Merge pull request #155 from seqan/actions/iwyu

[MISC] IWYU

include/hibf/hierarchical_interleaved_bloom_filter.hpp

@@ -4,10 +4,10 @@
 
 #pragma once
 
-#include <algorithm>  // for __sort_fn, sort
+#include <algorithm>  // for max, __sort_fn, fill, sort
 #include <cassert>    // for assert
 #include <cinttypes>  // for int64_t, uint16_t
-#include <concepts>   // for unsigned_integral
+#include <concepts>   // for integral, unsigned_integral
 #include <cstddef>    // for size_t
 #include <functional> // for identity, less
 #include <ranges>     // for forward_range, range, range_value_t
@@ -16,9 +16,10 @@
 
 #include <hibf/cereal/concepts.hpp>          // for cereal_archive
 #include <hibf/config.hpp>                   // for config
-#include <hibf/interleaved_bloom_filter.hpp> // for interleaved_bloom_filter
+#include <hibf/interleaved_bloom_filter.hpp> // for interleaved_bloom_filter, counting_vector
 #include <hibf/layout/layout.hpp>            // for layout
 #include <hibf/misc/timer.hpp>               // for concurrent, timer
+#include <hibf/platform.hpp>                 // for HIBF_CONSTEXPR_VECTOR
 
 #include <cereal/macros.hpp> // for CEREAL_SERIALIZE_FUNCTION_NAME
 

include/hibf/misc/bit_vector.hpp

@@ -32,21 +32,22 @@
 #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 <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 <type_traits>      // for conditional_t
 #include <utility>          // for swap
-#include <vector>           // for allocator, vector
+#include <vector>           // for 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/specialize.hpp>       // for specialization, specialize
 #include <cereal/types/base_class.hpp> // for base_class
-#include <cereal/types/vector.hpp>     // for base_class
+#include <cereal/types/vector.hpp>     // IWYU pragma: keep
 
 namespace seqan::hibf
 {

src/hierarchical_interleaved_bloom_filter.cpp

@@ -2,17 +2,16 @@
 // SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: BSD-3-Clause
 
-#include <algorithm>  // for max, fill_n, shuffle, __max_fn
-#include <cassert>    // for assert
-#include <cinttypes>  // for int64_t, uint64_t
-#include <cstddef>    // for size_t
-#include <functional> // for identity, less
-#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 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 <hibf/build/build_data.hpp>                      // for build_data
 #include <hibf/build/compute_kmers.hpp>                   // for compute_kmers

test/include/hibf/test/cereal.hpp

@@ -9,17 +9,19 @@
 
 #pragma once
 
-#include <gtest/gtest.h>
+#include <gtest/gtest.h> // for AssertionResult, EXPECT_TRUE, Message, TestPartResult
 
-#include <fstream>
+#include <fstream>     // for basic_ios, ios, basic_ifstream, basic_ofstream, ifstream, ofs...
+#include <type_traits> // for remove_cvref_t
 
-#include <hibf/cereal/concepts.hpp>
-#include <hibf/test/tmp_directory.hpp>
+#include <hibf/cereal/concepts.hpp>     // for cereal_input_archive, cereal_output_archive
+#include <hibf/test/sandboxed_path.hpp> // for sandboxed_path, operator/
+#include <hibf/test/tmp_directory.hpp>  // for tmp_directory
 
-#include <cereal/archives/binary.hpp>
-#include <cereal/archives/json.hpp>
-#include <cereal/archives/portable_binary.hpp>
-#include <cereal/archives/xml.hpp>
+#include <cereal/archives/binary.hpp>          // for BinaryInputArchive, BinaryOutputArchive
+#include <cereal/archives/json.hpp>            // for JSONInputArchive, JSONOutputArchive
+#include <cereal/archives/portable_binary.hpp> // for PortableBinaryInputArchive, PortableBinaryOutputArchive
+#include <cereal/archives/xml.hpp>             // for XMLInputArchive, XMLOutputArchive
 
 namespace seqan::hibf::test
 {

test/unit/hibf/hierarchical_interleaved_bloom_filter_test.cpp

@@ -8,7 +8,8 @@
 #include <cstddef>    // for size_t
 #include <functional> // for function
 #include <ranges>     // for _Iota, iota, views
-#include <sstream>    // for basic_stringstream, stringstream
+#include <sstream>    // for basic_stringstream, char_traits, stringstream
+#include <utility>    // for move
 #include <vector>     // for vector, allocator
 
 #include <hibf/config.hpp>                                // for insert_iterator, config

test/unit/hibf/interleaved_bloom_filter_test.cpp

@@ -2,7 +2,7 @@
 // SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: BSD-3-Clause
 
-#include <gtest/gtest.h> // for Test, Message, TestPartResult, AssertionResult, EXPECT_EQ, Test...
+#include <gtest/gtest.h> // for Test, Message, TestPartResult, AssertionResult, TestInfo, EXPEC...
 
 #include <algorithm>   // for __for_each_fn, for_each
 #include <array>       // for array
@@ -12,6 +12,7 @@
 #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 <utility>     // for move
 #include <vector>      // for vector, allocator
 
 #include <hibf/config.hpp>                   // for insert_iterator, config