
-#include <algorithm>        // for max, __for_each_fn, for_each, __all_of_fn, __any_of_fn, __fill_fn
+#include <algorithm>        // for __fn, for_each, all_of, any_of, copy, fill
 #include <bit>              // for countr_zero
 #include <cassert>          // for assert
 #include <cinttypes>        // for uint64_t
 #include <climits>          // for CHAR_BIT
 #include <compare>          // for strong_ordering, operator==
 #include <concepts>         // for assignable_from
 #include <cstddef>          // for size_t, ptrdiff_t
-#include <functional>       // for identity
 #include <initializer_list> // for initializer_list
-#include <iterator>         // for back_inserter, iter_reference_t, random_access_iterator_tag
-#include <memory>           // for allocator, assume_aligned, allocator_traits
-#include <ranges>           // for __next_fn, distance, next, _Begin, _End, __distance_fn, begin
+#include <iterator>         // for iter_reference_t, __fn, back_inserter, distance, iter_differen...
+#include <memory>           // for allocator, assume_aligned, allocator_traits, __compressed_pair
+#include <ranges>           // for __fn, begin, end
 #include <stdexcept>        // for out_of_range
-#include <string>           // for operator+, char_traits, to_string, operator""s
+#include <string>           // for char_traits, operator+, to_string, operator""s
 #include <type_traits>      // for conditional_t
 #include <utility>          // for swap
 #include <vector>           // for vector
 
-#include <cereal/cereal.hpp>     // for CEREAL_SERIALIZE_FUNCTION_NAME
-#include <cereal/macros.hpp>     // for CEREAL_SERIALIZE_FUNCTION_NAME
+#include <cereal/cereal.hpp>     // for binary_data
+#include <cereal/macros.hpp>     // for CEREAL_LOAD_FUNCTION_NAME, CEREAL_SAVE_FUNCTION_NAME
 #include <cereal/specialize.hpp> // for specialization, specialize
 
-#include <hibf/cereal/concepts.hpp>           // for cereal_archive
+#include <hibf/cereal/concepts.hpp>           // for cereal_archive, cereal_text_archive
 #include <hibf/contrib/aligned_allocator.hpp> // for aligned_allocator
-#include <hibf/platform.hpp>                  // for HIBF_CONSTEXPR_VECTOR
+#include <hibf/platform.hpp>                  // for HIBF_CONSTEXPR_VECTOR, _LIBCPP_HAS_NO_ASAN, _LIBCPP_VERSION
 
 namespace seqan::hibf
 {

include/hibf/misc/divide_and_ceil.hpp

@@ -7,6 +7,7 @@
 #include <cassert>  // for assert
 #include <concepts> // for unsigned_integral
 #include <cstddef>  // for size_t
+#include <limits>   // for numeric_limits
 
 #include <hibf/platform.hpp>
 

include/hibf/misc/insert_iterator.hpp

@@ -4,14 +4,15 @@
 
 #pragma once
 
-#include <cassert>   // for assert
-#include <cinttypes> // for uint64_t
-#include <cstddef>   // for ptrdiff_t
-#include <iterator>  // for output_iterator_tag
-#include <memory>    // for addressof
-#include <vector>    // for vector
+#include <cassert>    // for assert
+#include <cinttypes>  // for uint64_t
+#include <cstddef>    // for ptrdiff_t
+#include <functional> // for equal_to
+#include <iterator>   // for output_iterator_tag
+#include <memory>     // for addressof
+#include <vector>     // for vector
 
-#include <hibf/contrib/robin_hood.hpp> // for unordered_flat_set
+#include <hibf/contrib/robin_hood.hpp> // for unordered_flat_set, hash
 #include <hibf/platform.hpp>
 
 // IWYU pragma: private, include <hibf/config.hpp>

include/hibf/misc/timer.hpp

@@ -12,10 +12,10 @@
 #include <algorithm> // for max
 #include <atomic>    // for atomic, __atomic_base, memory_order_relaxed
 #include <cassert>   // for assert
-#include <chrono>    // for duration, time_point, operator-, steady_clock
+#include <chrono>    // for duration, time_point, operator-, operator<=>, steady_clock
 #include <cinttypes> // for uint64_t
+#include <compare>   // for operator>=, strong_ordering
 #include <concepts>  // for same_as
-#include <utility>   // for move
 
 #include <hibf/platform.hpp>
 

src/build/construct_ibf.cpp

@@ -2,19 +2,20 @@
 // SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: BSD-3-Clause
 
-#include <cassert>   // for assert
-#include <cinttypes> // for uint64_t
-#include <cmath>     // for ceil
-#include <cstddef>   // for size_t
-#include <vector>    // for vector
+#include <cassert>    // for assert
+#include <cinttypes>  // for uint64_t
+#include <cmath>      // for ceil
+#include <cstddef>    // for size_t
+#include <functional> // for equal_to
+#include <vector>     // for vector
 
