Merge pull request #153 from seqan/actions/iwyu

[MISC] IWYU

include/hibf/interleaved_bloom_filter.hpp

@@ -18,16 +18,17 @@
 #include <cstring>     // for size_t
 #include <functional>  // for plus
 #include <ranges>      // for range, forward_range, input_range, range_reference_t, range_value_t
-#include <tuple>       // for tie, operator==, tuple
 #include <type_traits> // for remove_cvref_t
 #include <utility>     // for addressof
 #include <vector>      // for vector
 
-#include <hibf/cereal/concepts.hpp> // for cereal_archive
-#include <hibf/config.hpp>          // for config
-#include <hibf/misc/bit_vector.hpp>
+#include <hibf/cereal/concepts.hpp>           // for cereal_archive
+#include <hibf/config.hpp>                    // for config
+#include <hibf/contrib/aligned_allocator.hpp> // for aligned_allocator
+#include <hibf/misc/bit_vector.hpp>           // for bit_vector
 
-#include <cereal/macros.hpp> // for CEREAL_SERIALIZE_FUNCTION_NAME
+#include <cereal/macros.hpp>           // for CEREAL_SERIALIZE_FUNCTION_NAME
+#include <cereal/types/base_class.hpp> // for base_class
 
 namespace seqan::hibf
 {

include/hibf/misc/bit_vector.hpp

@@ -21,15 +21,31 @@
 
 #pragma once
 
-#include <algorithm>
-#include <cassert>
-#include <climits>
-#include <vector>
-
-#include <hibf/cereal/concepts.hpp>
-#include <hibf/contrib/aligned_allocator.hpp>
-
-#include <cereal/types/base_class.hpp>
+#include <algorithm>        // for max, __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 <memory>           // for 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 <type_traits>      // for conditional_t
+#include <utility>          // for swap
+#include <vector>           // for allocator, vector
+
+#include <hibf/cereal/concepts.hpp>           // for cereal_archive
+#include <hibf/contrib/aligned_allocator.hpp> // for aligned_allocator
+#include <hibf/platform.hpp>                  // for HIBF_CONSTEXPR_VECTOR
+
+#include <cereal/macros.hpp>           // for CEREAL_SERIALIZE_FUNCTION_NAME
+#include <cereal/types/base_class.hpp> // for base_class
 
 namespace seqan::hibf
 {

include/hibf/misc/print.hpp

@@ -8,7 +8,8 @@
 #include <iostream>  // for cout, ostream
 #include <vector>    // for vector
 
-#include <hibf/interleaved_bloom_filter.hpp> // for counting_vector, bit_vector
+#include <hibf/interleaved_bloom_filter.hpp> // for counting_vector
+#include <hibf/misc/bit_vector.hpp>          // for bit_vector
 
 namespace seqan::hibf
 {

src/interleaved_bloom_filter.cpp

@@ -15,6 +15,7 @@
 #include <hibf/config.hpp>                   // for config, insert_iterator
 #include <hibf/contrib/robin_hood.hpp>       // for unordered_flat_set
 #include <hibf/interleaved_bloom_filter.hpp> // for interleaved_bloom_filter, bin_count, bin_index, bin_size, hash_...
+#include <hibf/misc/bit_vector.hpp>          // for bit_vector
 #include <hibf/misc/divide_and_ceil.hpp>     // for divide_and_ceil
 #include <hibf/platform.hpp>                 // for HIBF_COMPILER_IS_GCC
 

src/misc/print.cpp

@@ -8,7 +8,8 @@
 #include <ranges>    // for range_value_t, empty
 #include <vector>    // for vector
 
-#include <hibf/interleaved_bloom_filter.hpp> // for counting_vector, bit_vector
+#include <hibf/interleaved_bloom_filter.hpp> // for counting_vector
+#include <hibf/misc/bit_vector.hpp>          // for bit_vector
 #include <hibf/misc/print.hpp>               // for print_t
 
 namespace seqan::hibf

test/include/hibf/test/iterator_test_template.hpp

@@ -6,11 +6,15 @@
 
 #pragma once
 
-#include <gtest/gtest.h>
-
-#include <iterator>
-#include <memory>
-#include <ranges>
+#include <gtest/gtest.h> // for AssertionResult, Message, TestPartResult, EXPECT_TRUE, EXPECT_EQ, EXPECT_FALSE, Typ...
+
+#include <concepts>    // for derived_from, same_as, copy_constructible, equality_comparable_with
+#include <cstddef>     // for size_t
+#include <iterator>    // for random_access_iterator_tag, forward_iterator_tag, bidirectional_iterator_tag, input...
+#include <memory>      // for to_address
+#include <ranges>      // for begin, cbegin, next, end, cend, distance, iterator_t, range_difference_t
+#include <type_traits> // for remove_reference_t, conditional_t
+#include <utility>     // for as_const, addressof, pair
 
