[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 __sort_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 <ranges>    // for forward_range, range_value_t, range
+#include <utility>   // for addressof
+#include <vector>    // for vector, operator==
 
 #include <cereal/macros.hpp>       // for CEREAL_SERIALIZE_FUNCTION_NAME
 #include <cereal/types/vector.hpp> // IWYU pragma: keep

include/hibf/interleaved_bloom_filter.hpp

@@ -15,9 +15,9 @@
 #include <cinttypes>   // for uint16_t, uint64_t
 #include <concepts>    // for integral, same_as, unsigned_integral
 #include <cstring>     // for size_t
-#include <memory>      // for addressof
-#include <ranges>      // for range, forward_range, input_range, range_reference_t, range_va...
+#include <ranges>      // for range, range_reference_t, range_value_t, forward_range, input_...
 #include <type_traits> // for remove_cvref_t
+#include <utility>     // for addressof
 #include <vector>      // for operator==, vector
 
 #include <cereal/macros.hpp>           // for CEREAL_SERIALIZE_FUNCTION_NAME

include/hibf/layout/hierarchical_binning.hpp

@@ -6,8 +6,7 @@
 
 #include <cassert> // for assert
 #include <cstddef> // for size_t
-#include <memory>  // for addressof
-#include <utility> // for pair
+#include <utility> // for addressof, pair
 #include <vector>  // for vector
 
 #include <hibf/build/bin_size_in_bits.hpp> // for bin_size_in_bits

include/hibf/layout/simple_binning.hpp

@@ -6,8 +6,8 @@
 
 #include <cassert>   // for assert
 #include <cstddef>   // for size_t
-#include <memory>    // for addressof
 #include <stdexcept> // for runtime_error
+#include <utility>   // for addressof
 #include <vector>    // for vector
 
 #include <hibf/layout/data_store.hpp>        // for data_store

include/hibf/misc/bit_vector.hpp

@@ -21,30 +21,29 @@
 
 #pragma once
 
-#include <algorithm>        // for max, __for_each_fn, for_each, __all_of_fn, __any_of_fn, __fill_fn
+#include <algorithm>        // for __for_each_fn, for_each, __all_of_fn, __any_of_fn, __fill_fn
 #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 <iterator>         // for iter_reference_t, back_inserter, iter_difference_t, iter_value_t
 #include <memory>           // for allocator, assume_aligned, allocator_traits
 #include <ranges>           // for __next_fn, distance, next, _Begin, _End, __distance_fn, begin
 #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/misc/counting_vector.hpp

@@ -9,15 +9,14 @@
 
 #pragma once
 
-#include <algorithm>   // for transform
 #include <bit>         // for countr_zero
 #include <cassert>     // for assert
 #include <cinttypes>   // for uint64_t
 #include <climits>     // for CHAR_BIT
 #include <concepts>    // for integral
 #include <cstring>     // for size_t
 #include <functional>  // for minus, plus
-#include <type_traits> // for conditional_t
+#include <type_traits> // for conditional, conditional_t
 #include <vector>      // for vector
 
 #include <hibf/contrib/aligned_allocator.hpp> // for aligned_allocator

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 <utility>    // 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

@@ -12,11 +12,12 @@
 #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 <cinttypes> // for uint64_t
 #include <concepts>  // for same_as
 #include <utility>   // for move
 
+#include <bits/chrono.h> // for duration, time_point, operator-, steady_clock
+
 #include <hibf/platform.hpp>
 
 namespace seqan::hibf

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/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 <iostream>    // for basic_ostream, basic_istream, operator<<, stringstream, cerr
+#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>      // for char_traits, getline, operator<<, string
+#include <string_view> // for operator<<, operator==, basic_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
+#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 +2,11 @@
 // 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 __sort_fn, sort
+#include <cstddef>   // for size_t
+#include <sstream>   // for basic_stringstream, stringstream
+#include <utility>   // for addressof
+#include <vector>    // for vector
 
 #include <hibf/config.hpp>                        // for config
 #include <hibf/layout/compute_fpr_correction.hpp> // for compute_fpr_correction

src/layout/graph.cpp

@@ -6,8 +6,8 @@
 #include <cassert>          // for assert
 #include <cstddef>          // for size_t
 #include <initializer_list> // for initializer_list
-#include <iterator>         // for __fn, prev
-#include <optional>         // for optional, nullopt
+#include <optional>         // for optional, nullopt, nullopt_t
+#include <ranges>           // for __prev_fn, prev
 #include <vector>           // for vector
 
 #include <hibf/layout/graph.hpp>  // for graph

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 <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, basic_ostream::operator<<, operator<<, basic_ostream
+#include <iterator>    // for __iter_traits_impl
+#include <ranges>      // for range_value_t, empty
+#include <type_traits> // for remove_cvref
+#include <vector>      // for vector
 
 #include <hibf/misc/bit_vector.hpp>      // for bit_vector
 #include <hibf/misc/counting_vector.hpp> // for counting_vector

src/sketch/hyperloglog.cpp

@@ -3,17 +3,16 @@
 // SPDX-FileCopyrightText: 2013 Hideaki Ohno <hide.o.j55{at}gmail.com>
 // SPDX-License-Identifier: BSD-3-Clause AND MIT
 
-#include <algorithm> // for max, __fn, fill
+#include <algorithm> // for max, __fill_fn, fill
 #include <array>     // for array
 #include <bit>       // for countl_zero
 #include <cassert>   // for assert
 #include <cinttypes> // for uint64_t, uint8_t, uint32_t
 #include <cmath>     // for log
 #include <cstddef>   // for size_t
-#include <iostream>  // for basic_ostream, basic_istream, istream, ostream
-#include <memory>    // for addressof
+#include <iostream>  // for basic_ostream, basic_istream, basic_istream::read, basic_ostre...
 #include <stdexcept> // for runtime_error, invalid_argument
-#include <utility>   // for swap
+#include <utility>   // for addressof, swap
 #include <vector>    // for vector
 
 #include <simde/x86/avx.h>  // for simde__m256i, simde_mm256_add_ps, simde_mm256_set1_ps, simde_m...

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, greater
+#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/include/hibf/test/type_name_as_string.hpp

@@ -15,10 +15,11 @@
 
 #include <cstdlib>     // for free
 #include <functional>  // for function
-#include <memory>      // for allocator, addressof, unique_ptr
+#include <memory>      // for allocator, unique_ptr
 #include <string>      // for char_traits, operator+, string, to_string
 #include <type_traits> // for remove_reference_t
 #include <typeinfo>    // for type_info
+#include <utility>     // for addressof
 
 #include <hibf/platform.hpp>