 #include <hibf/build/bin_size_in_bits.hpp>    // for bin_size_in_bits
 #include <hibf/build/build_data.hpp>          // for build_data
 #include <hibf/build/construct_ibf.hpp>       // for construct_ibf
 #include <hibf/build/insert_into_ibf.hpp>     // for insert_into_ibf
 #include <hibf/build/update_parent_kmers.hpp> // for update_parent_kmers
 #include <hibf/config.hpp>                    // for config
-#include <hibf/contrib/robin_hood.hpp>        // for unordered_flat_set
+#include <hibf/contrib/robin_hood.hpp>        // for unordered_flat_set, hash
 #include <hibf/interleaved_bloom_filter.hpp>  // for interleaved_bloom_filter, bin_count, bin_size, hash_function_c...
 #include <hibf/layout/graph.hpp>              // for graph
 #include <hibf/misc/divide_and_ceil.hpp>      // for divide_and_ceil

src/build/insert_into_ibf.cpp

@@ -5,18 +5,17 @@
 #include <cassert>    // for assert
 #include <cinttypes>  // for uint64_t
 #include <cstddef>    // for size_t
-#include <functional> // for function
+#include <functional> // for equal_to, function
 #include <iterator>   // for counted_iterator
-#include <ranges>     // for all_t, operator==
 #include <vector>     // for vector
 
 #include <hibf/build/build_data.hpp>                // for build_data
 #include <hibf/build/insert_into_ibf.hpp>           // for insert_into_ibf
-#include <hibf/config.hpp>                          // for config, insert_iterator
-#include <hibf/contrib/robin_hood.hpp>              // for unordered_flat_set
-#include <hibf/contrib/std/chunk_view.hpp>          // for chunk_view, operator==, chunk, chunk_fn
+#include <hibf/config.hpp>                          // for insert_iterator, config
+#include <hibf/contrib/robin_hood.hpp>              // for Table, hash, unordered_flat_set
+#include <hibf/contrib/std/chunk_view.hpp>          // for chunk, chunk_fn, chunk_view
 #include <hibf/contrib/std/detail/adaptor_base.hpp> // for operator|
-#include <hibf/interleaved_bloom_filter.hpp>        // for interleaved_bloom_filter, bin_index
+#include <hibf/interleaved_bloom_filter.hpp>        // for bin_index, interleaved_bloom_filter
 #include <hibf/layout/layout.hpp>                   // for layout
 #include <hibf/misc/divide_and_ceil.hpp>            // for divide_and_ceil
 #include <hibf/misc/timer.hpp>                      // for serial_timer, concurrent_timer

src/config.cpp

@@ -3,12 +3,13 @@
 // SPDX-License-Identifier: BSD-3-Clause
 
 #include <cassert>     // for assert
-#include <cmath>       // for sqrt, ceil
+#include <cmath>       // for ceil, sqrt
 #include <functional>  // for function
 #include <iostream>    // for operator<<, basic_ostream, basic_istream, getline, stringstream
+#include <sstream>     // for basic_stringstream
 #include <stdexcept>   // for invalid_argument
 #include <string>      // for char_traits, string
-#include <string_view> // for operator==, basic_string_view
+#include <string_view> // for operator==, basic_string_view, string_view
 
 #include <cereal/archives/json.hpp> // for JSONInputArchive, JSONOutputArchive
 #include <cereal/cereal.hpp>        // for make_nvp, InputArchive, OutputArchive

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 <algorithm> // for max, fill_n, shuffle
-#include <cassert>   // for assert
-#include <cinttypes> // for uint64_t, int64_t
-#include <cstddef>   // for size_t
-#include <mutex>     // for mutex, lock_guard
-#include <numeric>   // for iota
-#include <optional>  // for optional
-#include <random>    // for random_device, mt19937_64
-#include <utility>   // for move
-#include <vector>    // for vector, erase
+#include <algorithm>  // for shuffle, __fn, none_of
+#include <cassert>    // for assert
+#include <cinttypes>  // for uint64_t, int64_t
+#include <cstddef>    // for size_t
+#include <functional> // for equal_to
+#include <mutex>      // for mutex, lock_guard
+#include <numeric>    // for iota
+#include <optional>   // for optional
+#include <random>     // for random_device, mt19937_64
+#include <utility>    // for move
+#include <vector>     // for vector, erase
 