 #include <hibf/platform.hpp>
 

test/performance/ibf/bit_vector_benchmark.cpp

@@ -4,11 +4,17 @@
 
 // Authored by: Rene Rahn <rene.rahn AT fu-berlin.de>
 
-#include <benchmark/benchmark.h>
+#include <benchmark/benchmark.h> // for Benchmark, State, BENCHMARK_CAPTURE, DoNotOptimize, BENCHMARK_MAIN
 
-#include <random>
+#include <algorithm>   // for __generate_fn, generate
+#include <cinttypes>   // for int32_t, uint8_t
+#include <cstddef>     // for size_t
+#include <memory>      // for allocator
+#include <random>      // for uniform_int_distribution, mt19937_64
+#include <type_traits> // for invoke_result_t
+#include <utility>     // for move, pair
 
-#include <hibf/misc/bit_vector.hpp>
+#include <hibf/misc/bit_vector.hpp> // for bit_vector
 
 seqan::hibf::bit_vector generate_bit_vector(size_t const size, size_t const seed)
 {

test/unit/hibf/bit_vector_test.cpp

@@ -4,13 +4,20 @@
 
 // Authored by: Rene Rahn <rene.rahn AT fu-berlin.de>
 
-#include <gtest/gtest.h>
-
-#include <concepts>
-#include <type_traits>
-
-#include <hibf/misc/bit_vector.hpp>
-#include <hibf/test/iterator_test_template.hpp>
+#include <gtest/gtest.h> // for AssertionResult, Message, TestPartResult, Test, EXPECT_TRUE
+
+#include <algorithm>        // for for_each
+#include <concepts>         // for convertible_to, same_as, integral
+#include <cstddef>          // for size_t
+#include <initializer_list> // for initializer_list
+#include <iterator>         // for output_iterator, random_access_iterator_tag
+#include <ranges>           // for _CBegin, _CEnd, cbegin, cend
+#include <stdexcept>        // for out_of_range
+#include <utility>          // for as_const, move
+#include <vector>           // for allocator, vector
+
+#include <hibf/misc/bit_vector.hpp>             // for bit_vector, operator&, operator^, operator|
+#include <hibf/test/iterator_test_template.hpp> // for iterator_fixture, gtest_registered_test_names_iterator_fixture_
 
 // ----------------------------------------------------------------------------
 // associated types

test/unit/hibf/interleaved_bloom_filter_test.cpp

@@ -2,18 +2,21 @@
 // SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: BSD-3-Clause
 
-#include <gtest/gtest.h> // for Message, TestPartResult, AssertionResult, EXPECT_EQ, TEST
-
-#include <algorithm>  // for for_each
-#include <array>      // for array
-#include <cstddef>    // for size_t
-#include <functional> // for function
-#include <ranges>     // for iota_view, operator==, _Iota, iota
-#include <stdexcept>  // for logic_error, invalid_argument
-#include <vector>     // for vector, allocator
+#include <gtest/gtest.h> // for Test, Message, TestPartResult, AssertionResult, EXPECT_EQ, Test...
+
+#include <algorithm>   // for __for_each_fn, for_each
+#include <array>       // for array
+#include <compare>     // for operator<, strong_ordering
+#include <cstddef>     // for size_t
+#include <functional>  // for identity, function
+#include <ranges>      // for iota_view, operator==, _Iota, iota, views
+#include <stdexcept>   // for logic_error, invalid_argument
+#include <type_traits> // for is_copy_assignable_v, is_copy_constructible_v, is_default_const...
+#include <vector>      // for vector, allocator
 
 #include <hibf/config.hpp>                   // for insert_iterator, config
-#include <hibf/interleaved_bloom_filter.hpp> // for bin_index, interleaved_bloom_filter, bin_count, bin_size, hash_...
+#include <hibf/interleaved_bloom_filter.hpp> // for interleaved_bloom_filter, bin_index, bin_count, bin_size, hash_...
+#include <hibf/misc/bit_vector.hpp>          // for bit_vector
 #include <hibf/test/expect_range_eq.hpp>     // for expect_range_eq, EXPECT_RANGE_EQ
 
 TEST(ibf_test, construction)

test/unit/hibf/print_test.cpp

@@ -10,7 +10,8 @@
 #include <ranges>    // for range_value_t
 #include <vector>    // for allocator, vector
 
-#include <hibf/interleaved_bloom_filter.hpp> // for counting_vector, bit_vector
+#include <hibf/interleaved_bloom_filter.hpp> // for counting_vector
+#include <hibf/misc/bit_vector.hpp>          // for bit_vector
 #include <hibf/misc/print.hpp>               // for print
 
 template <typename t>