 #include <hibf/build/build_data.hpp>                      // for build_data
 #include <hibf/build/compute_kmers.hpp>                   // for compute_kmers
@@ -20,15 +21,15 @@
 #include <hibf/build/update_parent_kmers.hpp>             // for update_parent_kmers
 #include <hibf/build/update_user_bins.hpp>                // for update_user_bins
 #include <hibf/config.hpp>                                // for config
-#include <hibf/contrib/robin_hood.hpp>                    // for unordered_flat_set
+#include <hibf/contrib/robin_hood.hpp>                    // for unordered_flat_set, hash
 #include <hibf/hierarchical_interleaved_bloom_filter.hpp> // for hierarchical_interleaved_bloom_filter
 #include <hibf/interleaved_bloom_filter.hpp>              // for interleaved_bloom_filter
 #include <hibf/layout/compute_fpr_correction.hpp>         // for compute_fpr_correction
 #include <hibf/layout/compute_layout.hpp>                 // for compute_layout
 #include <hibf/layout/graph.hpp>                          // for graph
 #include <hibf/layout/layout.hpp>                         // for layout
 #include <hibf/misc/divide_and_ceil.hpp>                  // for divide_and_ceil
-#include <hibf/misc/timer.hpp>                            // for timer
+#include <hibf/misc/timer.hpp>                            // for concurrent_timer
 #include <hibf/sketch/compute_sketches.hpp>               // for compute_sketches
 #include <hibf/sketch/hyperloglog.hpp>                    // for hyperloglog
 

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 <algorithm>  // for __fn, sort
-#include <cstddef>    // for size_t
-#include <functional> // for identity
-#include <memory>     // for addressof
-#include <sstream>    // for stringstream
-#include <vector>     // for vector
+#include <algorithm> // for __fn, sort
+#include <cstddef>   // for size_t
+#include <memory>    // for addressof
+#include <vector>    // for vector
 
 #include <hibf/config.hpp>                        // for config
 #include <hibf/layout/compute_fpr_correction.hpp> // for compute_fpr_correction

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 <cinttypes> // for uint16_t, int16_t, int64_t, int8_t, uint8_t, int32_t, uint32_t, uin...
-#include <cstddef>   // for size_t
-#include <iostream>  // for basic_ostream::operator<<, ostream, operator<<, basic_ostream
-#include <ranges>    // for range_value_t, empty
-#include <vector>    // for vector
+#include <cinttypes>   // for uint16_t, int16_t, int64_t, int8_t, uint8_t, int32_t, uint32_t, uin...
+#include <cstddef>     // for size_t
+#include <iostream>    // for ostream, operator<<, basic_ostream
+#include <ranges>      // for range_value_t, empty
+#include <type_traits> // for conditional
+#include <vector>      // for vector
 
 #include <hibf/misc/bit_vector.hpp>      // for bit_vector
 #include <hibf/misc/counting_vector.hpp> // for counting_vector

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 <algorithm> // for sort
-#include <cassert>   // for assert
-#include <cinttypes> // for uint64_t, int64_t
-#include <cmath>     // for sqrt, floor
-#include <cstddef>   // for size_t
-#include <limits>    // for numeric_limits
-#include <omp.h>     // for omp_get_thread_num
-#include <random>    // for uniform_int_distribution, mt19937_64
-#include <utility>   // for swap, move
-#include <vector>    // for vector
-
-#include <hibf/contrib/robin_hood.hpp> // for unordered_flat_map, pair
+#include <algorithm>  // for sort
+#include <cassert>    // for assert
+#include <cinttypes>  // for uint64_t, int64_t
+#include <cmath>      // for floor, sqrt
+#include <cstddef>    // for size_t
+#include <functional> // for equal_to
+#include <limits>     // for numeric_limits
+#include <omp.h>      // for omp_get_thread_num
+#include <random>     // for uniform_int_distribution, mt19937_64
+#include <utility>    // for swap, move
+#include <vector>     // for vector
+
+#include <hibf/contrib/robin_hood.hpp> // for hash, unordered_flat_map
 #include <hibf/sketch/hyperloglog.hpp> // for hyperloglog
 #include <hibf/sketch/toolbox.hpp>     // for clustering_node, entry, neighbor, prio_queue, distance_matrix, cluste...
 

test/include/hibf/test/sandboxed_path.hpp

@@ -11,7 +11,6 @@
 
 #include <filesystem>   // for path, filesystem_error, operator/
 #include <system_error> // for errc, make_error_code
-#include <type_traits>  // for __libcpp_remove_reference_t
 #include <utility>      // for move, forward
 
 #include <hibf/platform.hpp>

test/performance/ibf/interleaved_bloom_filter_benchmark.cpp

@@ -4,21 +4,22 @@
 
 #include <benchmark/benchmark.h> // for State, Benchmark, AddCustomContext, Counter, BENCHMARK
 
-#include <algorithm> // for copy, fill_n, __generate_fn, generate
-#include <cmath>     // for log, ceil, exp
-#include <cstddef>   // for size_t
-#include <random>    // for uniform_int_distribution, mt19937_64
-#include <ranges>    // for all_t, transform_view, iterator_t, iota_view, _Partial
-#include <string>    // for allocator, to_string, basic_string
-#include <tuple>     // for tuple, make_tuple
-#include <utility>   // for move, pair
-#include <vector>    // for vector
-
-#include <hibf/contrib/robin_hood.hpp>              // for pair, unordered_map
-#include <hibf/contrib/std/chunk_view.hpp>          // for chunk_view, operator==, chunk, chunk_fn
+#include <algorithm>  // for __fn, generate
+#include <cmath>      // for log, ceil, exp
+#include <cstddef>    // for size_t
+#include <functional> // for equal_to
+#include <random>     // for uniform_int_distribution, mt19937_64
+#include <ranges>     // for transform_view, iota_view, __range_adaptor_closure_t, __fn
+#include <string>     // for to_string, basic_string
+#include <tuple>      // for tuple, make_tuple
+#include <utility>    // for move, pair
+#include <vector>     // for vector
+
+#include <hibf/contrib/robin_hood.hpp>              // for hash, unordered_map
+#include <hibf/contrib/std/chunk_view.hpp>          // for chunk, chunk_fn, chunk_view
 #include <hibf/contrib/std/detail/adaptor_base.hpp> // for operator|
 #include <hibf/contrib/std/to.hpp>                  // for to
-#include <hibf/interleaved_bloom_filter.hpp>        // for interleaved_bloom_filter, bin_index, bin_count, bin_size
+#include <hibf/interleaved_bloom_filter.hpp>        // for bin_index, interleaved_bloom_filter, bin_count, bin_size
 #include <hibf/misc/divide_and_ceil.hpp>            // for divide_and_ceil
 #include <hibf/platform.hpp>                        // for HIBF_HAS_AVX512
 #include <hibf/test/bytes.hpp>                      // for operator""_MiB

test/unit/hibf/counting_vector_test.cpp

@@ -6,18 +6,17 @@
 #    define HIBF_HAS_AVX512 0
 #endif
 
-#include <gtest/gtest.h> // for TYPED_TEST, Message, TestPartResult, ASSERT_EQ, EXPECT_EQ, TYPED_TE...
+#include <gtest/gtest.h> // for Message, TYPED_TEST, TestPartResult, ASSERT_EQ, EXPECT_EQ, Types
 
 #include <algorithm> // for fill, fill_n
 #include <cinttypes> // for int16_t, int32_t, int64_t, int8_t, uint16_t, uint32_t, uint64_t
 #include <concepts>  // for signed_integral
 #include <cstddef>   // for size_t
 #include <limits>    // for numeric_limits
-#include <vector>    // for __sanitizer_annotate_contiguous_container
 
 #include <hibf/misc/bit_vector.hpp>      // for bit_vector
 #include <hibf/misc/counting_vector.hpp> // for counting_vector
-#include <hibf/platform.hpp>             // for _LIBCPP_VERSION
+#include <hibf/platform.hpp>             // for _LIBCPP_HAS_NO_ASAN, _LIBCPP_VERSION
 
 template <typename TypeParam>
 class counting_vector_test : public ::testing::Test

test/unit/hibf/sketch/hyperloglog_test.cpp

@@ -4,19 +4,20 @@
 
 #include <gtest/gtest.h> // for Test, Message, TestInfo, TestPartResult, TEST, EXPECT_EQ
 
-#include <algorithm>  // for __generate_fn, generate
+#include <algorithm>  // for __fn, generate
 #include <cinttypes>  // for uint64_t, uint8_t
 #include <cstddef>    // for size_t
 #include <filesystem> // for path
 #include <fstream>    // for basic_ofstream, basic_ifstream, ofstream, ifstream, basi...
+#include <functional> // for equal_to
 #include <random>     // for uniform_int_distribution, mt19937_64
-#include <ranges>     // for iterator_t, all_t, iota_view, operator==, _Iota, iota
+#include <ranges>     // for __fn, iota, iota_view, views
 #include <stdexcept>  // for runtime_error, invalid_argument
-#include <string>     // for allocator, basic_string, char_traits
+#include <string>     // for basic_string
 #include <vector>     // for vector
 
-#include <hibf/contrib/robin_hood.hpp>              // for unordered_flat_set
-#include <hibf/contrib/std/chunk_view.hpp>          // for chunk_view, operator==, chunk, chunk_fn
+#include <hibf/contrib/robin_hood.hpp>              // for hash, unordered_flat_set
+#include <hibf/contrib/std/chunk_view.hpp>          // for chunk, chunk_fn, chunk_view
 #include <hibf/contrib/std/detail/adaptor_base.hpp> // for operator|
 #include <hibf/misc/divide_and_ceil.hpp>            // for divide_and_ceil
 #include <hibf/sketch/hyperloglog.hpp>              // for hyperloglog